@article{
 title = {The effect of water availability on the carbon and nitrogen isotope composition of a C4 plant (pearl millet, Pennisetum glaucum)},
 type = {article},
 year = {2021},
 keywords = {African millet,Greenhouse experiment,Palaeoenvironmental reconstruction,Stable isotope analysis,Water restriction},
 pages = {103047},
 volume = {38},
 websites = {https://doi.org/10.1016/j.jasrep.2021.103047},
 publisher = {Elsevier Ltd},
 id = {b5b92182-74a7-3fe1-8c05-5aed06e4eaa9},
 created = {2021-06-14T16:15:15.676Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2021-06-14T16:15:26.881Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 bibtype = {article},
 author = {Sanborn, Lily H and Reid, Rachel E B and Bradley, Alexander S and Liu, Xinyi},
 doi = {10.1016/j.jasrep.2021.103047},
 journal = {Journal of Archaeological Science: Reports},
 number = {May 2020}
}

@article{
 title = {Statistical Uncertainty in Paleoclimate Proxy Reconstructions},
 type = {article},
 year = {2021},
 keywords = {calibration,confidence intervals,inverse prediction,paleoceanography,paleoclimate,proxies},
 pages = {1-11},
 volume = {48},
 id = {305e1e10-8d13-37a1-b3e5-11a587ea3460},
 created = {2021-09-16T12:52:50.833Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2022-01-12T15:29:59.232Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {McClelland2021},
 private_publication = {false},
 abstract = {A quantitative analysis of any environment older than the instrumental record relies on proxies. Uncertainties associated with proxy reconstructions are often underestimated, which can lead to artificial conflict between different proxies, and between data and models. In this paper, using ordinary least squares linear regression as a common example, we describe a simple, robust and generalizable method for quantifying uncertainty in proxy reconstructions. We highlight the primary controls on the magnitude of uncertainty, and compare this simple estimate to equivalent estimates from Bayesian, nonparametric and fiducial statistical frameworks. We discuss when it may be possible to reduce uncertainties, and conclude that the unexplained variance in the calibration must always feature in the uncertainty in the reconstruction. This directs future research toward explaining as much of the variance in the calibration data as possible. We also advocate for a “data-forward” approach, that clearly decouples the presentation of proxy data from plausible environmental inferences.},
 bibtype = {article},
 author = {McClelland, H. L.O. and Halevy, I. and Wolf-Gladrow, D. A. and Evans, D. and Bradley, A. S.},
 doi = {10.1029/2021GL092773},
 journal = {Geophysical Research Letters},
 number = {15}
}

A quantitative analysis of any environment older than the instrumental record relies on proxies. Uncertainties associated with proxy reconstructions are often underestimated, which can lead to artificial conflict between different proxies, and between data and models. In this paper, using ordinary least squares linear regression as a common example, we describe a simple, robust and generalizable method for quantifying uncertainty in proxy reconstructions. We highlight the primary controls on the magnitude of uncertainty, and compare this simple estimate to equivalent estimates from Bayesian, nonparametric and fiducial statistical frameworks. We discuss when it may be possible to reduce uncertainties, and conclude that the unexplained variance in the calibration must always feature in the uncertainty in the reconstruction. This directs future research toward explaining as much of the variance in the calibration data as possible. We also advocate for a “data-forward” approach, that clearly decouples the presentation of proxy data from plausible environmental inferences.

@article{
 title = {Effects of early marine diagenesis and site-specific depositional controls on carbonate-associated sulfate: Insights from paired S and O isotopic analyses},
 type = {article},
 year = {2021},
 keywords = {CAS,Carbonate-associated sulfate,Ireviken bioevent,Silurian,Sulfate oxygen isotopes,Sulfur isotopes},
 pages = {120525},
 volume = {584},
 websites = {https://doi.org/10.1016/j.chemgeo.2021.120525},
 publisher = {Elsevier B.V.},
 id = {c85b1b76-2065-3920-b96e-fed612650a77},
 created = {2021-11-11T00:52:29.903Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2022-01-13T18:41:54.966Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Richardson2021},
 private_publication = {false},
 abstract = {Carbon, sulfur and oxygen isotope profiles in Silurian strata of the Baltoscandian Basin (Estonia), coincident with the Ireviken Bioevent, provide insights into basin-scale and platform-specific depositional processes. Paired carbon isotope records preserve a positive isotope excursion during the early Wenlock, coincident with faunal turnover, yet δ13C variability of this excursion compared to other locations within the paleobasin reflects local depositional influences superimposed on a global signal. In comparison, sulfur isotope records do not preserve a systematic isotopic excursion over the same interval. Instead, sulfur isotope records have high sample-to-sample stratigraphic variability, particularly in shallow-water carbonate rocks (scatter up to ~10‰ for δ34SCAS and ~ 25‰ for δ34Spyr). This pattern of isotopic variability is also found between sites from the same carbonate platform, where the magnitude and isotopic variability in δ34SCAS and δ34Spyr differ depending on relative local sea level (and therefore facies). Such facies-dependent variability reflects more closed- versus more open-system diagenetic conditions where pulses of increased sedimentation rate in the shallow water environments generates greater isotopic variability in both δ34SCAS and δ34Spyr. Increased reworking and proximity to the shoreline results in local sulfide oxidation, seen as a decrease in δ34SCAS in the most proximal settings. Platform-scale evolution of isotopically distilled pore-fluids associated with dolomitization results in increased δ34SCAS in deep water settings. Correlations in paired δ34SCAS-δ18OCAS data support these conclusions, demonstrating the local alteration of CAS during deposition and early marine diagenesis. We present a framework to assess the sequence of diagenetic and depositional environmental processes that have altered δ34SCAS and find that δ34S of ~27–28‰ approximates Silurian seawater sulfate. Our findings provide a mechanism to understand the elevated variability in many deep-time δ34SCAS records that cannot otherwise be reconciled with behavior of the marine sulfate reservoir.},
 bibtype = {article},
 author = {Richardson, Jocelyn A. and Lepland, Aivo and Hints, Olle and Prave, Anthony R. and Gilhooly, William P. and Bradley, Alexander S. and Fike, David A.},
 doi = {10.1016/j.chemgeo.2021.120525},
 journal = {Chemical Geology},
 number = {September}
}

Carbon, sulfur and oxygen isotope profiles in Silurian strata of the Baltoscandian Basin (Estonia), coincident with the Ireviken Bioevent, provide insights into basin-scale and platform-specific depositional processes. Paired carbon isotope records preserve a positive isotope excursion during the early Wenlock, coincident with faunal turnover, yet δ13C variability of this excursion compared to other locations within the paleobasin reflects local depositional influences superimposed on a global signal. In comparison, sulfur isotope records do not preserve a systematic isotopic excursion over the same interval. Instead, sulfur isotope records have high sample-to-sample stratigraphic variability, particularly in shallow-water carbonate rocks (scatter up to ~10‰ for δ34SCAS and ~ 25‰ for δ34Spyr). This pattern of isotopic variability is also found between sites from the same carbonate platform, where the magnitude and isotopic variability in δ34SCAS and δ34Spyr differ depending on relative local sea level (and therefore facies). Such facies-dependent variability reflects more closed- versus more open-system diagenetic conditions where pulses of increased sedimentation rate in the shallow water environments generates greater isotopic variability in both δ34SCAS and δ34Spyr. Increased reworking and proximity to the shoreline results in local sulfide oxidation, seen as a decrease in δ34SCAS in the most proximal settings. Platform-scale evolution of isotopically distilled pore-fluids associated with dolomitization results in increased δ34SCAS in deep water settings. Correlations in paired δ34SCAS-δ18OCAS data support these conclusions, demonstrating the local alteration of CAS during deposition and early marine diagenesis. We present a framework to assess the sequence of diagenetic and depositional environmental processes that have altered δ34SCAS and find that δ34S of ~27–28‰ approximates Silurian seawater sulfate. Our findings provide a mechanism to understand the elevated variability in many deep-time δ34SCAS records that cannot otherwise be reconciled with behavior of the marine sulfate reservoir.

@article{
 title = {Controls of extreme isotopic enrichment in modern microbialites and associated abiogenic carbonates},
 type = {article},
 year = {2020},
 keywords = {biogenicity,depositional environment,isotopic enrichment,laguna negra,microbialite},
 pages = {136-149},
 volume = {269},
 websites = {https://doi.org/10.1016/j.gca.2019.10.022},
 publisher = {Elsevier Ltd},
 id = {fd26b69f-9738-3781-9450-53851a413930},
 created = {2019-12-13T18:06:44.703Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2020-12-09T17:06:16.854Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 citation_key = {Beeler2020},
 folder_uuids = {a645a47f-1ab0-40ef-ac0e-b4ed3e5e62e2},
 private_publication = {false},
 bibtype = {article},
 author = {Beeler, Scott R and Gomez, Fernando J and Bradley, Alexander S},
 doi = {10.1016/j.gca.2019.10.022},
 journal = {Geochimica et Cosmochimica Acta}
}

@article{
 title = {Oxygen isotope effects during microbial sulfate reduction: applications to sediment cell abundances},
 type = {article},
 year = {2020},
 keywords = {Biogeochemistry},
 pages = {1-12},
 websites = {http://www.nature.com/articles/s41396-020-0618-2},
 publisher = {Springer US},
 id = {fb050b33-4d13-30e5-89d4-76e09e12e1c1},
 created = {2020-03-23T19:36:48.618Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2022-01-13T18:50:06.749Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Bertran2020},
 private_publication = {false},
 abstract = {The majority of anaerobic biogeochemical cycling occurs within marine sediments. To understand these processes, quantifying the distribution of active cells and gross metabolic activity is essential. We present an isotope model rooted in thermodynamics to draw quantitative links between cell-specific sulfate reduction rates and active sedimentary cell abundances. This model is calibrated using data from a series of continuous culture experiments with two strains of sulfate reducing bacteria (freshwater bacterium Desulfovibrio vulgaris strain Hildenborough, and marine bacterium Desulfovibrio alaskensis strain G-20) grown on lactate across a range of metabolic rates and ambient sulfate concentrations. We use a combination of experimental sulfate oxygen isotope data and nonlinear regression fitting tools to solve for unknown kinetic, step-specific oxygen isotope effects. This approach enables identification of key isotopic reactions within the metabolic pathway, and defines a new, calibrated framework for understanding oxygen isotope variability in sulfate. This approach is then combined with porewater sulfate/sulfide concentration data and diagenetic modeling to reproduce measured 18O/16O in porewater sulfate. From here, we infer cell-specific sulfate reduction rates and predict abundance of active cells of sulfate reducing bacteria, the result of which is consistent with direct biological measurements.},
 bibtype = {article},
 author = {Bertran, E. and Waldeck, A. and Wing, B. A. and Halevy, I. and Leavitt, W. D. and Bradley, A. S. and Johnston, D. T.},
 doi = {10.1038/s41396-020-0618-2},
 journal = {The ISME Journal}
}

The majority of anaerobic biogeochemical cycling occurs within marine sediments. To understand these processes, quantifying the distribution of active cells and gross metabolic activity is essential. We present an isotope model rooted in thermodynamics to draw quantitative links between cell-specific sulfate reduction rates and active sedimentary cell abundances. This model is calibrated using data from a series of continuous culture experiments with two strains of sulfate reducing bacteria (freshwater bacterium Desulfovibrio vulgaris strain Hildenborough, and marine bacterium Desulfovibrio alaskensis strain G-20) grown on lactate across a range of metabolic rates and ambient sulfate concentrations. We use a combination of experimental sulfate oxygen isotope data and nonlinear regression fitting tools to solve for unknown kinetic, step-specific oxygen isotope effects. This approach enables identification of key isotopic reactions within the metabolic pathway, and defines a new, calibrated framework for understanding oxygen isotope variability in sulfate. This approach is then combined with porewater sulfate/sulfide concentration data and diagenetic modeling to reproduce measured 18O/16O in porewater sulfate. From here, we infer cell-specific sulfate reduction rates and predict abundance of active cells of sulfate reducing bacteria, the result of which is consistent with direct biological measurements.

@article{
 title = {Direct Observation of the Dynamics of Single-Cell Metabolic Activity during Microbial Diauxic Growth},
 type = {article},
 year = {2020},
 pages = {1-9},
 volume = {11},
 websites = {http://mbio.asm.org/lookup/doi/10.1128/mBio.01519-19},
 id = {983f432b-230b-38b8-813f-52f8e3381967},
 created = {2020-03-23T19:36:48.619Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2020-11-19T19:41:18.135Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {McClelland2020},
 private_publication = {false},
 abstract = {Population-level analyses are rapidly becoming inadequate to answer many of biomedical science and microbial ecology’s most pressing questions. The role of microbial populations within ecosystems and the evolutionary selective pressure on individuals depend fundamentally on the metabolic activity of single cells. Yet, many existing single-cell technologies provide only indirect evidence of metabolic specialization because they rely on correlations between transcription and phenotype established at the level of the population to infer activity. In this study, we take a top-down approach using isotope labels and secondary ion mass spectrometry to track the uptake of carbon and nitrogen atoms from different sources into biomass and directly observe dynamic changes in anabolic specialization at the level of single cells. We investigate the classic microbiological phenomenon of diauxic growth at the single-cell level in the model methylotroph Methylobacterium extorquens . In nature, this organism inhabits the phyllosphere, where it experiences diurnal changes in the available carbon substrates, necessitating an overhaul of central carbon metabolism. We show that the population exhibits a unimodal response to the changing availability of viable substrates, a conclusion that supports the canonical model but has thus far been supported by only indirect evidence. We anticipate that the ability to monitor the dynamics of anabolism in individual cells directly will have important applications across the fields of ecology, medicine, and biogeochemistry, especially where regulation downstream of transcription has the potential to manifest as heterogeneity that would be undetectable with other existing single-cell approaches.},
 bibtype = {article},
 author = {McClelland, H. L. O. and Jones, C and Chubiz, L. M. and Fike, D. A. and Bradley, A. S.},
 doi = {10.1128/mBio.01519-19},
 journal = {mBio},
 number = {2}
}

Population-level analyses are rapidly becoming inadequate to answer many of biomedical science and microbial ecology’s most pressing questions. The role of microbial populations within ecosystems and the evolutionary selective pressure on individuals depend fundamentally on the metabolic activity of single cells. Yet, many existing single-cell technologies provide only indirect evidence of metabolic specialization because they rely on correlations between transcription and phenotype established at the level of the population to infer activity. In this study, we take a top-down approach using isotope labels and secondary ion mass spectrometry to track the uptake of carbon and nitrogen atoms from different sources into biomass and directly observe dynamic changes in anabolic specialization at the level of single cells. We investigate the classic microbiological phenomenon of diauxic growth at the single-cell level in the model methylotroph Methylobacterium extorquens . In nature, this organism inhabits the phyllosphere, where it experiences diurnal changes in the available carbon substrates, necessitating an overhaul of central carbon metabolism. We show that the population exhibits a unimodal response to the changing availability of viable substrates, a conclusion that supports the canonical model but has thus far been supported by only indirect evidence. We anticipate that the ability to monitor the dynamics of anabolism in individual cells directly will have important applications across the fields of ecology, medicine, and biogeochemistry, especially where regulation downstream of transcription has the potential to manifest as heterogeneity that would be undetectable with other existing single-cell approaches.

@article{
 title = {Endosymbiotic adaptations in three new bacterial species associated with Dictyostelium discoideum: Burkholderia agricolaris sp. nov., Burkholderia hayleyella sp. nov., and Burkholderia bonniea sp. nov},
 type = {article},
 year = {2020},
 pages = {e9151},
 volume = {8},
 id = {8c09e540-505c-38fe-842e-93cadb94564e},
 created = {2020-05-26T17:23:12.306Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2022-01-13T18:48:30.072Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Brock2020},
 private_publication = {false},
 abstract = {Here we name three species of Burkholderia that can defeat the mechanisms by which bacteria are normally excluded from the spores of a soil dwelling eukaryote Dictyostelium discoideum , which is predatory on bacteria. They are B. agricolaris sp. nov., B. hayleyella sp. nov., and B. bonniea sp. nov. These new species are widespread across the eastern USA and were isolated as internal symbionts of wild collected D. discoideum . Evidence that they are each a distinct new species comes from their phylogenetic position, carbon usage, reduced cell length, cooler optimal growth temperature, and ability to invade D. discoideum amoebae and remain there for generations.},
 bibtype = {article},
 author = {Brock, Debra A. and Noh, Suegene and Hubert, Alicia N.M. and Haselkorn, Tamara and DiSalvo, Susanne and Suess, Melanie K. and Bradley, Alexander S. and Tavakoli-Nezhad, Mahhboubeh and Geist, Katherinne S. and Queller, David C. and Strassmann, Joan E.},
 doi = {10.1101/304352},
 journal = {PeerJ}
}

Here we name three species of Burkholderia that can defeat the mechanisms by which bacteria are normally excluded from the spores of a soil dwelling eukaryote Dictyostelium discoideum , which is predatory on bacteria. They are B. agricolaris sp. nov., B. hayleyella sp. nov., and B. bonniea sp. nov. These new species are widespread across the eastern USA and were isolated as internal symbionts of wild collected D. discoideum . Evidence that they are each a distinct new species comes from their phylogenetic position, carbon usage, reduced cell length, cooler optimal growth temperature, and ability to invade D. discoideum amoebae and remain there for generations.

@article{
 title = {Isotopic fractionation associated with sulfate import and activation by Desulfovibrio vulgaris str. Hildenborough},
 type = {article},
 year = {2020},
 keywords = {adenylyl transferase,ch,chemostat,enzymes,isotope fractionation,oxygen,sulfate,sulfate permease,sulfate reduction,sulfur},
 pages = {1-14},
 volume = {11},
 id = {4b68f6a6-fdfb-38dc-addb-2f76e2ba93a1},
 created = {2020-09-25T17:28:16.952Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2020-11-19T19:41:17.658Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Smith2020},
 private_publication = {false},
 abstract = {The use of stable isotopes to trace biogeochemical sulfur cycling relies on an understanding of how isotopic fractionation is imposed by metabolic networks. We investigated the effects of the first two enzymatic steps in the dissimilatory sulfate reduction (DSR) network – sulfate permease and sulfate adenylyl transferase (Sat) – on the sulfur and oxygen isotopic composition of residual sulfate. Mutant strains of Desulfovibrio vulgaris str. Hildenborough (DvH) with perturbed expression of these enzymes were grown in batch culture, with a subset grown in continuous culture, to examine the impact of these enzymatic steps on growth rate, cell specific sulfate reduction rate and isotopic fractionations in comparison to the wild type strain. Deletion of several permease genes resulted in only small (∼1?) changes in sulfur isotope fractionation, a difference that approaches the uncertainties of the measurement. Mutants that perturb Sat expression show higher fractionations than the wild type strain. This increase probably relates to an increased material flux between sulfate and APS, allowing an increase in the expressed fractionation of rate-limiting APS reductase. This work illustrates that flux through the initial steps of the DSR pathway can affect the fractionation imposed by the overall pathway, even though these steps are themselves likely to impose only small fractionations.},
 bibtype = {article},
 author = {Smith, D and Fike, David A. and Johnston, David T. and Bradley, Alexander S.},
 doi = {10.3389/fmicb.2020.529317},
 journal = {Frontiers in Microbiology},
 number = {September}
}

The use of stable isotopes to trace biogeochemical sulfur cycling relies on an understanding of how isotopic fractionation is imposed by metabolic networks. We investigated the effects of the first two enzymatic steps in the dissimilatory sulfate reduction (DSR) network – sulfate permease and sulfate adenylyl transferase (Sat) – on the sulfur and oxygen isotopic composition of residual sulfate. Mutant strains of Desulfovibrio vulgaris str. Hildenborough (DvH) with perturbed expression of these enzymes were grown in batch culture, with a subset grown in continuous culture, to examine the impact of these enzymatic steps on growth rate, cell specific sulfate reduction rate and isotopic fractionations in comparison to the wild type strain. Deletion of several permease genes resulted in only small (∼1?) changes in sulfur isotope fractionation, a difference that approaches the uncertainties of the measurement. Mutants that perturb Sat expression show higher fractionations than the wild type strain. This increase probably relates to an increased material flux between sulfate and APS, allowing an increase in the expressed fractionation of rate-limiting APS reductase. This work illustrates that flux through the initial steps of the DSR pathway can affect the fractionation imposed by the overall pathway, even though these steps are themselves likely to impose only small fractionations.

@article{
 title = {The Isotopic Imprint of Life on an Evolving Planet},
 type = {article},
 year = {2020},
 keywords = {Biogeochemical cycles,Carbon,Evolution of life,Geobiology,Isotope geochemistry,Nitrogen,Sulfur},
 volume = {216},
 id = {1d07f961-21b8-3be2-aea4-7ac202fe7bf3},
 created = {2020-10-10T23:59:00.000Z},
 file_attached = {false},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2020-11-19T19:41:17.664Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 citation_key = {Lloyd2020},
 private_publication = {false},
 abstract = {© 2020, Springer Nature B.V. Stable isotope compositions of biologically cycled elements encode information about the interaction between life and environment. On Earth, geochemical biomarkers have been used to probe the extent, nature, and activity of modern and ancient organisms. However, extracting biological information from stable isotopic compositions requires untangling the interconnected nature of the Earth’s biogeochemical system, and must be viewed through the lens of evolving metabolisms on an evolving planet. In this chapter, we provide an introduction to isotope geobiology and to the geobiological history of Earth. We discuss the isotope biogeochemistry of the biologically essential elements carbon, nitrogen and sulfur, and we summarize their distribution on the modern Earth as an interconnected network of isotopically fractionated reservoirs with contrasting residence times. We show how this framework can be used to explore the evolution of life and environments on the ancient Earth, which is our closest accessible analogue for an extraterrestrial planet.},
 bibtype = {article},
 author = {Lloyd, M.K. and McClelland, H.L.O. and Antler, G. and Bradley, A.S. and Halevy, I. and Junium, C.K. and Wankel, S.D. and Zerkle, A.L.},
 doi = {10.1007/s11214-020-00730-6},
 journal = {Space Science Reviews},
 number = {7}
}

© 2020, Springer Nature B.V. Stable isotope compositions of biologically cycled elements encode information about the interaction between life and environment. On Earth, geochemical biomarkers have been used to probe the extent, nature, and activity of modern and ancient organisms. However, extracting biological information from stable isotopic compositions requires untangling the interconnected nature of the Earth’s biogeochemical system, and must be viewed through the lens of evolving metabolisms on an evolving planet. In this chapter, we provide an introduction to isotope geobiology and to the geobiological history of Earth. We discuss the isotope biogeochemistry of the biologically essential elements carbon, nitrogen and sulfur, and we summarize their distribution on the modern Earth as an interconnected network of isotopically fractionated reservoirs with contrasting residence times. We show how this framework can be used to explore the evolution of life and environments on the ancient Earth, which is our closest accessible analogue for an extraterrestrial planet.

@article{
 title = {Proteomic and Isotopic Response of Desulfovibrio vulgaris to DsrC Perturbation},
 type = {article},
 year = {2019},
 keywords = {chemostat,microbial energy,microbial energy metabolism,microbial sulfate reduction,proteomics,sulfur isotope fractionation},
 pages = {1-13},
 volume = {10},
 id = {763c0a65-27b5-3cf7-9144-c12093b89c8f},
 created = {2019-12-13T18:05:43.981Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2020-11-19T19:41:17.898Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Leavitt2019},
 private_publication = {false},
 abstract = {Dissimilatory sulfate reduction is a microbial energy metabolism that can produce sulfur isotopic fractionations over a large range in magnitude. Calibrating sulfur isotopic fractionation in laboratory experiments allows for better interpretations of sulfur isotopes in modern sediments and ancient sedimentary rocks. The proteins involved in sulfate reduction are expressed in response to environmental conditions, and are collectively responsible for the net isotopic fractionation between sulfate and sulfide. We examined the role of DsrC, a key component of the sulfate reduction pathway, by comparing wildtype Desulfovibrio vulgaris DSM 644T to strain IPFG07, a mutant deficient in DsrC production. Both strains were cultivated in parallel chemostat reactors at identical turnover times and cell specific sulfate reduction rates. Under these conditions, sulfur isotopic fractionations between sulfate and sulfide of 17.3 ± 0.5 permil or 12.6 ± 0.5 permil were recorded for the wildtype or mutant, respectively. The enzymatic machinery that produced these different fractionations was revealed by quantitative proteomics. Results are consistent with a cellular-level response that throttled the supply of electrons and sulfur supply through the sulfate reduction pathway more in the mutant relative to the wildtype, independent of rate. We conclude that the smaller fractionation observed in the mutant strain is a consequence of sulfate reduction that proceeded at a rate that consumed a greater proportion of the strains overall capacity for sulfate reduction. These observations have consequences for models of sulfate reducer metabolism and how it yields different isotopic fractionations, notably, the role of DsrC in central energy metabolism.},
 bibtype = {article},
 author = {Leavitt, William D and Venceslau, Sofia S and Waldbauer, Jacob and Smith, Derek A and Pereira, Inês A Cardoso and Bradley, Alexander S},
 doi = {10.3389/fmicb.2019.00658},
 journal = {Frontiers in Microbiology},
 number = {April}
}

Dissimilatory sulfate reduction is a microbial energy metabolism that can produce sulfur isotopic fractionations over a large range in magnitude. Calibrating sulfur isotopic fractionation in laboratory experiments allows for better interpretations of sulfur isotopes in modern sediments and ancient sedimentary rocks. The proteins involved in sulfate reduction are expressed in response to environmental conditions, and are collectively responsible for the net isotopic fractionation between sulfate and sulfide. We examined the role of DsrC, a key component of the sulfate reduction pathway, by comparing wildtype Desulfovibrio vulgaris DSM 644T to strain IPFG07, a mutant deficient in DsrC production. Both strains were cultivated in parallel chemostat reactors at identical turnover times and cell specific sulfate reduction rates. Under these conditions, sulfur isotopic fractionations between sulfate and sulfide of 17.3 ± 0.5 permil or 12.6 ± 0.5 permil were recorded for the wildtype or mutant, respectively. The enzymatic machinery that produced these different fractionations was revealed by quantitative proteomics. Results are consistent with a cellular-level response that throttled the supply of electrons and sulfur supply through the sulfate reduction pathway more in the mutant relative to the wildtype, independent of rate. We conclude that the smaller fractionation observed in the mutant strain is a consequence of sulfate reduction that proceeded at a rate that consumed a greater proportion of the strains overall capacity for sulfate reduction. These observations have consequences for models of sulfate reducer metabolism and how it yields different isotopic fractionations, notably, the role of DsrC in central energy metabolism.

@article{
 title = {Sulfur isotope analysis of microcrystalline iron sulfides using secondary ion mass spectrometry imaging : Extracting local paleo ‐ environmental information from modern and ancient sediments},
 type = {article},
 year = {2019},
 pages = {491-502},
 volume = {33},
 id = {43e8c5ca-9801-3ff3-bbc8-3f8c5cfc70b6},
 created = {2019-12-13T18:05:44.049Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2020-11-19T19:41:17.909Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 citation_key = {Bryant2019},
 private_publication = {false},
 abstract = {Rationale: Sulfur isotope ratio measurements of bulk sulfide from marine sediments have often been used to reconstruct environmental conditions associated with their formation. In situ microscale spot analyses by secondary ion mass spectrometry (SIMS) and laser ablation multiple‐collector inductively coupled plasma mass spectrometry (LA‐MC‐ICP‐MS) have been utilized for the same purpose. However, these techniques are often not suitable for studying small (≤10μm) grains or for detecting intra‐grain variability. Methods: Here, we present a method for the physical extraction (using lithium polytungstate heavy liquid) and subsequent sulfur isotope analysis (using SIMS; CAMECA IMS 7f‐GEO) of microcrystalline iron sulfides. SIMS sulfur isotope ratio measurements were made via Cs+ bombardment of raster squares with sides of 20–130μm, using an electron multiplier (EM) detector to collect counts of 32S− and 34S− for each pixel (128 ×128 pixel grids) for between 20 and 960 cycles. Results: The extraction procedure did not discernibly alter pyrite grain‐size distributions. The apparent inter‐grain variability in 34S/32Sin1–4μm‐sized pyrite and marcasite fragments from isotopically homogeneous hydrothermal crystals was ~ ±2‰ (1σ), comparable with the standard error of the mean for individual measurements (≤±2‰,1σ). In contrast, grain‐specific 34S/32S ratios inmodern and ancient sedimentary pyrites and marcasites can have inter‐ and intra‐grain variability >60‰. The distributions of intra‐sample isotopic variability are consistent with bulk 34S/32S values. Conclusions: SIMS analyses of isolated iron sulfide grains yielded distributions that are isotopically representative of bulk 34S/32S values. Populations of iron sulfide grains from sedimentary samples record the evolution of the S‐isotopic composition of pore water sulfide in their S‐isotopic compositions. These data allow past local environmental conditions to be inferred. 1},
 bibtype = {article},
 author = {Bryant, Roger N and Jones, Clive and Raven, Morgan R and Gomes, Maya L and Berelson, William M and Bradley, Alexander S and Fike, David A},
 doi = {10.1002/rcm.8375},
 journal = {Rapid Communications in Mass Spectrometry}
}

Rationale: Sulfur isotope ratio measurements of bulk sulfide from marine sediments have often been used to reconstruct environmental conditions associated with their formation. In situ microscale spot analyses by secondary ion mass spectrometry (SIMS) and laser ablation multiple‐collector inductively coupled plasma mass spectrometry (LA‐MC‐ICP‐MS) have been utilized for the same purpose. However, these techniques are often not suitable for studying small (≤10μm) grains or for detecting intra‐grain variability. Methods: Here, we present a method for the physical extraction (using lithium polytungstate heavy liquid) and subsequent sulfur isotope analysis (using SIMS; CAMECA IMS 7f‐GEO) of microcrystalline iron sulfides. SIMS sulfur isotope ratio measurements were made via Cs+ bombardment of raster squares with sides of 20–130μm, using an electron multiplier (EM) detector to collect counts of 32S− and 34S− for each pixel (128 ×128 pixel grids) for between 20 and 960 cycles. Results: The extraction procedure did not discernibly alter pyrite grain‐size distributions. The apparent inter‐grain variability in 34S/32Sin1–4μm‐sized pyrite and marcasite fragments from isotopically homogeneous hydrothermal crystals was ~ ±2‰ (1σ), comparable with the standard error of the mean for individual measurements (≤±2‰,1σ). In contrast, grain‐specific 34S/32S ratios inmodern and ancient sedimentary pyrites and marcasites can have inter‐ and intra‐grain variability >60‰. The distributions of intra‐sample isotopic variability are consistent with bulk 34S/32S values. Conclusions: SIMS analyses of isolated iron sulfide grains yielded distributions that are isotopically representative of bulk 34S/32S values. Populations of iron sulfide grains from sedimentary samples record the evolution of the S‐isotopic composition of pore water sulfide in their S‐isotopic compositions. These data allow past local environmental conditions to be inferred. 1

@article{
 title = {Paired organic matter and pyrite δ34S records reveal mechanisms of carbon , sulfur , and iron cycle disruption during Ocean Anoxic Event 2},
 type = {article},
 year = {2019},
 pages = {27-38},
 volume = {512},
 websites = {https://doi.org/10.1016/j.epsl.2019.01.048},
 publisher = {Elsevier B.V.},
 id = {d2ac0287-a98a-34d3-9a17-5a4e1a48f063},
 created = {2019-12-13T18:05:52.238Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2020-11-19T19:41:17.993Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 citation_key = {Raven2019},
 private_publication = {false},
 abstract = {The sulfur (S) isotope composition of pyrite in the sedimentary record has played an important part in our understanding of the evolution of biogeochemical cycles throughout Earth history. However, the kinetics of pyritization are complex and depend strongly on the reactivity and mineralogy of available iron. As a second major sink for sulfide in anoxic sediments, organic matter (OM) provides essential context for reconstructing the distribution and isotopic composition of environmental sulfide. To first order, roughly parallel pyrite and OM δ34S profiles reflect changes in sulfide, while independent patterns require alternative explanations, including changes in iron availability or OM characteristics. We apply this framework to Ocean Anoxic Event 2 (OAE-2, ∼94 Mya), a period of enhanced burial of reduced C and S (in OM and pyrite) that has been associated with an expansion of reducing marine conditions. We present paired S-isotope records for pyrite and OM along with profiles of OM S:C ratio and S redox speciation from four well-characterized lithologic sections with a range of depositional environments (Pont d’Issole, Cismon, Tarfaya Basin, and Demerara Rise) to reconstruct both local redox structure and global mechanisms impacting the C, S and Fe cycles around OAE-2. OM sulfurization appears to be a major control on OM preservation at all four sites. Similar to modern anoxic environments, there is a positive correlation between OM S:C ratios and TOC concentrations for sites with more reducing conditions, implying a link between OM sulfurization and burial. At consistently anoxic sites like Tarfaya Basin and Demerara Rise, strongly sulfurized OM with a consistent S redox speciation and S-isotope composition most likely formed rapidly in sinking particles before, during, and after OAE-2. Particle-hosted OM sulfurization may therefore have been a central mechanism facilitating the massive burial of OM in anoxic environments during this and other periods of enhanced global carbon burial. At the same time, a nearly 25h negative shift in the δ34S values of pyrite – but not OM – occurs at multiple, globally distributed sites prior to the onset of OAE-2, indicating slower pyritization reactions that likely reflect changes in iron delivery due to expanding regional or global anoxia. The combination of pyrite and organic S isotopes thus provides novel constraints on the interwoven cycles of carbon, iron, and sulfur across a major carbon cycle perturbation.},
 bibtype = {article},
 author = {Raven, Morgan Reed and Fike, David A and Bradley, Alexander S and Gomes, Maya L and Owens, Jeremy D and Webb, Samuel A},
 doi = {10.1016/j.epsl.2019.01.048},
 journal = {Earth and Planetary Science Letters}
}

The sulfur (S) isotope composition of pyrite in the sedimentary record has played an important part in our understanding of the evolution of biogeochemical cycles throughout Earth history. However, the kinetics of pyritization are complex and depend strongly on the reactivity and mineralogy of available iron. As a second major sink for sulfide in anoxic sediments, organic matter (OM) provides essential context for reconstructing the distribution and isotopic composition of environmental sulfide. To first order, roughly parallel pyrite and OM δ34S profiles reflect changes in sulfide, while independent patterns require alternative explanations, including changes in iron availability or OM characteristics. We apply this framework to Ocean Anoxic Event 2 (OAE-2, ∼94 Mya), a period of enhanced burial of reduced C and S (in OM and pyrite) that has been associated with an expansion of reducing marine conditions. We present paired S-isotope records for pyrite and OM along with profiles of OM S:C ratio and S redox speciation from four well-characterized lithologic sections with a range of depositional environments (Pont d’Issole, Cismon, Tarfaya Basin, and Demerara Rise) to reconstruct both local redox structure and global mechanisms impacting the C, S and Fe cycles around OAE-2. OM sulfurization appears to be a major control on OM preservation at all four sites. Similar to modern anoxic environments, there is a positive correlation between OM S:C ratios and TOC concentrations for sites with more reducing conditions, implying a link between OM sulfurization and burial. At consistently anoxic sites like Tarfaya Basin and Demerara Rise, strongly sulfurized OM with a consistent S redox speciation and S-isotope composition most likely formed rapidly in sinking particles before, during, and after OAE-2. Particle-hosted OM sulfurization may therefore have been a central mechanism facilitating the massive burial of OM in anoxic environments during this and other periods of enhanced global carbon burial. At the same time, a nearly 25h negative shift in the δ34S values of pyrite – but not OM – occurs at multiple, globally distributed sites prior to the onset of OAE-2, indicating slower pyritization reactions that likely reflect changes in iron delivery due to expanding regional or global anoxia. The combination of pyrite and organic S isotopes thus provides novel constraints on the interwoven cycles of carbon, iron, and sulfur across a major carbon cycle perturbation.

@article{
 title = {Silurian records of carbon and sulfur cycling from Estonia : The importance of depositional environment on isotopic trends},
 type = {article},
 year = {2019},
 pages = {71-82},
 volume = {512},
 websites = {https://doi.org/10.1016/j.epsl.2019.01.055},
 publisher = {Elsevier B.V.},
 id = {b1f59df1-f498-3c67-8460-0c80a25f30d3},
 created = {2019-12-13T18:05:52.342Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2020-11-19T19:41:17.940Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 citation_key = {Richardson2019},
 private_publication = {false},
 abstract = {The Llandovery–Wenlock carbonate-marl succession of the Baltoscandian Basin has been analyzed in the Viki drill core, western Estonia, for carbonate carbon (δ13Ccarb), organic carbon (δ13Corg), carbonate- associated sulfate (δ34SCAS) and pyrite (δ34Spyr) isotopes, along with trace element concentrations. Following the End-Ordovician glaciation and the Hirnantian carbon isotope excursion, δ13Ccarb values rise to an early Llandovery carbon isotope maximum (+2h). Subsequently, δ13Ccarb and coeval δ13Corg record a large ∼+4.5h excursion in the early Wenlock, associated with a regression and biotic turnover known as the Ireviken bioevent (IBE). Overall, δ34SCAS values generally fall within a range (25h to 35h) similar to that reported in other sections of comparable age. Two distinct trends are observed: low and stable δ34SCAS values are associated with deep-water facies, while δ34SCAS becomes higher and more variable in the shallow-water facies. Similarly, δ34Spyr values are low and invariant (∼−15h) in deep- water facies but become higher and more variable (ranging between −35h and 16h) in shallow-water deposits. Despite abundant recrystallization, no obvious evidence for large-scale alteration of proxies is apparent in concentrations of Fe, Sr, Mn and Mg, or in isotopic correlations, although increased variability and lower values of δ34SCAS are observed where CAS abundance is low. A large, well-resolved positive excursion in δ34SCAS observed during the IBE from a time-correlative section on Gotland (Sweden) is absent in the data presented here. This difference demonstrates that, counter to general understanding, local environmental variations can give rise to divergent δ34SCAS profiles in coeval sections. The S-isotope fluctuations in CAS and pyrite in the Viki drill core can be explained by local processes involving facies changes, early diagenetic processes and associated open vs. closed system behavior that can overprint and potentially mask basin or global signals.},
 bibtype = {article},
 author = {Richardson, Jocelyn A and Keating, Colin and Lepland, Aivo and Hints, Olle and Bradley, Alexander S and Fike, David A},
 doi = {10.1016/j.epsl.2019.01.055},
 journal = {Earth and Planetary Science Letters}
}

The Llandovery–Wenlock carbonate-marl succession of the Baltoscandian Basin has been analyzed in the Viki drill core, western Estonia, for carbonate carbon (δ13Ccarb), organic carbon (δ13Corg), carbonate- associated sulfate (δ34SCAS) and pyrite (δ34Spyr) isotopes, along with trace element concentrations. Following the End-Ordovician glaciation and the Hirnantian carbon isotope excursion, δ13Ccarb values rise to an early Llandovery carbon isotope maximum (+2h). Subsequently, δ13Ccarb and coeval δ13Corg record a large ∼+4.5h excursion in the early Wenlock, associated with a regression and biotic turnover known as the Ireviken bioevent (IBE). Overall, δ34SCAS values generally fall within a range (25h to 35h) similar to that reported in other sections of comparable age. Two distinct trends are observed: low and stable δ34SCAS values are associated with deep-water facies, while δ34SCAS becomes higher and more variable in the shallow-water facies. Similarly, δ34Spyr values are low and invariant (∼−15h) in deep- water facies but become higher and more variable (ranging between −35h and 16h) in shallow-water deposits. Despite abundant recrystallization, no obvious evidence for large-scale alteration of proxies is apparent in concentrations of Fe, Sr, Mn and Mg, or in isotopic correlations, although increased variability and lower values of δ34SCAS are observed where CAS abundance is low. A large, well-resolved positive excursion in δ34SCAS observed during the IBE from a time-correlative section on Gotland (Sweden) is absent in the data presented here. This difference demonstrates that, counter to general understanding, local environmental variations can give rise to divergent δ34SCAS profiles in coeval sections. The S-isotope fluctuations in CAS and pyrite in the Viki drill core can be explained by local processes involving facies changes, early diagenetic processes and associated open vs. closed system behavior that can overprint and potentially mask basin or global signals.

@article{
 title = {Insights into past ocean proxies from micron-scale mapping of sulfur species in carbonates},
 type = {article},
 year = {2019},
 pages = {833-837},
 volume = {47},
 id = {064b2b0c-74ba-3f32-a33d-16ba69899ee1},
 created = {2019-12-13T18:06:48.287Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2022-01-13T18:51:23.874Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 citation_key = {Rose2019},
 private_publication = {false},
 abstract = {Geological reconstructions of global ocean chemistry and atmospheric oxygen concentrations over Earth history commonly rely on the abundance and stable isotopic composition (δ34S) of sulfur-bearing compounds. Carbonate-associated sulfate (CAS), sulfate bound within a calcium carbonate mineral matrix, is among the most commonly interrogated sulfur mineral phases. However, recent work has revealed variability in δ34SCAS values that cannot be explained by evolution of the marine sulfate reservoir, challenging the common interpretation that CAS is inherently a high-fidelity record of seawater sulfate. To investigate the source of this inconsistency, we used X-ray spectromicroscopy to map the micron-scale distribution of S-bearing sedimentary phases in Ordovician-aged (ca. 444 Ma) shallow marine carbonates from Anticosti Island, Québec, Canada. Clear differences in the abundance of CAS are observed between cements and fossils, suggesting that variance in bulk-rock data could be a consequence of component mixing and that coupled synchrotron-petrographic screening can identify the carbonate components that are most likely to retain primary CAS. Furthermore, we observe multiple, distinct forms of sulfate (both inorganic and organic). Differences in these forms among fossil clades could provide new insights into biomineralization mechanisms in extinct organisms.},
 bibtype = {article},
 author = {Rose, Catherine V and Webb, Samuel M and Newville, Matthew and Lanzirotti, Antonio and Richardson, Jocelyn A and Tosca, Nicholas J and Catalano, Jeffrey G and Bradley, Alexander S and Fike, David A},
 doi = {10.1130/G46228.1},
 journal = {Geology},
 number = {9}
}

Geological reconstructions of global ocean chemistry and atmospheric oxygen concentrations over Earth history commonly rely on the abundance and stable isotopic composition (δ34S) of sulfur-bearing compounds. Carbonate-associated sulfate (CAS), sulfate bound within a calcium carbonate mineral matrix, is among the most commonly interrogated sulfur mineral phases. However, recent work has revealed variability in δ34SCAS values that cannot be explained by evolution of the marine sulfate reservoir, challenging the common interpretation that CAS is inherently a high-fidelity record of seawater sulfate. To investigate the source of this inconsistency, we used X-ray spectromicroscopy to map the micron-scale distribution of S-bearing sedimentary phases in Ordovician-aged (ca. 444 Ma) shallow marine carbonates from Anticosti Island, Québec, Canada. Clear differences in the abundance of CAS are observed between cements and fossils, suggesting that variance in bulk-rock data could be a consequence of component mixing and that coupled synchrotron-petrographic screening can identify the carbonate components that are most likely to retain primary CAS. Furthermore, we observe multiple, distinct forms of sulfate (both inorganic and organic). Differences in these forms among fossil clades could provide new insights into biomineralization mechanisms in extinct organisms.

@article{
 title = {Organic carbon burial during OAE2 driven by changes in the locus of organic matter sulfurization},
 type = {article},
 year = {2018},
 pages = {3409},
 volume = {9},
 websites = {www.nature.com/naturecommunications},
 publisher = {Springer US},
 id = {8269c7f4-9cbd-34c9-85c8-95eabedf1795},
 created = {2018-10-06T20:38:50.471Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2020-11-19T19:41:18.064Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Raven2018},
 private_publication = {false},
 abstract = {Ocean Anoxic Event 2 (OAE2) was a period of dramatic disruption to the global carbon cycle when massive amounts of organic matter (OM) were buried in marine sediments via complex and controversial mechanisms. Here we investigate the role of OM sulfurization, which makes OM less available for microbial respiration, in driving variable OM preservation in OAE2 sedimentary strata from Pont d'Issole (France). We find correlations between the concentration, S:C ratio, S-isotope composition, and sulfur speciation of OM suggesting that sulfurization facilitated changes in carbon burial at this site as the chemocline moved in and out of the sediments during deposition. These patterns are reproduced by a simple model, suggesting that small changes in primary productivity could drive large changes in local OM burial in environments poised near a critical redox threshold. This amplifying mechanism may be central to understanding the magnitude of global carbon cycle response to environmental perturbations.},
 bibtype = {article},
 author = {Raven, Morgan Reed and Fike, David A and Gomes, Maya L and Webb, Samuel M and Bradley, Alexander S and Mcclelland, Harry-Luke O},
 doi = {10.1038/s41467-018-05943-6},
 journal = {Nature Communications}
}

Ocean Anoxic Event 2 (OAE2) was a period of dramatic disruption to the global carbon cycle when massive amounts of organic matter (OM) were buried in marine sediments via complex and controversial mechanisms. Here we investigate the role of OM sulfurization, which makes OM less available for microbial respiration, in driving variable OM preservation in OAE2 sedimentary strata from Pont d'Issole (France). We find correlations between the concentration, S:C ratio, S-isotope composition, and sulfur speciation of OM suggesting that sulfurization facilitated changes in carbon burial at this site as the chemocline moved in and out of the sediments during deposition. These patterns are reproduced by a simple model, suggesting that small changes in primary productivity could drive large changes in local OM burial in environments poised near a critical redox threshold. This amplifying mechanism may be central to understanding the magnitude of global carbon cycle response to environmental perturbations.

@article{
 title = {Hopanoid-free Methylobacterium extorquens DM4 overproduces carotenoids and has widespread growth impairment},
 type = {article},
 year = {2017},
 pages = {e0173323},
 volume = {12},
 websites = {http://dx.plos.org/10.1371/journal.pone.0173323},
 id = {5b52bdb6-c723-3988-bc6b-34c73bfbb5b0},
 created = {2017-04-04T18:05:58.560Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2017-07-25T21:51:12.870Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Bradley2017},
 private_publication = {false},
 bibtype = {article},
 author = {Bradley, Alexander S. and Swanson, Paige K. and Muller, Emilie E. L. and Bringel, Françoise and Caroll, Sean M. and Pearson, Ann and Vuilleumier, Stéphane and Marx, Christopher J.},
 doi = {10.1371/journal.pone.0173323},
 journal = {PLoS One},
 number = {3}
}

@article{
 title = {Heritability of the Structures and 13C Fractionation in Tomato Leaf Wax Alkanes: A Genetic Model System to Inform Paleoenvironmental Reconstructions},
 type = {article},
 year = {2017},
 keywords = {anteiso -alkanes,frontiers in earth science,frontiersin,introgression line,iso -alkanes,n -alkanes,n-alkanes, iso-alkanes, anteiso-alkanes, tomato, i,org,qtl,stable carbon isotopes,tomato,www},
 pages = {1-13},
 volume = {5},
 websites = {http://journal.frontiersin.org/article/10.3389/feart.2017.00047/full},
 id = {efbeea3f-5b92-3923-a35c-7a4750149fb2},
 created = {2017-06-16T14:41:59.625Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2017-07-25T21:51:12.861Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Bender2017},
 private_publication = {false},
 bibtype = {article},
 author = {Bender, Amanda L. D. and Chitwood, Daniel H. and Bradley, Alexander S.},
 doi = {10.3389/feart.2017.00047},
 journal = {Frontiers in Earth Science},
 number = {June}
}

@article{
 title = {Hydrogen isotope composition of Thermoanaerobacterium saccharolyticum lipids : Comparing wild type with a nfn- transhydrogenase mutant},
 type = {article},
 year = {2017},
 keywords = {anaerobe energy metabolism,compound specific hydrogen isotopes,electron bifurcating transhydrogenase},
 pages = {239-241},
 volume = {113},
 websites = {https://doi.org/10.1016/j.orggeochem.2017.06.020},
 publisher = {Elsevier Ltd},
 id = {73dc4bf2-deb1-37e6-8b9a-f3ec7ded5166},
 created = {2017-09-24T09:37:50.498Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2019-12-13T21:04:29.785Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 citation_key = {Leavitt2017},
 private_publication = {false},
 bibtype = {article},
 author = {Leavitt, William D and Murphy, Sean Jean-loup and Lynd, Lee R and Bradley, Alexander S},
 doi = {10.1016/j.orggeochem.2017.06.020},
 journal = {Organic Geochemistry}
}

@article{
 title = {Patterns of sulfur isotope fractionation during Microbial Sulfate Reduction},
 type = {article},
 year = {2016},
 pages = {91-101},
 volume = {14},
 websites = {http://doi.wiley.com/10.1111/gbi.12149},
 id = {a827691a-9e91-3391-bcc7-7778b8390993},
 created = {2015-07-24T22:14:21.000Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2021-06-10T13:09:26.782Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Bradley2015},
 private_publication = {false},
 bibtype = {article},
 author = {Bradley, A.S. and Leavitt, W.D. and Schmidt, M. and Knoll, A.H. and Girguis, P.R. and Johnston, D.T.},
 doi = {10.1111/gbi.12149},
 journal = {Geobiology}
}

@article{
 title = {Thiosulfate oxidation by Thiomicrospira thermophila: Metabolic flexibility in response to ambient geochemistry},
 type = {article},
 year = {2016},
 pages = {3057-3072},
 volume = {18},
 id = {0111f09f-a5d9-38f1-bd39-204809564da3},
 created = {2016-05-27T08:02:06.000Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2019-12-13T18:07:28.653Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Houghton2016},
 private_publication = {false},
 abstract = {Previous studies of the stoichiometry of thiosulfateoxidation by colorless sulfur bacteria have failed todemonstrate mass balance of sulfur, indicating thatunidentified oxidized products must be present. Herethe reaction stoichiometry and kinetics undervariable pH conditions during the growth of Thiomi-crospira thermophila strain EPR85, isolated fromdiffuse hydrothermal fluids at the East Pacific Rise, ispresented. At pH 8.0, thiosulfate was stoichiometri-cally converted to sulfate. At lower pH, the productsof thiosulfate oxidation were extracellular elementalsulfur and sulfate. We were able to replicate previousexperiments and identify the missing sulfur as tetra-thionate, consistent with previous reports of theactivity of thiosulfate dehydrogenase. Tetrathionatewas formed under slightly acidic conditions.Genomic DNA from T. thermophila strain EPR85 con-tains genes homologous to those in the Sox pathway(soxAXYZBCDL), as well as rhodanese and thiosul-fate dehydrogenase. No other sulfur oxidizingbacteria containing sox(CD)2genes have beenrepor ted to produce extracellular elemental sulfur. Ifthe apparent modified Sox pathway we observed in T.thermophila is present in marine Thiobacillus andThiomicrospira species, production of extracellularelemental sulfur may be biogeochemically importantin marine sulfur cycling.},
 bibtype = {article},
 author = {Houghton, J. L. and Foustoukos, D. I. and Flynn, T. M. and Vetriani, C. and Bradley, Alexander S. and Fike, D. A.},
 doi = {10.1111/1462-2920.13232},
 journal = {Environmental Microbiology}
}

Previous studies of the stoichiometry of thiosulfateoxidation by colorless sulfur bacteria have failed todemonstrate mass balance of sulfur, indicating thatunidentified oxidized products must be present. Herethe reaction stoichiometry and kinetics undervariable pH conditions during the growth of Thiomi-crospira thermophila strain EPR85, isolated fromdiffuse hydrothermal fluids at the East Pacific Rise, ispresented. At pH 8.0, thiosulfate was stoichiometri-cally converted to sulfate. At lower pH, the productsof thiosulfate oxidation were extracellular elementalsulfur and sulfate. We were able to replicate previousexperiments and identify the missing sulfur as tetra-thionate, consistent with previous reports of theactivity of thiosulfate dehydrogenase. Tetrathionatewas formed under slightly acidic conditions.Genomic DNA from T. thermophila strain EPR85 con-tains genes homologous to those in the Sox pathway(soxAXYZBCDL), as well as rhodanese and thiosul-fate dehydrogenase. No other sulfur oxidizingbacteria containing sox(CD)2genes have beenrepor ted to produce extracellular elemental sulfur. Ifthe apparent modified Sox pathway we observed in T.thermophila is present in marine Thiobacillus andThiomicrospira species, production of extracellularelemental sulfur may be biogeochemically importantin marine sulfur cycling.

@article{
 title = {Transhydrogenase and growth substrate influence lipid hydrogen isotope ratios in Desulfovibrio alaskensis G20},
 type = {article},
 year = {2016},
 volume = {7},
 id = {7da52c6f-6f88-33a2-ae91-c9bc2d7dd724},
 created = {2016-07-13T23:22:39.000Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2017-07-25T21:51:12.862Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 citation_key = {Leavitt2016},
 private_publication = {false},
 abstract = {Microbial fatty acids preserve metabolic and environmental information in their hydrogen isotope ratios (2H/1H). This ratio is influenced by parameters that include the 2H/1H of water in the microbial growth environment, and biosynthetic fractionations between water and lipid. In some microbes, this biosynthetic fractionation has been shown to vary systematically with central energy metabolism, and controls on fatty acid 2H/1H may be linked to the intracellular production of NADPH. We examined the apparent fractionation between media water and the fatty acids produced by Desulfovibrio alaskensis G20. Growth was in batch culture with malate as an electron donor for sulfate respiration, and with pyruvate and fumarate as substrates for fermentation and for sulfate respiration. A larger fractionation was observed as a consequence of respiratory or fermentative growth on pyruvate than growth on fumarate or malate. This difference correlates with opposite apparent flows of electrons through the electron bifurcating/confurcating transhydrogenase NfnAB. When grown on malate or fumarate, mutant strains of D. alaskensis G20 containing transposon disruptions in a copy of nfnAB show different fractionations than the wild type strain. This phenotype is muted during fermentative growth on pyruvate, and it is absent when pyruvate is a substrate for sulfate reduction. All strains and conditions produced similar fatty acid profiles, and the 2H/1H of individual lipids changed in concert with the mass-weighted average. Unsaturated fatty acids were generally depleted in 2H relative to their saturated homologs, and anteiso-branched fatty acids were generally depleted in 2H relative to straight-chain fatty acids. Fractionation correlated with growth rate, a pattern that has also been observed in the fractionation of sulfur isotopes during dissimilatory sulfate reduction by sulfate-reducing bacteria.},
 bibtype = {article},
 author = {Leavitt, William D and Flynn, Theodore M and Suess, Melanie K and Bradley, Alexander S},
 doi = {10.3389/fmicb.2016.00918},
 journal = {Frontiers in Microbiology},
 number = {918}
}

Microbial fatty acids preserve metabolic and environmental information in their hydrogen isotope ratios (2H/1H). This ratio is influenced by parameters that include the 2H/1H of water in the microbial growth environment, and biosynthetic fractionations between water and lipid. In some microbes, this biosynthetic fractionation has been shown to vary systematically with central energy metabolism, and controls on fatty acid 2H/1H may be linked to the intracellular production of NADPH. We examined the apparent fractionation between media water and the fatty acids produced by Desulfovibrio alaskensis G20. Growth was in batch culture with malate as an electron donor for sulfate respiration, and with pyruvate and fumarate as substrates for fermentation and for sulfate respiration. A larger fractionation was observed as a consequence of respiratory or fermentative growth on pyruvate than growth on fumarate or malate. This difference correlates with opposite apparent flows of electrons through the electron bifurcating/confurcating transhydrogenase NfnAB. When grown on malate or fumarate, mutant strains of D. alaskensis G20 containing transposon disruptions in a copy of nfnAB show different fractionations than the wild type strain. This phenotype is muted during fermentative growth on pyruvate, and it is absent when pyruvate is a substrate for sulfate reduction. All strains and conditions produced similar fatty acid profiles, and the 2H/1H of individual lipids changed in concert with the mass-weighted average. Unsaturated fatty acids were generally depleted in 2H relative to their saturated homologs, and anteiso-branched fatty acids were generally depleted in 2H relative to straight-chain fatty acids. Fractionation correlated with growth rate, a pattern that has also been observed in the fractionation of sulfur isotopes during dissimilatory sulfate reduction by sulfate-reducing bacteria.

@article{
 title = {The sluggish speed of making abiotic methane},
 type = {article},
 year = {2016},
 pages = {13944-13946},
 volume = {113},
 websites = {http://www.pnas.org/lookup/doi/10.1073/pnas.1617103113},
 id = {70ace463-b247-3dcb-9659-6761d69d3b18},
 created = {2016-12-22T15:30:04.000Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2017-06-30T19:27:43.964Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Bradley2016},
 private_publication = {false},
 bibtype = {article},
 author = {Bradley, Alexander S.},
 doi = {10.1073/pnas.1617103113},
 journal = {Proceedings of the National Academy of Sciences},
 number = {49}
}

@article{
 title = {Fractionation of sulfur and hydrogen isotopes in Desulfovibrio vulgaris with perturbed DsrC expression},
 type = {article},
 year = {2016},
 keywords = {Anaerobic energy metabolism,Biomarkers,Compound specific hydrogen isotopes,Dissimilatory sulfate reduction,Sulfur isotopes},
 pages = {1-8},
 volume = {363},
 id = {c88622cd-a213-388e-8bfe-0e7ef166beda},
 created = {2017-02-21T02:12:17.000Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2019-12-13T18:07:29.330Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Leavitt2016a},
 private_publication = {false},
 bibtype = {article},
 author = {Leavitt, William D. and Venceslau, Sofia S. and Pereira, In??s A C and Johnston, David T. and Bradley, Alexander S.},
 doi = {10.1093/femsle/fnw226},
 journal = {FEMS Microbiology Letters},
 number = {20}
}

@inbook{
 type = {inbook},
 year = {2016},
 pages = {479-515},
 id = {968146bf-beb6-3184-807f-93edd8af79ae},
 created = {2017-10-21T00:55:18.286Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2019-12-13T21:05:53.123Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {false},
 hidden = {false},
 citation_key = {Fike2016},
 private_publication = {false},
 bibtype = {inbook},
 author = {Fike, David A and Bradley, Alexander S and Leavitt, William D},
 chapter = {Geomicrobiology of Sulfur},
 title = {Erlich's Geomicrobiology}
}

@article{
 title = {Rethinking the Ancient Sulfur Cycle},
 type = {article},
 year = {2015},
 keywords = {carbonate-associated sulfate,microbial sulfate reduction,pyrite,seawater sulfate,sulfur isotopes},
 pages = {593-622},
 volume = {43},
 websites = {http://www.annualreviews.org/doi/abs/10.1146/annurev-earth-060313-054802},
 id = {9c852b58-ec10-3fe5-aa53-ae3e7a7882e2},
 created = {2015-06-03T23:08:14.000Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2020-07-09T23:44:48.283Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Fike2013},
 private_publication = {false},
 abstract = {The sulfur biogeochemical cycle integrates the metabolic activity ofmultiple microbial pathways (e.g., sulfate reduction, disproportionation, and sulfide oxidation) along with abiotic reactions and geological processes that cycle sulfur through various reservoirs. The sulfur cycle impacts the global carbon cycle and climate primarily through the remineralization of organic carbon. Over geological timescales, cycling of sulfur is closely tied to the redox state of Earth’s exosphere through the burial of oxidized (sulfate) and reduced (sulfide) sulfur species in marine sediments. Biological sulfur cycling is associated with isotopic fractionations that can be used to trace the fluxes through various metabolic pathways. The resulting isotopic data provide insights into sulfur cycling in both modern and ancient environments via isotopic signatures in sedimentary sulfate and sulfide phases. Here, we review the deep-time δ34S record of marine sulfates and sulfides in light of recent advances in understanding how isotopic signatures are generated by microbial activity, how these signatures are encoded in marine sediments, and how they may be altered following deposition. The resulting picture shows a sulfur cycle intimately coupled to ambient carbon cycling, where sulfur isotopic records preserved in sedimentary rocks are critically depen- dent on sedimentological and geochemical conditions (e.g., iron availability) during deposition.},
 bibtype = {article},
 author = {Fike, David A. and Bradley, Alexander S. and Rose, Catherine V.},
 doi = {10.1146/annurev-earth-060313-054802},
 journal = {Annual Review of Earth and Planetary Sciences},
 number = {1}
}

The sulfur biogeochemical cycle integrates the metabolic activity ofmultiple microbial pathways (e.g., sulfate reduction, disproportionation, and sulfide oxidation) along with abiotic reactions and geological processes that cycle sulfur through various reservoirs. The sulfur cycle impacts the global carbon cycle and climate primarily through the remineralization of organic carbon. Over geological timescales, cycling of sulfur is closely tied to the redox state of Earth’s exosphere through the burial of oxidized (sulfate) and reduced (sulfide) sulfur species in marine sediments. Biological sulfur cycling is associated with isotopic fractionations that can be used to trace the fluxes through various metabolic pathways. The resulting isotopic data provide insights into sulfur cycling in both modern and ancient environments via isotopic signatures in sedimentary sulfate and sulfide phases. Here, we review the deep-time δ34S record of marine sulfates and sulfides in light of recent advances in understanding how isotopic signatures are generated by microbial activity, how these signatures are encoded in marine sediments, and how they may be altered following deposition. The resulting picture shows a sulfur cycle intimately coupled to ambient carbon cycling, where sulfur isotopic records preserved in sedimentary rocks are critically depen- dent on sedimentological and geochemical conditions (e.g., iron availability) during deposition.

@article{
 title = {Hopanoids as functional analogues of cholesterol in bacterial membranes},
 type = {article},
 year = {2015},
 pages = {11971-11976},
 volume = {112},
 websites = {http://www.pnas.org/lookup/doi/10.1073/pnas.1515607112},
 id = {0149fc61-bc60-31a7-acc6-65548364821a},
 created = {2015-09-27T11:38:42.000Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2017-03-10T07:28:27.036Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Saenz2015a},
 private_publication = {false},
 bibtype = {article},
 author = {Sáenz, James P. and Grosser, Daniel and Bradley, Alexander S. and Lagny, Thibaut J. and Lavrynenko, Oksana and Broda, Martyna and Simons, Kai},
 doi = {10.1073/pnas.1515607112},
 journal = {Proceedings of the National Academy of Sciences},
 number = {38}
}

@article{
 title = {Sulfur Isotope Effects of Dissimilatory Sulfite Reductase},
 type = {article},
 year = {2015},
 keywords = {cycle,dissimilatory sulfite reductase,enzyme-specific isotope fractionation,global sulfur,global sulfur cycle,microbial sulfate reduction,minor sulfur isotopes},
 pages = {1-38},
 volume = {6},
 id = {ef93fed7-b0d5-312b-bc0d-6f10cc91bff4},
 created = {2015-12-28T22:30:16.000Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2017-07-25T21:51:12.876Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Leavitt2015},
 private_publication = {false},
 bibtype = {article},
 author = {Leavitt, William D and Bradley, Alexander S and Santos, André A and Inês A. C. Pereira, undefined and Johnston, David T.},
 doi = {10.3389/fmicb.2015.01392},
 journal = {Frontiers in Microbiology},
 number = {December}
}

@article{
 title = {Determination and application of the equilibrium oxygen isotope effect between water and sulfite},
 type = {article},
 year = {2014},
 pages = {694-711},
 volume = {125},
 websites = {http://linkinghub.elsevier.com/retrieve/pii/S0016703713005073},
 month = {1},
 publisher = {Elsevier Ltd},
 id = {389eed81-6aac-3b96-a93f-ca8d07393854},
 created = {2014-01-19T03:57:36.000Z},
 accessed = {2014-01-19},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2019-12-13T22:56:51.099Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Wankel2014},
 private_publication = {false},
 bibtype = {article},
 author = {Wankel, Scott D. and Bradley, Alexander S. and Eldridge, Daniel L. and Johnston, David T.},
 doi = {10.1016/j.gca.2013.08.039},
 journal = {Geochimica et Cosmochimica Acta}
}

@article{
 title = {Multiple sulfur isotope signatures of sulfite and thiosulfate reduction by the model dissimilatory sulfate-reducer, Desulfovibrio alaskensis str. G20},
 type = {article},
 year = {2014},
 keywords = {biogeochemical sulfur cycle,microbial sulfate reduction,microbial sulfate reduction, multiple sulfur isoto,multiple sulfur isotopes,sulfur,thionates},
 pages = {1-16},
 volume = {5},
 websites = {http://www.frontiersin.org/Microbiological_Chemistry_and_Geomicrobiology/10.3389/fmicb.2014.00591/abstract},
 month = {11},
 day = {25},
 id = {acff3c89-20a6-3d58-877d-e6bc4d60b8cf},
 created = {2014-11-28T21:36:18.000Z},
 accessed = {2014-11-28},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2017-07-25T21:51:12.890Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Leavitt2014},
 folder_uuids = {17a7dc4f-ef34-43b7-8510-92f8cf4136fc},
 private_publication = {false},
 bibtype = {article},
 author = {Leavitt, William D. and Cummins, Renata and Schmidt, Marian L. and Sim, Min S. and Ono, Shuhei and Bradley, Alexander S. and Johnston, David T.},
 doi = {10.3389/fmicb.2014.00591},
 journal = {Frontiers in Microbiology},
 number = {November}
}

@article{
 title = {Spatial and temporal variability of biomarkers and microbial diversity reveal metabolic and community flexibility in Streamer Biofilm Communities in the Lower Geyser Basin, Yellowstone National Park.},
 type = {article},
 year = {2013},
 keywords = {16S,16S: genetics,Archaea,Archaea: classification,Archaea: genetics,Archaeal,Archaeal: chemistry,Archaeal: genetics,Bacteria,Bacteria: classification,Bacteria: genetics,Bacterial,Bacterial: chemistry,Bacterial: genetics,Biofilms,Biota,Cluster Analysis,DNA,Genes,Hot Springs,Hot Springs: microbiology,Lipids,Lipids: analysis,Molecular Sequence Data,Nucleic Acid,Phylogeny,RNA,Ribosomal,Ribosomal: chemistry,Ribosomal: genetics,Sequence Analysis,Sequence Homology,Temperature,United States,rRNA},
 pages = {549-69},
 volume = {11},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/23981055},
 month = {11},
 id = {300f0f7f-4fff-38f3-9974-eb70cf0f5c97},
 created = {2014-01-19T03:57:36.000Z},
 accessed = {2014-01-19},
 file_attached = {false},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2017-03-10T07:28:21.318Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Schubotz2013},
 private_publication = {false},
 abstract = {Detailed analysis of 16S rRNA and intact polar lipids (IPLs) from streamer biofilm communities (SBCs), collected from geochemically similar hot springs in the Lower Geyser Basin, Yellowstone National Park, shows good agreement and affirm that IPLs can be used as reliable markers for the microbial constituents of SBCs. Uncultured Crenarchaea are prominent in SBS, and their IPLs contain both glycosidic and mixed glyco-phospho head groups with tetraether cores, having 0-4 rings. Archaeal IPL contributions increase with increasing temperature and comprise up to one-fourth of the total IPL inventory at >84 °C. At elevated temperatures, bacterial IPLs contain abundant glycosidic glycerol diether lipids. Diether and diacylglycerol (DAG) lipids with aminopentanetetrol and phosphatidylinositol head groups were identified as lipids diagnostic of Aquificales, while DAG glycolipids and glyco-phospholipids containing N-acetylgycosamine as head group were assigned to members of the Thermales. With decreasing temperature and concomitant changes in water chemistry, IPLs typical of phototrophic bacteria, such as mono-, diglycosyl, and sulfoquinovosyl DAG, which are specific for cyanobacteria, increase in abundance, consistent with genomic data from the same samples. Compound-specific stable carbon isotope analysis of IPL breakdown products reveals a large isotopic diversity among SBCs in different hot springs. At two of the hot springs, 'Bison Pool' and Flat Cone, lipids derived from Aquificales are enriched in (13) C relative to biomass and approach values close to dissolved inorganic carbon (DIC) (approximately 0‰), consistent with fractionation during autotrophic carbon fixation via the reversed tricarboxylic acid pathway. At a third site, Octopus Spring, the same Aquificales-diagnostic lipids are 10‰ depleted relative to biomass and resemble stable carbon isotope values of dissolved organic carbon (DOC), indicative of heterotrophy. Other bacterial and archaeal lipids show a similar variance, with values resembling the DIC or DOC pool or a mixture thereof. This variance cannot be explained by hot spring chemistry or temperature alone, but instead, we argue that intermittent input of exogenous organic carbon can result in metabolic shifts of the chemotrophic communities from autotrophy to heterotrophy and vice versa.},
 bibtype = {article},
 author = {Schubotz, F. and Meyer-Dombard, D.R. and Bradley, A.S. and Fredricks, H.F. and Hinrichs, K-U. and Shock, E.L. and Summons, R.E.},
 doi = {10.1111/gbi.12051},
 journal = {Geobiology},
 number = {6}
}

Detailed analysis of 16S rRNA and intact polar lipids (IPLs) from streamer biofilm communities (SBCs), collected from geochemically similar hot springs in the Lower Geyser Basin, Yellowstone National Park, shows good agreement and affirm that IPLs can be used as reliable markers for the microbial constituents of SBCs. Uncultured Crenarchaea are prominent in SBS, and their IPLs contain both glycosidic and mixed glyco-phospho head groups with tetraether cores, having 0-4 rings. Archaeal IPL contributions increase with increasing temperature and comprise up to one-fourth of the total IPL inventory at >84 °C. At elevated temperatures, bacterial IPLs contain abundant glycosidic glycerol diether lipids. Diether and diacylglycerol (DAG) lipids with aminopentanetetrol and phosphatidylinositol head groups were identified as lipids diagnostic of Aquificales, while DAG glycolipids and glyco-phospholipids containing N-acetylgycosamine as head group were assigned to members of the Thermales. With decreasing temperature and concomitant changes in water chemistry, IPLs typical of phototrophic bacteria, such as mono-, diglycosyl, and sulfoquinovosyl DAG, which are specific for cyanobacteria, increase in abundance, consistent with genomic data from the same samples. Compound-specific stable carbon isotope analysis of IPL breakdown products reveals a large isotopic diversity among SBCs in different hot springs. At two of the hot springs, 'Bison Pool' and Flat Cone, lipids derived from Aquificales are enriched in (13) C relative to biomass and approach values close to dissolved inorganic carbon (DIC) (approximately 0‰), consistent with fractionation during autotrophic carbon fixation via the reversed tricarboxylic acid pathway. At a third site, Octopus Spring, the same Aquificales-diagnostic lipids are 10‰ depleted relative to biomass and resemble stable carbon isotope values of dissolved organic carbon (DOC), indicative of heterotrophy. Other bacterial and archaeal lipids show a similar variance, with values resembling the DIC or DOC pool or a mixture thereof. This variance cannot be explained by hot spring chemistry or temperature alone, but instead, we argue that intermittent input of exogenous organic carbon can result in metabolic shifts of the chemotrophic communities from autotrophy to heterotrophy and vice versa.

@article{
 title = {Archaeal and bacterial glycerol dialkyl glycerol tetraether lipids in chimneys of the Lost City Hydrothermal Field},
 type = {article},
 year = {2013},
 pages = {45-53},
 volume = {60},
 websites = {http://linkinghub.elsevier.com/retrieve/pii/S0146638013000934,http://dx.doi.org/10.1016/j.orggeochem.2013.04.010},
 month = {7},
 publisher = {Elsevier Ltd},
 id = {83bd9217-a218-32dd-8d89-0920486d064f},
 created = {2014-01-19T03:57:35.000Z},
 accessed = {2014-01-19},
 file_attached = {false},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2017-03-10T07:28:21.318Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Lincoln2013},
 private_publication = {false},
 abstract = {We detected archaeal and bacterial glycerol dialkyl glycerol tetraether (GDGT) lipids in carbonate chimneys of the Lost City Hydrothermal Field, an alkaline system near the mid-Atlantic Ridge. Isoprenoidal, archaeal tetraethers from this site include “H-shaped” GDGTs, crenarchaeol and GDGTs with 0–3 cyclopentane moieties (here referred to as GDGTs 0–3). Concentrations of GDGT-3 do not track those of GDGTs 0–2 across the sample set, suggesting that its biosynthesis may be subject to different controls. Two branched, bacterial GDGTs (brGDGTs) common in terrigenous environments were also detected. Consulting previously published surveys of microbial diversity at Lost City and literature on known precursor-product relationships, we investigated the provenance of these GDGTs. The principal source of GDGTs 0–3 is likely ANME-1 archaea, abundant at Lost City. H-shaped GDGTs are likely derived from thermophilic Methanobacteria and Thermoprotei. Marine Group I Thaumarchaea detected in Lost City chimneys are a potential source of crenarchaeol, but it is unclear whether they are autotrophic nitrifiers or representatives of a hydrothermal ecotype with different physiology. The detection of branched GDGTs, possibly synthesized by Acidobacteria at Lost City, adds to a growing body of evidence that the capacity for their biosynthesis is not restricted to acidophilic soil bacteria and that they cannot strictly be considered indicators of terrigenous contributions to marine sediments. Input of hydrothermally derived lipids has the potential to complicate paleoproxy applications based on GDGTs. We propose that H-GDGTs be viewed as indicators of hydrothermal input and that their detection in sediments warrants caution in proxy application when a hydrothermal origin for co-occurring isoprenoidal and brGDGTs cannot be excluded.},
 bibtype = {article},
 author = {Lincoln, Sara A. and Bradley, Alexander S. and Newman, Sharon A. and Summons, Roger E.},
 doi = {10.1016/j.orggeochem.2013.04.010},
 journal = {Organic Geochemistry}
}

We detected archaeal and bacterial glycerol dialkyl glycerol tetraether (GDGT) lipids in carbonate chimneys of the Lost City Hydrothermal Field, an alkaline system near the mid-Atlantic Ridge. Isoprenoidal, archaeal tetraethers from this site include “H-shaped” GDGTs, crenarchaeol and GDGTs with 0–3 cyclopentane moieties (here referred to as GDGTs 0–3). Concentrations of GDGT-3 do not track those of GDGTs 0–2 across the sample set, suggesting that its biosynthesis may be subject to different controls. Two branched, bacterial GDGTs (brGDGTs) common in terrigenous environments were also detected. Consulting previously published surveys of microbial diversity at Lost City and literature on known precursor-product relationships, we investigated the provenance of these GDGTs. The principal source of GDGTs 0–3 is likely ANME-1 archaea, abundant at Lost City. H-shaped GDGTs are likely derived from thermophilic Methanobacteria and Thermoprotei. Marine Group I Thaumarchaea detected in Lost City chimneys are a potential source of crenarchaeol, but it is unclear whether they are autotrophic nitrifiers or representatives of a hydrothermal ecotype with different physiology. The detection of branched GDGTs, possibly synthesized by Acidobacteria at Lost City, adds to a growing body of evidence that the capacity for their biosynthesis is not restricted to acidophilic soil bacteria and that they cannot strictly be considered indicators of terrigenous contributions to marine sediments. Input of hydrothermally derived lipids has the potential to complicate paleoproxy applications based on GDGTs. We propose that H-GDGTs be viewed as indicators of hydrothermal input and that their detection in sediments warrants caution in proxy application when a hydrothermal origin for co-occurring isoprenoidal and brGDGTs cannot be excluded.

@article{
 title = {Influence of sulfate reduction rates on the Phanerozoic sulfur isotope record.},
 type = {article},
 year = {2013},
 pages = {11244-9},
 volume = {110},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/23733944},
 month = {7},
 day = {9},
 id = {02d2fd2b-6eff-32bb-add1-08210d9943d1},
 created = {2014-01-19T03:57:35.000Z},
 accessed = {2014-01-11},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2020-11-19T19:41:17.879Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Leavitt2013},
 private_publication = {false},
 abstract = {Phanerozoic levels of atmospheric oxygen relate to the burial histories of organic carbon and pyrite sulfur. The sulfur cycle remains poorly constrained, however, leading to concomitant uncertainties in O2 budgets. Here we present experiments linking the magnitude of fractionations of the multiple sulfur isotopes to the rate of microbial sulfate reduction. The data demonstrate that such fractionations are controlled by the availability of electron donor (organic matter), rather than by the concentration of electron acceptor (sulfate), an environmental constraint that varies among sedimentary burial environments. By coupling these results with a sediment biogeochemical model of pyrite burial, we find a strong relationship between observed sulfur isotope fractionations over the last 200 Ma and the areal extent of shallow seafloor environments. We interpret this as a global dependency of the rate of microbial sulfate reduction on the availability of organic-rich sea-floor settings. However, fractionation during the early/mid-Paleozoic fails to correlate with shelf area. We suggest that this decoupling reflects a shallower paleoredox boundary, primarily confined to the water column in the early Phanerozoic. The transition between these two states begins during the Carboniferous and concludes approximately around the Triassic-Jurassic boundary, indicating a prolonged response to a Carboniferous rise in O2. Together, these results lay the foundation for decoupling changes in sulfate reduction rates from the global average record of pyrite burial, highlighting how the local nature of sedimentary processes affects global records. This distinction greatly refines our understanding of the S cycle and its relationship to the history of atmospheric oxygen.},
 bibtype = {article},
 author = {Leavitt, William D. and Halevy, Itay and Bradley, Alexander S. and Johnston, David T.},
 doi = {10.1073/pnas.1218874110},
 journal = {Proceedings of the National Academy of Sciences of the United States of America},
 number = {28}
}

Phanerozoic levels of atmospheric oxygen relate to the burial histories of organic carbon and pyrite sulfur. The sulfur cycle remains poorly constrained, however, leading to concomitant uncertainties in O2 budgets. Here we present experiments linking the magnitude of fractionations of the multiple sulfur isotopes to the rate of microbial sulfate reduction. The data demonstrate that such fractionations are controlled by the availability of electron donor (organic matter), rather than by the concentration of electron acceptor (sulfate), an environmental constraint that varies among sedimentary burial environments. By coupling these results with a sediment biogeochemical model of pyrite burial, we find a strong relationship between observed sulfur isotope fractionations over the last 200 Ma and the areal extent of shallow seafloor environments. We interpret this as a global dependency of the rate of microbial sulfate reduction on the availability of organic-rich sea-floor settings. However, fractionation during the early/mid-Paleozoic fails to correlate with shelf area. We suggest that this decoupling reflects a shallower paleoredox boundary, primarily confined to the water column in the early Phanerozoic. The transition between these two states begins during the Carboniferous and concludes approximately around the Triassic-Jurassic boundary, indicating a prolonged response to a Carboniferous rise in O2. Together, these results lay the foundation for decoupling changes in sulfate reduction rates from the global average record of pyrite burial, highlighting how the local nature of sedimentary processes affects global records. This distinction greatly refines our understanding of the S cycle and its relationship to the history of atmospheric oxygen.

@article{
 title = {Influence of subsurface biosphere on geochemical fluxes from diffuse hydrothermal fluids},
 type = {article},
 year = {2011},
 pages = {461-468},
 volume = {4},
 websites = {http://www.nature.com/doifinder/10.1038/ngeo1183},
 month = {6},
 publisher = {Nature Publishing Group},
 day = {19},
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 accessed = {2014-01-19},
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 citation_key = {Wankel2011},
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 bibtype = {article},
 author = {Wankel, Scott D. and Germanovich, Leonid N. and Lilley, Marvin D. and Genc, Gence and DiPerna, Christopher J. and Bradley, Alexander S. and Olson, Eric J. and Girguis, Peter R.},
 doi = {10.1038/ngeo1183},
 journal = {Nature Geoscience},
 number = {7}
}

@article{
 title = {Revisiting the dissimilatory sulfate reduction pathway.},
 type = {article},
 year = {2011},
 keywords = {Archaea,Archaea: metabolism,Bacteria,Bacteria: metabolism,Chemical Fractionation,Oxidation-Reduction,Sulfides,Sulfides: metabolism,Sulfites,Sulfites: metabolism,Sulfur,Sulfur Acids,Sulfur Acids: metabolism,Sulfur Isotopes,Sulfur Isotopes: chemistry,Sulfur Isotopes: metabolism,Sulfur: chemistry,Sulfur: metabolism,Thiosulfates,Thiosulfates: metabolism},
 pages = {446-57},
 volume = {9},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/21884365},
 month = {9},
 id = {e8b9d676-0b16-3c60-a324-b0eb04e46e3a},
 created = {2014-01-19T03:57:34.000Z},
 accessed = {2014-01-18},
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 last_modified = {2019-12-13T21:03:13.907Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Bradley2011},
 private_publication = {false},
 abstract = {Sulfur isotopes in the geological record integrate a combination of biological and diagenetic influences, but a key control on the ratio of sulfur isotopes in sedimentary materials is the magnitude of isotope fractionation imparted during dissimilatory sulfate reduction. This fractionation is controlled by the flux of sulfur through the network of chemical reactions involved in sulfate reduction and by the isotope effect associated with each of these chemical reactions. Despite its importance, the network of reactions constituting sulfate reduction is not fully understood, with two principle networks underpinning most isotope models. In this study, we build on biochemical data and recently solved crystal structures of enzymes to propose a revised network topology for the flow of sulfur through the sulfate reduction metabolism. This network is highly branched and under certain conditions produces results consistent with the observations that motivated previous sulfate reduction models. Our revised network suggests that there are two main paths to sulfide production: one that involves the production of thionate intermediates, and one that does not. We suggest that a key factor in determining sulfur isotope fractionation associated with sulfate reduction is the ratio of the rate at which electrons are supplied to subunits of Dsr vs. the rate of sulfite delivery to the active site of Dsr. This reaction network may help geochemists to better understand the relationship between the physiology of sulfate reduction and the isotopic record it produces.},
 bibtype = {article},
 author = {Bradley, Alexander S. and Leavitt, William D. and Johnston, David T.},
 doi = {10.1111/j.1472-4669.2011.00292.x},
 journal = {Geobiology},
 number = {5}
}

Sulfur isotopes in the geological record integrate a combination of biological and diagenetic influences, but a key control on the ratio of sulfur isotopes in sedimentary materials is the magnitude of isotope fractionation imparted during dissimilatory sulfate reduction. This fractionation is controlled by the flux of sulfur through the network of chemical reactions involved in sulfate reduction and by the isotope effect associated with each of these chemical reactions. Despite its importance, the network of reactions constituting sulfate reduction is not fully understood, with two principle networks underpinning most isotope models. In this study, we build on biochemical data and recently solved crystal structures of enzymes to propose a revised network topology for the flow of sulfur through the sulfate reduction metabolism. This network is highly branched and under certain conditions produces results consistent with the observations that motivated previous sulfate reduction models. Our revised network suggests that there are two main paths to sulfide production: one that involves the production of thionate intermediates, and one that does not. We suggest that a key factor in determining sulfur isotope fractionation associated with sulfate reduction is the ratio of the rate at which electrons are supplied to subunits of Dsr vs. the rate of sulfite delivery to the active site of Dsr. This reaction network may help geochemists to better understand the relationship between the physiology of sulfate reduction and the isotopic record it produces.

@article{
 title = {Multiple origins of methane at the Lost City Hydrothermal Field},
 type = {article},
 year = {2010},
 keywords = {lost city hydrothermal field},
 pages = {34-41},
 volume = {297},
 websites = {http://linkinghub.elsevier.com/retrieve/pii/S0012821X10003638},
 month = {8},
 publisher = {Elsevier B.V.},
 id = {2db79e13-74d8-3093-8ac2-26e580fc83be},
 created = {2014-01-19T03:57:33.000Z},
 accessed = {2014-01-19},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2017-03-10T07:28:21.318Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Bradley2010a},
 private_publication = {false},
 bibtype = {article},
 author = {Bradley, Alexander S. and Summons, Roger E.},
 doi = {10.1016/j.epsl.2010.05.034},
 journal = {Earth and Planetary Science Letters},
 number = {1-2}
}

@article{
 title = {Adenosylhopane: The first intermediate in hopanoid side chain biosynthesis},
 type = {article},
 year = {2010},
 pages = {1075-1081},
 volume = {41},
 websites = {http://linkinghub.elsevier.com/retrieve/pii/S0146638010001853},
 month = {10},
 publisher = {Elsevier Ltd},
 id = {ff91149c-8246-3568-894f-9a86b06459c1},
 created = {2014-01-19T03:57:34.000Z},
 accessed = {2014-01-09},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2018-06-01T19:28:06.635Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Bradley2010},
 folder_uuids = {9878a07d-c63c-4df7-829f-649893c9580f},
 private_publication = {false},
 bibtype = {article},
 author = {Bradley, Alexander S. and Pearson, Ann and Sáenz, James P. and Marx, Christopher J.},
 doi = {10.1016/j.orggeochem.2010.07.003},
 journal = {Organic Geochemistry},
 number = {10}
}

@article{
 title = {Expanding the limits of life.},
 type = {article},
 year = {2009},
 keywords = {Atlantic Ocean,Biogenesis,Biological Evolution,Carbon Isotopes,Carbon Isotopes: analysis,Ecosystem,Geologic Sediments,Geologic Sediments: chemistry,Geologic Sediments: microbiology,Hot Temperature,Hydrogen-Ion Concentration,Methane,Methane: chemistry},
 pages = {62-67},
 volume = {301},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/20058641},
 month = {12},
 id = {1b6ab34f-13a2-3f47-8de6-bed2391b9996},
 created = {2014-01-19T03:57:33.000Z},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2017-03-10T07:28:21.318Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Bradley2009a},
 private_publication = {false},
 bibtype = {article},
 author = {Bradley, Alexander S},
 journal = {Scientific American},
 number = {6}
}

@article{
 title = {Extraordinary 13C enrichment of diether lipids at the Lost City Hydrothermal Field indicates a carbon-limited ecosystem},
 type = {article},
 year = {2009},
 pages = {102-118},
 volume = {73},
 websites = {http://linkinghub.elsevier.com/retrieve/pii/S0016703708005899},
 month = {1},
 publisher = {Elsevier Ltd},
 id = {d6aaac2e-7222-39ae-a01d-b2de1ff1d41b},
 created = {2014-01-19T03:57:33.000Z},
 accessed = {2014-01-19},
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 last_modified = {2017-07-15T19:59:31.944Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Bradley2009b},
 private_publication = {false},
 bibtype = {article},
 author = {Bradley, Alexander S. and Hayes, John M. and Summons, Roger E.},
 doi = {10.1016/j.gca.2008.10.005},
 journal = {Geochimica et Cosmochimica Acta},
 number = {1}
}

@article{
 title = {Tubular compression fossils from the Ediacaran Nama Group, Namibia},
 type = {article},
 year = {2009},
 pages = {110-122},
 volume = {83},
 websites = {http://www.bioone.org/doi/abs/10.1666/09-040R.1},
 id = {46308c31-17b7-37a1-8dd8-fe529f91490c},
 created = {2014-01-19T03:57:34.000Z},
 file_attached = {true},
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 last_modified = {2017-03-10T07:28:21.318Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Cohen2009},
 private_publication = {false},
 bibtype = {article},
 author = {Cohen, Phoebe A. and Bradley, Alexander S. and Knoll, Andrew H. and Grotzinger, John P. and Jensen, S. and Abelson, J. and Hand, K. and Love, Gordon D. and Metz, J. and McLoughlin, N. and Meister, P. and Shepard, R. and Tice, M. and Wilson, J.P.},
 journal = {Journal of Paleontology},
 number = {1}
}

@article{
 title = {Fossil steroids record the appearance of Demospongiae during the Cryogenian period.},
 type = {article},
 year = {2009},
 keywords = {Ancient,Animals,Arabia,Biological Evolution,Biological Markers,Biological Markers: analysis,Biological Markers: chemistry,Cholestanes,Cholestanes: analysis,Cholestanes: chemistry,Cholestanes: isolation & purification,Fossils,Gas Chromatography-Mass Spectrometry,Geologic Sediments,Geologic Sediments: chemistry,History,Hydrocarbons,Hydrocarbons: analysis,Hydrocarbons: chemistry,Ice Cover,Oceans and Seas,Oxygen,Oxygen: analysis,Porifera,Porifera: physiology,Seawater,Seawater: chemistry},
 pages = {718-21},
 volume = {457},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/19194449},
 month = {2},
 publisher = {Nature Publishing Group},
 day = {5},
 id = {7e764581-9c18-30f3-9574-33469fff3162},
 created = {2014-01-19T03:57:35.000Z},
 accessed = {2014-01-17},
 file_attached = {false},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2017-03-10T07:28:21.318Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Love2009},
 folder_uuids = {8a3d41ab-8bb7-4032-a2c4-981411878979},
 private_publication = {false},
 abstract = {The Neoproterozoic era (1,000-542 Myr ago) was an era of climatic extremes and biological evolutionary developments culminating in the emergence of animals (Metazoa) and new ecosystems. Here we show that abundant sedimentary 24-isopropylcholestanes, the hydrocarbon remains of C(30) sterols produced by marine demosponges, record the presence of Metazoa in the geological record before the end of the Marinoan glaciation ( approximately 635 Myr ago). These sterane biomarkers are abundant in all formations of the Huqf Supergroup, South Oman Salt Basin, and, based on a new high-precision geochronology, constitute a continuous 100-Myr-long chemical fossil record of demosponges through the terminal Neoproterozoic and into the Early Cambrian epoch. The demosponge steranes occur in strata that underlie the Marinoan cap carbonate (>635 Myr ago). They currently represent the oldest evidence for animals in the fossil record, and are evidence for animals pre-dating the termination of the Marinoan glaciation. This suggests that shallow shelf waters in some late Cryogenian ocean basins (>635 Myr ago) contained dissolved oxygen in concentrations sufficient to support basal metazoan life at least 100 Myr before the rapid diversification of bilaterians during the Cambrian explosion. Biomarker analysis has yet to reveal any convincing evidence for ancient sponges pre-dating the first globally extensive Neoproterozoic glacial episode (the Sturtian, approximately 713 Myr ago in Oman).},
 bibtype = {article},
 author = {Love, Gordon D and Grosjean, Emmanuelle and Stalvies, Charlotte and Fike, David A and Grotzinger, John P and Bradley, Alexander S and Kelly, Amy E and Bhatia, Maya and Meredith, William and Snape, Colin E and Bowring, Samuel a and Condon, Daniel J and Summons, Roger E},
 doi = {10.1038/nature07673},
 journal = {Nature},
 number = {7230}
}

The Neoproterozoic era (1,000-542 Myr ago) was an era of climatic extremes and biological evolutionary developments culminating in the emergence of animals (Metazoa) and new ecosystems. Here we show that abundant sedimentary 24-isopropylcholestanes, the hydrocarbon remains of C(30) sterols produced by marine demosponges, record the presence of Metazoa in the geological record before the end of the Marinoan glaciation ( approximately 635 Myr ago). These sterane biomarkers are abundant in all formations of the Huqf Supergroup, South Oman Salt Basin, and, based on a new high-precision geochronology, constitute a continuous 100-Myr-long chemical fossil record of demosponges through the terminal Neoproterozoic and into the Early Cambrian epoch. The demosponge steranes occur in strata that underlie the Marinoan cap carbonate (>635 Myr ago). They currently represent the oldest evidence for animals in the fossil record, and are evidence for animals pre-dating the termination of the Marinoan glaciation. This suggests that shallow shelf waters in some late Cryogenian ocean basins (>635 Myr ago) contained dissolved oxygen in concentrations sufficient to support basal metazoan life at least 100 Myr before the rapid diversification of bilaterians during the Cambrian explosion. Biomarker analysis has yet to reveal any convincing evidence for ancient sponges pre-dating the first globally extensive Neoproterozoic glacial episode (the Sturtian, approximately 713 Myr ago in Oman).

@article{
 title = {Structural diversity of diether lipids in carbonate chimneys at the Lost City Hydrothermal Field},
 type = {article},
 year = {2009},
 pages = {1169-1178},
 volume = {40},
 websites = {http://linkinghub.elsevier.com/retrieve/pii/S0146638009002022},
 month = {12},
 publisher = {Elsevier Ltd},
 id = {f938c7e7-0853-35e8-a09c-5a38ef166a86},
 created = {2014-01-19T03:57:34.000Z},
 accessed = {2014-01-19},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2017-03-10T07:28:21.318Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Bradley2009},
 private_publication = {false},
 bibtype = {article},
 author = {Bradley, Alexander S. and Fredricks, Helen and Hinrichs, Kai-uwe and Summons, Roger E.},
 doi = {10.1016/j.orggeochem.2009.09.004},
 journal = {Organic Geochemistry},
 number = {12}
}

@article{
 title = {Stable carbon isotope fractionation between substrates and products of Methanosarcina barkeri},
 type = {article},
 year = {2008},
 pages = {608-621},
 volume = {39},
 websites = {http://linkinghub.elsevier.com/retrieve/pii/S0146638008000764},
 month = {5},
 id = {4bc962ce-5b93-33d8-b1f3-9c278bbe6a18},
 created = {2014-01-19T03:57:35.000Z},
 accessed = {2014-01-19},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2017-07-25T21:51:12.874Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Londry2008},
 private_publication = {false},
 bibtype = {article},
 author = {Londry, Kathleen L. and Dawson, Kathleen G. and Grover, Heather D. and Summons, Roger E. and Bradley, Alexander S.},
 doi = {10.1016/j.orggeochem.2008.03.002},
 journal = {Organic Geochemistry},
 number = {5}
}

@article{
 title = {Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host.},
 type = {article},
 year = {2007},
 keywords = {Adenosine Triphosphate,Adenosine Triphosphate: chemistry,Archaeal Proteins,Archaeal Proteins: chemistry,Bacterial Proteins,Bacterial Proteins: chemistry,Cell Membrane,Cell Membrane: metabolism,Chemical,Escherichia coli,Escherichia coli: metabolism,Gene Expression Regulation,Gene Library,Gene Transfer,Genetic,Horizontal,Light,Models,Molecular Sequence Data,Phosphorylation,Photosynthetic Reaction Center Complex Proteins,Plant,Rhodopsin,Rhodopsin: genetics},
 pages = {5590-5595},
 volume = {104},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1838496&tool=pmcentrez&rendertype=abstract},
 month = {3},
 day = {27},
 id = {f49af8c1-38a3-3fbb-bdb0-1a4afa0df506},
 created = {2014-01-19T03:57:35.000Z},
 accessed = {2014-01-19},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2017-03-10T07:28:21.318Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Martinez2007},
 private_publication = {false},
 abstract = {Proteorhodopsins (PRs) are retinal-containing proteins that catalyze light-activated proton efflux across the cell membrane. These photoproteins are known to be globally distributed in the ocean's photic zone, and they are found in a diverse array of Bacteria and Archaea. Recently, light-enhanced growth rates and yields have been reported in at least one PR-containing marine bacterium, but the physiological basis of light-activated growth stimulation has not yet been determined. To describe more fully PR photosystem genetics and biochemistry, we functionally surveyed a marine picoplankton large-insert genomic library for recombinant clones expressing PR photosystems in vivo. Our screening approach exploited transient increases in vector copy number that significantly enhanced the sensitivity of phenotypic detection. Two genetically distinct recombinants, initially identified by their orange pigmentation, expressed a small cluster of genes encoding a complete PR-based photosystem. Genetic and biochemical analyses of transposon mutants verified the function of gene products in the photopigment and opsin biosynthetic pathways. Heterologous expression of six genes, five encoding photopigment biosynthetic proteins and one encoding a PR, generated a fully functional PR photosystem that enabled photophosphorylation in recombinant Escherichia coli cells exposed to light. Our results demonstrate that a single genetic event can result in the acquisition of phototrophic capabilities in an otherwise chemoorganotrophic microorganism, and they explain in part the ubiquity of PR photosystems among diverse microbial taxa.},
 bibtype = {article},
 author = {Martinez, A. and Bradley, Alexander S. and Waldbauer, Jacob R. and Summons, Roger E. and DeLong, Edward F.},
 doi = {10.1073/pnas.0611470104},
 journal = {Proceedings of the National Academy of Sciences of the United States of America},
 number = {13}
}

Proteorhodopsins (PRs) are retinal-containing proteins that catalyze light-activated proton efflux across the cell membrane. These photoproteins are known to be globally distributed in the ocean's photic zone, and they are found in a diverse array of Bacteria and Archaea. Recently, light-enhanced growth rates and yields have been reported in at least one PR-containing marine bacterium, but the physiological basis of light-activated growth stimulation has not yet been determined. To describe more fully PR photosystem genetics and biochemistry, we functionally surveyed a marine picoplankton large-insert genomic library for recombinant clones expressing PR photosystems in vivo. Our screening approach exploited transient increases in vector copy number that significantly enhanced the sensitivity of phenotypic detection. Two genetically distinct recombinants, initially identified by their orange pigmentation, expressed a small cluster of genes encoding a complete PR-based photosystem. Genetic and biochemical analyses of transposon mutants verified the function of gene products in the photopigment and opsin biosynthetic pathways. Heterologous expression of six genes, five encoding photopigment biosynthetic proteins and one encoding a PR, generated a fully functional PR photosystem that enabled photophosphorylation in recombinant Escherichia coli cells exposed to light. Our results demonstrate that a single genetic event can result in the acquisition of phototrophic capabilities in an otherwise chemoorganotrophic microorganism, and they explain in part the ubiquity of PR photosystems among diverse microbial taxa.

@article{
 title = {Steroids, triterpenoids and molecular oxygen.},
 type = {article},
 year = {2006},
 keywords = {Amino Acid Sequence,Cyanobacteria,Cyanobacteria: enzymology,Cyanobacteria: genetics,Cyanobacteria: metabolism,Evolution, Molecular,Intramolecular Transferases,Intramolecular Transferases: chemistry,Intramolecular Transferases: genetics,Intramolecular Transferases: metabolism,Models, Molecular,Molecular Sequence Data,Oxygen,Oxygen: metabolism,Sequence Alignment,Steroids,Steroids: biosynthesis,Triterpenes,Triterpenes: metabolism},
 pages = {951-68},
 volume = {361},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1578733&tool=pmcentrez&rendertype=abstract},
 month = {6},
 day = {29},
 id = {0cfc547e-fbc9-30ea-b390-35bf38221932},
 created = {2014-10-17T02:21:36.000Z},
 accessed = {2014-10-17},
 file_attached = {true},
 profile_id = {fd85b893-2275-3774-9b29-c65b0275f3f3},
 last_modified = {2017-03-10T07:28:21.318Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Summons2006},
 private_publication = {false},
 abstract = {There is a close connection between modern-day biosynthesis of particular triterpenoid biomarkers and presence of molecular oxygen in the environment. Thus, the detection of steroid and triterpenoid hydrocarbons far back in Earth history has been used to infer the antiquity of oxygenic photosynthesis. This prompts the question: were these compounds produced similarly in the past? In this paper, we address this question with a review of the current state of knowledge surrounding the oxygen requirement for steroid biosynthesis and phylogenetic patterns in the distribution of steroid and triterpenoid biosynthetic pathways. The hopanoid and steroid biosynthetic pathways are very highly conserved within the bacterial and eukaryotic domains, respectively. Bacteriohopanepolyols are produced by a wide range of bacteria, and are methylated in significant abundance at the C2 position by oxygen-producing cyanobacteria. On the other hand, sterol biosynthesis is sparsely distributed in distantly related bacterial taxa and the pathways do not produce the wide range of products that characterize eukaryotes. In particular, evidence for sterol biosynthesis by cyanobacteria appears flawed. Our experiments show that cyanobacterial cultures are easily contaminated by sterol-producing rust fungi, which can be eliminated by treatment with cycloheximide affording sterol-free samples. Sterols are ubiquitous features of eukaryotic membranes, and it appears likely that the initial steps in sterol biosynthesis were present in their modern form in the last common ancestor of eukaryotes. Eleven molecules of O2 are required by four enzymes to produce one molecule of cholesterol. Thermodynamic arguments, optimization of function and parsimony all indicate that an ancestral anaerobic pathway is highly unlikely. The known geological record of molecular fossils, especially steranes and triterpanes, is notable for the limited number of structural motifs that have been observed. With a few exceptions, the carbon skeletons are the same as those found in the lipids of extant organisms and no demonstrably extinct structures have been reported. Furthermore, their patterns of occurrence over billion year time-scales correlate strongly with environments of deposition. Accordingly, biomarkers are excellent indicators of environmental conditions even though the taxonomic affinities of all biomarkers cannot be precisely specified. Biomarkers are ultimately tied to biochemicals with very specific functional properties, and interpretations of the biomarker record will benefit from increased understanding of the biological roles of geologically durable molecules.},
 bibtype = {article},
 author = {Summons, Roger E and Bradley, Alexander S and Jahnke, Linda L and Waldbauer, Jacob R},
 doi = {10.1098/rstb.2006.1837},
 journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
 number = {1470}
}

There is a close connection between modern-day biosynthesis of particular triterpenoid biomarkers and presence of molecular oxygen in the environment. Thus, the detection of steroid and triterpenoid hydrocarbons far back in Earth history has been used to infer the antiquity of oxygenic photosynthesis. This prompts the question: were these compounds produced similarly in the past? In this paper, we address this question with a review of the current state of knowledge surrounding the oxygen requirement for steroid biosynthesis and phylogenetic patterns in the distribution of steroid and triterpenoid biosynthetic pathways. The hopanoid and steroid biosynthetic pathways are very highly conserved within the bacterial and eukaryotic domains, respectively. Bacteriohopanepolyols are produced by a wide range of bacteria, and are methylated in significant abundance at the C2 position by oxygen-producing cyanobacteria. On the other hand, sterol biosynthesis is sparsely distributed in distantly related bacterial taxa and the pathways do not produce the wide range of products that characterize eukaryotes. In particular, evidence for sterol biosynthesis by cyanobacteria appears flawed. Our experiments show that cyanobacterial cultures are easily contaminated by sterol-producing rust fungi, which can be eliminated by treatment with cycloheximide affording sterol-free samples. Sterols are ubiquitous features of eukaryotic membranes, and it appears likely that the initial steps in sterol biosynthesis were present in their modern form in the last common ancestor of eukaryotes. Eleven molecules of O2 are required by four enzymes to produce one molecule of cholesterol. Thermodynamic arguments, optimization of function and parsimony all indicate that an ancestral anaerobic pathway is highly unlikely. The known geological record of molecular fossils, especially steranes and triterpanes, is notable for the limited number of structural motifs that have been observed. With a few exceptions, the carbon skeletons are the same as those found in the lipids of extant organisms and no demonstrably extinct structures have been reported. Furthermore, their patterns of occurrence over billion year time-scales correlate strongly with environments of deposition. Accordingly, biomarkers are excellent indicators of environmental conditions even though the taxonomic affinities of all biomarkers cannot be precisely specified. Biomarkers are ultimately tied to biochemicals with very specific functional properties, and interpretations of the biomarker record will benefit from increased understanding of the biological roles of geologically durable molecules.

@article{
 title = {A serpentinite-hosted ecosystem: the Lost City Hydrothermal Field},
 type = {article},
 year = {2005},
 pages = {1428-1434},
 volume = {307},
 websites = {https://www.sciencemag.org/content/307/5714/1428},
 id = {89c3a7c8-2246-315a-b752-0b1f8537b716},
 created = {2014-01-19T03:57:34.000Z},
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 last_modified = {2017-03-10T07:28:21.318Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Kelley2005},
 private_publication = {false},
 bibtype = {article},
 author = {Kelley, Deborah S and Karson, Jeffrey A and Fru, Gretchen L and Yoerger, Dana R and Shank, Timothy M and Butterfield, David A and Hayes, John M and Schrenk, Matthew O and Olson, Eric J and Proskurowski, Giora and Jakuba, Mike and Bradley, Al and Larson, Ben and Ludwig, Kristin and Glickson, Deborah and Buckman, Kate and Bradley, Alexander S and Brazelton, William J and Roe, Kevin and Bernasconi, Stefano M and Elend, Mitch J and Lilley, Marvin D and Baross, John A and Summons, Roger E and Sylva, Sean P},
 doi = {10.1126/science.1102556},
 journal = {Science},
 number = {March}
}