Resistance and Resilience of the Forest Soil Microbiome to Logging-Associated Compaction. Hartmann, M., Niklaus, P. A., Zimmermann, S., Schmutz, S., Kremer, J., Abarenkov, K., Luscher, P., Widmer, F., & Frey, B. 8(1):226–244.
Resistance and Resilience of the Forest Soil Microbiome to Logging-Associated Compaction [link]Paper  doi  abstract   bibtex   
Soil compaction is a major disturbance associated with logging, but we lack a fundamental understanding of how this affects the soil microbiome. We assessed the structural resistance and resilience of the microbiome using a high-throughput pyrosequencing approach in differently compacted soils at two forest sites and correlated these findings with changes in soil physical properties and functions. Alterations in soil porosity after compaction strongly limited the air and water conductivity. Compaction significantly reduced abundance, increased diversity, and persistently altered the structure of the microbiota. Fungi were less resistant and resilient than bacteria; clayey soils were less resistant and resilient than sandy soils. The strongest effects were observed in soils with unfavorable moisture conditions, where air and water conductivities dropped well below 10\,% of their initial value. Maximum impact was observed around 6-12 months after compaction, and microbial communities showed resilience in lightly but not in severely compacted soils 4 years post disturbance. Bacteria capable of anaerobic respiration, including sulfate, sulfur, and metal reducers of the Proteobacteria and Firmicutes, were significantly associated with compacted soils. Compaction detrimentally affected ectomycorrhizal species, whereas saprobic and parasitic fungi proportionally increased in compacted soils. Structural shifts in the microbiota were accompanied by significant changes in soil processes, resulting in reduced carbon dioxide, and increased methane and nitrous oxide emissions from compacted soils. This study demonstrates that physical soil disturbance during logging induces profound and long-lasting changes in the soil microbiome and associated soil functions, raising awareness regarding sustainable management of economically driven logging operations. [Excerpt] Soil is an essential component of forest ecosystems, mediating fundamental nutrient and energy flow patterns that ensure forest productivity, sustain biodiversity and regulate climate stability (Bonan, 2008; Reay et al., 2008; Dominati et al., 2010; Normile, 2010). Soils are dynamic biological matrices featuring a complex microbiome that has an integral role in virtually all ecosystem processes (Barrios, 2007). At the system level, microbial metabolism regulates ecosystem functioning and modulates resistance and resilience to perturbations (Allison and Martiny, 2008). It is likely that measuring the microbial community structure and associated functions can improve the ability (1) to monitor alterations of the soil system after disturbances, (2) to evaluate its capacity to recover and perhaps (3) to detect adverse effects in ecosystem functioning before they are irreversible. [\n] Soil compaction has been recognized as a major disturbance associated with forest management (Van-Camp et al., 2004). Economically efficient harvesting requires the use of heavy machines, causing severe compaction of the soil particularly during wet conditions and along skid trails and landings (Grigal, 2000; Marshall, 2000). Alterations in soil porosity affect pore connectivity, water infiltration, air permeability, temperature, rooting space, nutrient flow and biological activity (Greacen and Sands, 1980; Kozlowski, 1999; Richard et al., 2001; Mooney and Nipattasuk, 2003), often resulting in increased surface runoff, soil erosion, nutrient leaching and greenhouse gas emission (Worrell and Hampson, 1997; Powers et al., 2005). As a consequence, the soil system can suffer substantial, persistent and sometimes irreversible damage, which ultimately reduces forest productivity and ecosystem functionality. Given that the affected area can range between 10 and 40\,% of the total logged stand, the impact on the ecosystem can be substantial (Grigal, 2000; Luckow and Guldin, 2007; Frey et al., 2009). [\n] The negative impact of soil compaction caused by logging on physicochemical properties has been demonstrated for years (for example, McNabb et al., 2001; Horn et al., 2007; Ampoorter et al., 2010). [...] [Conclusions] Soil compaction is a major problem inherently linked to economically efficient logging operations. Once a soil has been compacted, a return to the initial state can be very slow, and recovery from severe compaction might take centuries rather than decades (Webb, 2002; von Wilpert and Schäffer, 2006). As the degree of disturbance depends on factors like harvesting equipment, operation condition and site characteristics, careful operational design can substantially mitigate the environmental impact. We observed that site characteristics such as soil type were important determinants of the degree of impact, with clayey soils exhibiting less resistance and resilience than sandy soils. However, high moisture contents as simulated in the severely compacted skid trails led to a strong and persistent impact on the soil microbiota and functions at both forest sites. Ultimately, site conditions and characteristics (for example, soil moisture, texture) should drive the decisions about the time of logging (for example, rainfall, storms) and type of equipment used (for example, machine load, type of tires). We demonstrated that the combined investigation of soil physical, microbial and functional characteristics represents a powerful tool to measure resistance and resilience of the soil system to compaction (Figure 7). The deep sequencing approach identified microbial indicators that can assist in monitoring such disturbances in forest ecosystems and determining compaction thresholds below which there is no detrimental impact on ecosystem functioning in the long term.
@article{hartmannResistanceResilienceForest2013,
  title = {Resistance and Resilience of the Forest Soil Microbiome to Logging-Associated Compaction},
  author = {Hartmann, Martin and Niklaus, Pascal A. and Zimmermann, Stephan and Schmutz, Stefan and Kremer, Johann and Abarenkov, Kessy and Luscher, Peter and Widmer, Franco and Frey, Beat},
  date = {2013-09},
  journaltitle = {The ISME Journal},
  volume = {8},
  pages = {226--244},
  issn = {1751-7362},
  doi = {10.1038/ismej.2013.141},
  url = {https://doi.org/10.1038/ismej.2013.141},
  abstract = {Soil compaction is a major disturbance associated with logging, but we lack a fundamental understanding of how this affects the soil microbiome. We assessed the structural resistance and resilience of the microbiome using a high-throughput pyrosequencing approach in differently compacted soils at two forest sites and correlated these findings with changes in soil physical properties and functions. Alterations in soil porosity after compaction strongly limited the air and water conductivity. Compaction significantly reduced abundance, increased diversity, and persistently altered the structure of the microbiota. Fungi were less resistant and resilient than bacteria; clayey soils were less resistant and resilient than sandy soils. The strongest effects were observed in soils with unfavorable moisture conditions, where air and water conductivities dropped well below 10\,\% of their initial value. Maximum impact was observed around 6-12 months after compaction, and microbial communities showed resilience in lightly but not in severely compacted soils 4 years post disturbance. Bacteria capable of anaerobic respiration, including sulfate, sulfur, and metal reducers of the Proteobacteria and Firmicutes, were significantly associated with compacted soils. Compaction detrimentally affected ectomycorrhizal species, whereas saprobic and parasitic fungi proportionally increased in compacted soils. Structural shifts in the microbiota were accompanied by significant changes in soil processes, resulting in reduced carbon dioxide, and increased methane and nitrous oxide emissions from compacted soils. This study demonstrates that physical soil disturbance during logging induces profound and long-lasting changes in the soil microbiome and associated soil functions, raising awareness regarding sustainable management of economically driven logging operations.

[Excerpt] Soil is an essential component of forest ecosystems, mediating fundamental nutrient and energy flow patterns that ensure forest productivity, sustain biodiversity and regulate climate stability (Bonan, 2008; Reay et al., 2008; Dominati et al., 2010; Normile, 2010). Soils are dynamic biological matrices featuring a complex microbiome that has an integral role in virtually all ecosystem processes (Barrios, 2007). At the system level, microbial metabolism regulates ecosystem functioning and modulates resistance and resilience to perturbations (Allison and Martiny, 2008). It is likely that measuring the microbial community structure and associated functions can improve the ability (1) to monitor alterations of the soil system after disturbances, (2) to evaluate its capacity to recover and perhaps (3) to detect adverse effects in ecosystem functioning before they are irreversible.

[\textbackslash n] Soil compaction has been recognized as a major disturbance associated with forest management (Van-Camp et al., 2004). Economically efficient harvesting requires the use of heavy machines, causing severe compaction of the soil particularly during wet conditions and along skid trails and landings (Grigal, 2000; Marshall, 2000). Alterations in soil porosity affect pore connectivity, water infiltration, air permeability, temperature, rooting space, nutrient flow and biological activity (Greacen and Sands, 1980; Kozlowski, 1999; Richard et al., 2001; Mooney and Nipattasuk, 2003), often resulting in increased surface runoff, soil erosion, nutrient leaching and greenhouse gas emission (Worrell and Hampson, 1997; Powers et al., 2005). As a consequence, the soil system can suffer substantial, persistent and sometimes irreversible damage, which ultimately reduces forest productivity and ecosystem functionality. Given that the affected area can range between 10 and 40\,\% of the total logged stand, the impact on the ecosystem can be substantial (Grigal, 2000; Luckow and Guldin, 2007; Frey et al., 2009).

[\textbackslash n] The negative impact of soil compaction caused by logging on physicochemical properties has been demonstrated for years (for example, McNabb et al., 2001; Horn et al., 2007; Ampoorter et al., 2010). [...]

[Conclusions] Soil compaction is a major problem inherently linked to economically efficient logging operations. Once a soil has been compacted, a return to the initial state can be very slow, and recovery from severe compaction might take centuries rather than decades (Webb, 2002; von Wilpert and Schäffer, 2006). As the degree of disturbance depends on factors like harvesting equipment, operation condition and site characteristics, careful operational design can substantially mitigate the environmental impact. We observed that site characteristics such as soil type were important determinants of the degree of impact, with clayey soils exhibiting less resistance and resilience than sandy soils. However, high moisture contents as simulated in the severely compacted skid trails led to a strong and persistent impact on the soil microbiota and functions at both forest sites. Ultimately, site conditions and characteristics (for example, soil moisture, texture) should drive the decisions about the time of logging (for example, rainfall, storms) and type of equipment used (for example, machine load, type of tires). We demonstrated that the combined investigation of soil physical, microbial and functional characteristics represents a powerful tool to measure resistance and resilience of the soil system to compaction (Figure 7). The deep sequencing approach identified microbial indicators that can assist in monitoring such disturbances in forest ecosystems and determining compaction thresholds below which there is no detrimental impact on ecosystem functioning in the long term.},
  keywords = {*imported-from-citeulike-INRMM,~INRMM-MiD:c-13886680,~to-add-doi-URL,forest-management,forest-resources,ghg,logging,precipitation,runoff,soil-compactation,soil-erosion,soil-microbial-properties,soil-resources,storm,trade-offs},
  number = {1}
}
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