Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods

Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods. Pierella Karlusich, J. J., Pelletier, E., Lombard, F., Carsique, M., Dvorak, E., Colin, S., Picheral, M., Cornejo-Castillo, F. M., Acinas, S. G., Pepperkok, R., Karsenti, E., de Vargas, C., Wincker, P., Bowler, C., & Foster, R. A. Nat Commun, 12(1):4160, 2021. Pierella Karlusich, Juan Jose Pelletier, Eric Lombard, Fabien Carsique, Madeline Dvorak, Etienne Colin, Sebastien Picheral, Marc Cornejo-Castillo, Francisco M Acinas, Silvia G Pepperkok, Rainer Karsenti, Eric de Vargas, Colomban Wincker, Patrick Bowler, Chris Foster, Rachel A eng Research Support, Non-U.S. Gov't England Nat Commun. 2021 Jul 6;12(1):4160. doi: 10.1038/s41467-021-24299-y.

Paper doi abstract bibtex 2 downloads

Nitrogen fixation has a critical role in marine primary production, yet our understanding of marine nitrogen-fixers (diazotrophs) is hindered by limited observations. Here, we report a quantitative image analysis pipeline combined with mapping of molecular markers for mining >2,000,000 images and >1300 metagenomes from surface, deep chlorophyll maximum and mesopelagic seawater samples across 6 size fractions (<0.2-2000 mum). We use this approach to characterise the diversity, abundance, biovolume and distribution of symbiotic, colony-forming and particle-associated diazotrophs at a global scale. We show that imaging and PCR-free molecular data are congruent. Sequence reads indicate diazotrophs are detected from the ultrasmall bacterioplankton (<0.2 mum) to mesoplankton (180-2000 mum) communities, while images predict numerous symbiotic and colony-forming diazotrophs (>20 microm). Using imaging and molecular data, we estimate that polyploidy can substantially affect gene abundances of symbiotic versus colony-forming diazotrophs. Our results support the canonical view that larger diazotrophs (>10 mum) dominate the tropical belts, while unicellular cyanobacterial and non-cyanobacterial diazotrophs are globally distributed in surface and mesopelagic layers. We describe co-occurring diazotrophic lineages of different lifestyles and identify high-density regions of diazotrophs in the global ocean. Overall, we provide an update of marine diazotroph biogeographical diversity and present a new bioimaging-bioinformatic workflow.

@article{RN254,
   author = {Pierella Karlusich, J. J. and Pelletier, E. and Lombard, F. and Carsique, M. and Dvorak, E. and Colin, S. and Picheral, M. and Cornejo-Castillo, F. M. and Acinas, S. G. and Pepperkok, R. and Karsenti, E. and de Vargas, C. and Wincker, P. and Bowler, C. and Foster, R. A.},
   title = {Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods},
   journal = {Nat Commun},
   volume = {12},
   number = {1},
   pages = {4160},
   note = {Pierella Karlusich, Juan Jose
Pelletier, Eric
Lombard, Fabien
Carsique, Madeline
Dvorak, Etienne
Colin, Sebastien
Picheral, Marc
Cornejo-Castillo, Francisco M
Acinas, Silvia G
Pepperkok, Rainer
Karsenti, Eric
de Vargas, Colomban
Wincker, Patrick
Bowler, Chris
Foster, Rachel A
eng
Research Support, Non-U.S. Gov't
England
Nat Commun. 2021 Jul 6;12(1):4160. doi: 10.1038/s41467-021-24299-y.},
   abstract = {Nitrogen fixation has a critical role in marine primary production, yet our understanding of marine nitrogen-fixers (diazotrophs) is hindered by limited observations. Here, we report a quantitative image analysis pipeline combined with mapping of molecular markers for mining >2,000,000 images and >1300 metagenomes from surface, deep chlorophyll maximum and mesopelagic seawater samples across 6 size fractions (<0.2-2000 mum). We use this approach to characterise the diversity, abundance, biovolume and distribution of symbiotic, colony-forming and particle-associated diazotrophs at a global scale. We show that imaging and PCR-free molecular data are congruent. Sequence reads indicate diazotrophs are detected from the ultrasmall bacterioplankton (<0.2 mum) to mesoplankton (180-2000 mum) communities, while images predict numerous symbiotic and colony-forming diazotrophs (>20 microm). Using imaging and molecular data, we estimate that polyploidy can substantially affect gene abundances of symbiotic versus colony-forming diazotrophs. Our results support the canonical view that larger diazotrophs (>10 mum) dominate the tropical belts, while unicellular cyanobacterial and non-cyanobacterial diazotrophs are globally distributed in surface and mesopelagic layers. We describe co-occurring diazotrophic lineages of different lifestyles and identify high-density regions of diazotrophs in the global ocean. Overall, we provide an update of marine diazotroph biogeographical diversity and present a new bioimaging-bioinformatic workflow.},
   keywords = {Aquatic Organisms
Bacteria/genetics/metabolism
Cyanobacteria/genetics/metabolism
Molecular Imprinting/*methods
Nitrogen/*metabolism
Nitrogen Fixation/*genetics/physiology
Oceans and Seas
Phylogeny
Plankton/metabolism
Seawater/*chemistry/microbiology
Symbiosis/genetics/physiology},
   ISSN = {2041-1723 (Electronic)
2041-1723 (Linking)},
   DOI = {10.1038/s41467-021-24299-y},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/34230473},
   year = {2021},
   type = {Journal Article}
}

Downloads: 2

{"_id":"u4HdxGdKBXx8inYee","bibbaseid":"pierellakarlusich-pelletier-lombard-carsique-dvorak-colin-picheral-cornejocastillo-etal-globaldistributionpatternsofmarinenitrogenfixersbyimagingandmolecularmethods-2021","author_short":["Pierella Karlusich, J. J.","Pelletier, E.","Lombard, F.","Carsique, M.","Dvorak, E.","Colin, S.","Picheral, M.","Cornejo-Castillo, F. M.","Acinas, S. G.","Pepperkok, R.","Karsenti, E.","de Vargas, C.","Wincker, P.","Bowler, C.","Foster, R. A."],"bibdata":{"bibtype":"article","type":"Journal Article","author":[{"propositions":[],"lastnames":["Pierella","Karlusich"],"firstnames":["J.","J."],"suffixes":[]},{"propositions":[],"lastnames":["Pelletier"],"firstnames":["E."],"suffixes":[]},{"propositions":[],"lastnames":["Lombard"],"firstnames":["F."],"suffixes":[]},{"propositions":[],"lastnames":["Carsique"],"firstnames":["M."],"suffixes":[]},{"propositions":[],"lastnames":["Dvorak"],"firstnames":["E."],"suffixes":[]},{"propositions":[],"lastnames":["Colin"],"firstnames":["S."],"suffixes":[]},{"propositions":[],"lastnames":["Picheral"],"firstnames":["M."],"suffixes":[]},{"propositions":[],"lastnames":["Cornejo-Castillo"],"firstnames":["F.","M."],"suffixes":[]},{"propositions":[],"lastnames":["Acinas"],"firstnames":["S.","G."],"suffixes":[]},{"propositions":[],"lastnames":["Pepperkok"],"firstnames":["R."],"suffixes":[]},{"propositions":[],"lastnames":["Karsenti"],"firstnames":["E."],"suffixes":[]},{"propositions":["de"],"lastnames":["Vargas"],"firstnames":["C."],"suffixes":[]},{"propositions":[],"lastnames":["Wincker"],"firstnames":["P."],"suffixes":[]},{"propositions":[],"lastnames":["Bowler"],"firstnames":["C."],"suffixes":[]},{"propositions":[],"lastnames":["Foster"],"firstnames":["R.","A."],"suffixes":[]}],"title":"Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods","journal":"Nat Commun","volume":"12","number":"1","pages":"4160","note":"Pierella Karlusich, Juan Jose Pelletier, Eric Lombard, Fabien Carsique, Madeline Dvorak, Etienne Colin, Sebastien Picheral, Marc Cornejo-Castillo, Francisco M Acinas, Silvia G Pepperkok, Rainer Karsenti, Eric de Vargas, Colomban Wincker, Patrick Bowler, Chris Foster, Rachel A eng Research Support, Non-U.S. Gov't England Nat Commun. 2021 Jul 6;12(1):4160. doi: 10.1038/s41467-021-24299-y.","abstract":"Nitrogen fixation has a critical role in marine primary production, yet our understanding of marine nitrogen-fixers (diazotrophs) is hindered by limited observations. Here, we report a quantitative image analysis pipeline combined with mapping of molecular markers for mining >2,000,000 images and >1300 metagenomes from surface, deep chlorophyll maximum and mesopelagic seawater samples across 6 size fractions (<0.2-2000 mum). We use this approach to characterise the diversity, abundance, biovolume and distribution of symbiotic, colony-forming and particle-associated diazotrophs at a global scale. We show that imaging and PCR-free molecular data are congruent. Sequence reads indicate diazotrophs are detected from the ultrasmall bacterioplankton (<0.2 mum) to mesoplankton (180-2000 mum) communities, while images predict numerous symbiotic and colony-forming diazotrophs (>20 microm). Using imaging and molecular data, we estimate that polyploidy can substantially affect gene abundances of symbiotic versus colony-forming diazotrophs. Our results support the canonical view that larger diazotrophs (>10 mum) dominate the tropical belts, while unicellular cyanobacterial and non-cyanobacterial diazotrophs are globally distributed in surface and mesopelagic layers. We describe co-occurring diazotrophic lineages of different lifestyles and identify high-density regions of diazotrophs in the global ocean. Overall, we provide an update of marine diazotroph biogeographical diversity and present a new bioimaging-bioinformatic workflow.","keywords":"Aquatic Organisms Bacteria/genetics/metabolism Cyanobacteria/genetics/metabolism Molecular Imprinting/*methods Nitrogen/*metabolism Nitrogen Fixation/*genetics/physiology Oceans and Seas Phylogeny Plankton/metabolism Seawater/*chemistry/microbiology Symbiosis/genetics/physiology","issn":"2041-1723 (Electronic) 2041-1723 (Linking)","doi":"10.1038/s41467-021-24299-y","url":"https://www.ncbi.nlm.nih.gov/pubmed/34230473","year":"2021","bibtex":"@article{RN254,\r\n author = {Pierella Karlusich, J. J. and Pelletier, E. and Lombard, F. and Carsique, M. and Dvorak, E. and Colin, S. and Picheral, M. and Cornejo-Castillo, F. M. and Acinas, S. G. and Pepperkok, R. and Karsenti, E. and de Vargas, C. and Wincker, P. and Bowler, C. and Foster, R. A.},\r\n title = {Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods},\r\n journal = {Nat Commun},\r\n volume = {12},\r\n number = {1},\r\n pages = {4160},\r\n note = {Pierella Karlusich, Juan Jose\r\nPelletier, Eric\r\nLombard, Fabien\r\nCarsique, Madeline\r\nDvorak, Etienne\r\nColin, Sebastien\r\nPicheral, Marc\r\nCornejo-Castillo, Francisco M\r\nAcinas, Silvia G\r\nPepperkok, Rainer\r\nKarsenti, Eric\r\nde Vargas, Colomban\r\nWincker, Patrick\r\nBowler, Chris\r\nFoster, Rachel A\r\neng\r\nResearch Support, Non-U.S. Gov't\r\nEngland\r\nNat Commun. 2021 Jul 6;12(1):4160. doi: 10.1038/s41467-021-24299-y.},\r\n abstract = {Nitrogen fixation has a critical role in marine primary production, yet our understanding of marine nitrogen-fixers (diazotrophs) is hindered by limited observations. Here, we report a quantitative image analysis pipeline combined with mapping of molecular markers for mining >2,000,000 images and >1300 metagenomes from surface, deep chlorophyll maximum and mesopelagic seawater samples across 6 size fractions (<0.2-2000 mum). We use this approach to characterise the diversity, abundance, biovolume and distribution of symbiotic, colony-forming and particle-associated diazotrophs at a global scale. We show that imaging and PCR-free molecular data are congruent. Sequence reads indicate diazotrophs are detected from the ultrasmall bacterioplankton (<0.2 mum) to mesoplankton (180-2000 mum) communities, while images predict numerous symbiotic and colony-forming diazotrophs (>20 microm). Using imaging and molecular data, we estimate that polyploidy can substantially affect gene abundances of symbiotic versus colony-forming diazotrophs. Our results support the canonical view that larger diazotrophs (>10 mum) dominate the tropical belts, while unicellular cyanobacterial and non-cyanobacterial diazotrophs are globally distributed in surface and mesopelagic layers. We describe co-occurring diazotrophic lineages of different lifestyles and identify high-density regions of diazotrophs in the global ocean. Overall, we provide an update of marine diazotroph biogeographical diversity and present a new bioimaging-bioinformatic workflow.},\r\n keywords = {Aquatic Organisms\r\nBacteria/genetics/metabolism\r\nCyanobacteria/genetics/metabolism\r\nMolecular Imprinting/*methods\r\nNitrogen/*metabolism\r\nNitrogen Fixation/*genetics/physiology\r\nOceans and Seas\r\nPhylogeny\r\nPlankton/metabolism\r\nSeawater/*chemistry/microbiology\r\nSymbiosis/genetics/physiology},\r\n ISSN = {2041-1723 (Electronic)\r\n2041-1723 (Linking)},\r\n DOI = {10.1038/s41467-021-24299-y},\r\n url = {https://www.ncbi.nlm.nih.gov/pubmed/34230473},\r\n year = {2021},\r\n type = {Journal Article}\r\n}\r\n\r\n","author_short":["Pierella Karlusich, J. J.","Pelletier, E.","Lombard, F.","Carsique, M.","Dvorak, E.","Colin, S.","Picheral, M.","Cornejo-Castillo, F. M.","Acinas, S. G.","Pepperkok, R.","Karsenti, E.","de Vargas, C.","Wincker, P.","Bowler, C.","Foster, R. A."],"key":"RN254","id":"RN254","bibbaseid":"pierellakarlusich-pelletier-lombard-carsique-dvorak-colin-picheral-cornejocastillo-etal-globaldistributionpatternsofmarinenitrogenfixersbyimagingandmolecularmethods-2021","role":"author","urls":{"Paper":"https://www.ncbi.nlm.nih.gov/pubmed/34230473"},"keyword":["Aquatic Organisms Bacteria/genetics/metabolism Cyanobacteria/genetics/metabolism Molecular Imprinting/*methods Nitrogen/*metabolism Nitrogen Fixation/*genetics/physiology Oceans and Seas Phylogeny Plankton/metabolism Seawater/*chemistry/microbiology Symbiosis/genetics/physiology"],"metadata":{"authorlinks":{}},"downloads":2},"bibtype":"article","biburl":"https://bibbase.org/network/files/CzfdMm64N7sna2FRu","dataSources":["t7xPM8AA6iLF6Ckv9","jJ47DxiMR6MjLSFRc","9s8gPwvuScLx6XcJT","CG9K4BdddQWrftb7x","gaxrsokLT3SXSaGrY","GXJLvS6cuRBu7DapG","MuWdkm3uCTrikLpw2","oN8Wd4zAfgwaCR7pT","Ly5oTfXjg2ogJZ3Mt","WBzsMjaYZGMDcZMoy","4koo5y9mSNT7X3ZyK","vAJa6ptXSf5sWDNtC","TkaCSd5Aj84jXPcpB"],"keywords":["aquatic organisms bacteria/genetics/metabolism cyanobacteria/genetics/metabolism molecular imprinting/*methods nitrogen/*metabolism nitrogen fixation/*genetics/physiology oceans and seas phylogeny plankton/metabolism seawater/*chemistry/microbiology symbiosis/genetics/physiology"],"search_terms":["global","distribution","patterns","marine","nitrogen","fixers","imaging","molecular","methods","pierella karlusich","pelletier","lombard","carsique","dvorak","colin","picheral","cornejo-castillo","acinas","pepperkok","karsenti","de vargas","wincker","bowler","foster"],"title":"Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods","year":2021,"downloads":2}