Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale

Bru, David; Ramette, Alban; Saby, Nicolas P.A.; Dequiedt, Samuel; Ranjard, Lionel; Jolivet, Claudy; Arrouays, Dominique; Philippot, Laurent

doi:10.1038/ismej.2010.130

Cited by 358 publications

(251 citation statements)

References 56 publications

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“…In a large-scale field study, Enwall et al [67] found a positive relationship between soil Cu content and the abundance of nirK genes. Thus, Cu plays a key role in both NO 2 2 and N 2 O reduction [68]. With approximately 40 per cent of Europe's arable soils being Cu deficient (less than 2 mg Cu kg 21 ), the potential for N 2 O mitigation (with a simultaneous crop yield increase) is high.…”

Section: Nitrous Oxide Emissions From Soilsmentioning

confidence: 99%

Biological sources and sinks of nitrous oxide and strategies to mitigate emissions

Thomson

Giannopoulos

Pretty

et al. 2012

Phil. Trans. R. Soc. B

433

282

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Nitrous oxide (N 2 O) is a powerful atmospheric greenhouse gas and cause of ozone layer depletion. Global emissions continue to rise. More than two-thirds of these emissions arise from bacterial and fungal denitrification and nitrification processes in soils, largely as a result of the application of nitrogenous fertilizers. This article summarizes the outcomes of an interdisciplinary meeting, ‘Nitrous oxide (N 2 O) the forgotten greenhouse gas’, held at the Kavli Royal Society International Centre, from 23 to 24 May 2011. It provides an introduction and background to the nature of the problem, and summarizes the conclusions reached regarding the biological sources and sinks of N 2 O in oceans, soils and wastewaters, and discusses the genetic regulation and molecular details of the enzymes responsible. Techniques for providing global and local N 2 O budgets are discussed. The findings of the meeting are drawn together in a review of strategies for mitigating N 2 O emissions, under three headings, namely: (i) managing soil chemistry and microbiology, (ii) engineering crop plants to fix nitrogen, and (iii) sustainable agricultural intensification.

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Section: Nitrous Oxide Emissions From Soilsmentioning

confidence: 99%

Biological sources and sinks of nitrous oxide and strategies to mitigate emissions

Thomson

Giannopoulos

Pretty

et al. 2012

Phil. Trans. R. Soc. B

433

282

View full text Add to dashboard Cite

show abstract

“…For the latter, a recent DNA fingerprinting experiment showed that CopA genes were strongly influenced by pH (Lejon et al, 2007). pH has also been shown to affect both ammonia-oxidizing archaea and ammonia-oxidizing bacteria (Bru et al, 2010). Therefore, the correlation between pH and amoA-ammonia-oxidizing archaea/amoA-ammonia-oxidizing bacteria ratios was examined.…”

Section: Microbial Mediation Of Responses To Warmingmentioning

confidence: 99%

“…pH was shown to be a major factor in shaping soil microbial community at the global scale (Fierer and Jackson, 2006) and to affect certain genes such as those involved in nitrification (Bru et al, 2010). Pearson's correlation tests indicated that a total of 65 genes spanning a number of categories such as the C cycle, N cycle, antibiotic and metal resistance were significantly (r ¼ À 0.62B0.84, Po0.010) correlated with pH (Supplementary Table S7).…”

Section: Microbial Mediation Of Responses To Warmingmentioning

confidence: 99%

Microbial mediation of biogeochemical cycles revealed by simulation of global changes with soil transplant and cropping

et al. 2014

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Despite microbes’ key roles in driving biogeochemical cycles, the mechanism of microbe-mediated feedbacks to global changes remains elusive. Recently, soil transplant has been successfully established as a proxy to simulate climate changes, as the current trend of global warming coherently causes range shifts toward higher latitudes. Four years after southward soil transplant over large transects in China, we found that microbial functional diversity was increased, in addition to concurrent changes in microbial biomass, soil nutrient content and functional processes involved in the nitrogen cycle. However, soil transplant effects could be overridden by maize cropping, which was attributed to a negative interaction. Strikingly, abundances of nitrogen and carbon cycle genes were increased by these field experiments simulating global change, coinciding with higher soil nitrification potential and carbon dioxide (CO2) efflux. Further investigation revealed strong correlations between carbon cycle genes and CO2 efflux in bare soil but not cropped soil, and between nitrogen cycle genes and nitrification. These findings suggest that changes of soil carbon and nitrogen cycles by soil transplant and cropping were predictable by measuring microbial functional potentials, contributing to a better mechanistic understanding of these soil functional processes and suggesting a potential to incorporate microbial communities in greenhouse gas emission modeling.

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“…Subsequently, the spatial variation of pollutants and other soil chemical parameters may regulate the spatial patterns of microbial communities (Tö rneman et al, 2008;Bengtsson et al, 2010). Association between spatial patterns of environmental factors and the distribution of microbial taxa as well as their activities can be elucidated via geostatistical modelling (Philippot et al, 2009;Bru et al, 2010;Enwall et al, 2010;Wessén et al, 2011). Furthermore, the choice of taxonomic level to address the microbial community responses is a crucial issue.…”

Section: Introductionmentioning

confidence: 99%

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

et al. 2014

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Restoration of polluted sites via in situ bioremediation relies heavily on the indigenous microbes and their activities. Spatial heterogeneity of microbial populations, contaminants and soil chemical parameters on such sites is a major hurdle in optimizing and implementing an appropriate bioremediation regime. We performed a grid-based sampling of an aged creosote-contaminated site followed by geostatistical modelling to illustrate the spatial patterns of microbial diversity and activity and to relate these patterns to the distribution of pollutants. Spatial distribution of bacterial groups unveiled patterns of niche differentiation regulated by patchy distribution of pollutants and an east-to-west pH gradient at the studied site. Proteobacteria clearly dominated in the hot spots of creosote pollution, whereas the abundance of Actinobacteria, TM7 and Planctomycetes was considerably reduced from the hot spots. The pH preferences of proteobacterial groups dominating in pollution could be recognized by examining the order and family-level responses. Acidobacterial classes came across as generalists in hydrocarbon pollution whose spatial distribution seemed to be regulated solely by the pH gradient. Although the community evenness decreased in the heavily polluted zones, basal respiration and fluorescein diacetate hydrolysis rates were higher, indicating the adaptation of specific indigenous microbial populations to hydrocarbon pollution. Combining the information from the kriged maps of microbial and soil chemistry data provided a comprehensive understanding of the long-term impacts of creosote pollution on the subsurface microbial communities. This study also highlighted the prospect of interpreting taxa-specific spatial patterns and applying them as indicators or proxies for monitoring polluted sites.

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Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale

Cited by 358 publications

References 56 publications

Biological sources and sinks of nitrous oxide and strategies to mitigate emissions

Biological sources and sinks of nitrous oxide and strategies to mitigate emissions

Microbial mediation of biogeochemical cycles revealed by simulation of global changes with soil transplant and cropping

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

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