Microbial modulators of soil carbon storage: integrating genomic and metabolic knowledge for global prediction

Trivedi, Pankaj; Anderson, Ian C.; Singh, Brajesh K.

doi:10.1016/j.tim.2013.09.005

Cited by 426 publications

(224 citation statements)

References 80 publications

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“…However, the functional potential of the microbial community will be driven by the selection of active taxa within different lineages. Functional attributes are embedded in the genomic blueprint and the capacity to produce extracellular enzymes varies at relatively fine-scale phylogenetic resolution (Philippot et al, 2010;Trivedi et al, 2013;Zimmerman et al, 2013). Because the composition of microbial community does not correlate strongly with the enzyme activity, functional genes and processes may offer a better predictive framework for investigating the ecological consequences of microbial traits conserved at higher phylogenetic resolutions than inferring function based on phylogenetic marker genes.…”

Section: Discussionmentioning

confidence: 99%

“…Managing soils to obtain multiple economic, societal and environmental benefits requires integrated policies and incentives that maintain and enhance soil C (Singh et al, 2010;Victoria et al, 2012;Trivedi et al, 2013). Soil microorganisms contribute greatly to ecosystem C budgets through their roles as decomposers, plant symbionts or pathogens, thereby modifying nutrient availability and influencing C turnover and retention in soil (Bardgett et al, 2008;Singh et al, 2010;Bardgett and van der Putten, 2014).…”

Section: Introductionmentioning

confidence: 99%

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Microbial regulation of the soil carbon cycle: evidence from gene–enzyme relationships

et al. 2016

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A lack of empirical evidence for the microbial regulation of ecosystem processes, including carbon (C) degradation, hinders our ability to develop a framework to directly incorporate the genetic composition of microbial communities in the enzyme-driven Earth system models. Herein we evaluated the linkage between microbial functional genes and extracellular enzyme activity in soil samples collected across three geographical regions of Australia. We found a strong relationship between different functional genes and their corresponding enzyme activities. This relationship was maintained after considering microbial community structure, total C and soil pH using structural equation modelling. Results showed that the variations in the activity of enzymes involved in C degradation were predicted by the functional gene abundance of the soil microbial community (R 2 40.90 in all cases). Our findings provide a strong framework for improved predictions on soil C dynamics that could be achieved by adopting a gene-centric approach incorporating the abundance of functional genes into process models.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Microbial regulation of the soil carbon cycle: evidence from gene–enzyme relationships

et al. 2016

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“…In addition, the majority of related studies focus on large, charismatic organisms, whereas soil microbes, the most diverse and abundant taxa in these systems, have received far less attention, despite their critical roles in ecosystem function and recovery from forest disturbance [9][10][11]. Since a variety of biotic and abiotic factors known to structure soil microbial communities are significantly altered in degraded forests that have been logged or converted to agricultural production areas [12,13], it is likely that microbial taxa will be dramatically different in these humandominated systems with important consequences for altered plant-soil-atmosphere feedbacks [14,15].…”

Section: Introductionmentioning

confidence: 99%

“…Compositional changes in fungal communities have been linked to altered plant dynamics [20], changes in nutrient cycling [21,22], and shifts in soil carbon pools and fluxes [23]. However, few belowground studies have evaluated the responses of soil fungi to landuse conversion in tropical forests and more work has focused on how bacterial communities are structured by the biotic and abiotic soil properties that can be altered with land-use change [15,[24][25][26]. However, fungi and bacteria have different physiologies [11,27] and display differential responses and feedbacks to factors such as pH [28] and soil C [29], so fungal responses cannot necessarily be inferred from the responses of soil bacteria.…”

Section: Introductionmentioning

confidence: 99%

“…In addition, these fungal community shifts can lead to altered soil process rates that can have long-lasting effects with uncertain recovery times [31]. Understanding the resistance and resilience of the dynamic soil microbial community is essential for predicting soil-plant-atmosphere feedbacks, as these nutrient and energy exchanges are regulated through microbial processes [15,32].…”

Section: Introductionmentioning

confidence: 99%

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Responses of Soil Fungi to Logging and Oil Palm Agriculture in Southeast Asian Tropical Forests

et al. 2014

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Human land use alters soil microbial composition and function in a variety of systems, although few comparable studies have been done in tropical forests and tropical agricultural production areas. Logging and the expansion of oil palm agriculture are two of the most significant drivers of tropical deforestation, and the latter is most prevalent in Southeast Asia. The aim of this study was to compare soil fungal communities from three sites in Malaysia that represent three of the most dominant land-use types in the Southeast Asia tropics: a primary forest, a regenerating forest that had been selectively logged 50 years previously, and a 25-year-old oil palm plantation. Soil cores were collected from three replicate plots at each site, and fungal communities were sequenced using the Illumina platform. Extracellular enzyme assays were assessed as a proxy for soil microbial function. We found that fungal communities were distinct across all sites, although fungal composition in the regenerating forest was more similar to the primary forest than either forest community was to the oil palm site. Ectomycorrhizal fungi, which are important associates of the dominant Dipterocarpaceae tree family in this region, were compositionally distinct across forests, but were nearly absent from oil palm soils. Extracellular enzyme assays indicated that the soil ecosystem in oil palm plantations experienced altered nutrient cycling dynamics, but there were few differences between regenerating and primary forest soils. Together, these results show that logging and the replacement of primary forest with oil palm plantations alter fungal community and function, although forests regenerating from logging had more similarities with primary forests in terms of fungal composition and nutrient cycling potential. Since oil palm agriculture is currently the mostly rapidly expanding equatorial crop and logging is pervasive across tropical ecosystems, these findings may have broad applicability.

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Modeling Microbial Dynamics and Heterotrophic Soil Respiration

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Ferrière

2020

Biogeochemical Cycles

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Microbial modulators of soil carbon storage: integrating genomic and metabolic knowledge for global prediction

Cited by 426 publications

References 80 publications

Microbial regulation of the soil carbon cycle: evidence from gene–enzyme relationships

Microbial regulation of the soil carbon cycle: evidence from gene–enzyme relationships

Responses of Soil Fungi to Logging and Oil Palm Agriculture in Southeast Asian Tropical Forests

Modeling Microbial Dynamics and Heterotrophic Soil Respiration

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