Temporal dynamics of the compositions and activities of soil microbial communities post-application of the insecticide chlorantraniliprole in paddy soils

ABSTRACT Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from dead cells or secreted extracellular DNA) may dampen temporal signals. Here, we disentangle the relationships among spatial, temporal, and relic DNA effects on prokaryotic and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over 6 months to discriminate between temporal variability, intraplot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intraplot spatial variability in microbial community composition was strong and independent of relic DNA effects and that these spatial patterns persisted throughout the study. When controlling for intraplot spatial variability, we identified significant temporal variability in both plots over the 6-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show that these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes. IMPORTANCE Nearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here, we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling was required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from nonliving sources masks important temporal patterns. We identified groups of microbes with shared temporal responses and show that these patterns were predictable from changes in soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.

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Temporal Dynamics of Soil Microbial Communities below the Seedbed under Two Contrasting Tillage Regimes

Frontiers in Microbiology ◽

10.3389/fmicb.2017.01127 ◽

2017 ◽

Vol 8 ◽

Cited By ~ 42

Author(s):

Florine Degrune ◽

Nicolas Theodorakopoulos ◽

Gilles Colinet ◽

Marie-Pierre Hiel ◽

Bernard Bodson ◽

...

Keyword(s):

Microbial Communities ◽

Temporal Dynamics ◽

Soil Microbial Communities ◽

Soil Microbial

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Diversity and asynchrony in soil microbial communities stabilizes ecosystem functioning

10.1101/2020.10.02.324012 ◽

2020 ◽

Author(s):

Cameron Wagg ◽

Yann Hautier ◽

Sarah Pellkofer ◽

Samiran Banerjee ◽

Bernhard Schmid ◽

...

Keyword(s):

Microbial Diversity ◽

Microbial Communities ◽

Ecosystem Functioning ◽

Temporal Dynamics ◽

Temporal Stability ◽

Soil Microbial Communities ◽

Ecosystem Functions ◽

Soil Microbial Diversity ◽

Soil Biodiversity ◽

Soil Microbial

AbstractTheoretical and empirical advances have revealed the importance of biodiversity for stabilizing ecosystem functions through time. Yet despite the global degradation of soils, how the loss of soil microbial diversity can de-stabilizes ecosystem functioning is unknown. Here we experimentally quantified the contribution diversity and the temporal dynamics in the composition of soil microbial communities to the temporal stability of four key ecosystem functions related to nutrient and carbon cycling. Soil microbial diversity loss reduced the temporal stability of all ecosystem functions and was particularly strong when over 50% of microbial taxa were lost. The stabilizing effect of soil biodiversity was linked to asynchrony among microbial taxa whereby different soil fungi and bacteria were associated with different ecosystem functions at different times. Our results emphasize the need to conserve soil biodiversity in order to ensure the reliable provisioning of multiple ecosystems functions that soils provide to society.

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Methylmercury production and degradation by soil microbial communities

10.5194/egusphere-egu2020-6441 ◽

2020 ◽

Author(s):

Yu-Rong Liu ◽

Qiaoyun Huang

Keyword(s):

Microbial Communities ◽

Bacterial Community Composition ◽

Inorganic Mercury ◽

Soil Microbial Communities ◽

Paddy Soils ◽

Equation Modeling ◽

Soil Microbial ◽

Anaerobic Microorganisms ◽

Water Saturated ◽

Reducing Bacteria

<p>Rice consumption is now recognized as an important pathway of human exposure to the neurotoxin methylmercury (MeHg), particularly in countries where rice is a staple food. Although the discovery of a two-gene cluster hgcAB has linked Hg methylation to several phylogenetically diverse groups of anaerobic microorganisms converting inorganic mercury (Hg) to MeHg, the prevalence and diversity of microbial communities associated with MeHg production and degradation in paddy soils remain unclear. Both Illumina and PacBio sequencing analyses revealed that Hg methylating communities were dominated by iron-reducing bacteria (i.e., Geobacter) and methanogens, with a relatively low abundance of hgcA+ sulfate-reducing bacteria in the soil. A positive correlation was observed between the MeHg content in soil and the relative abundance of Geobacter carrying the hgcA gene. Our structure equation modeling suggested a much stronger link between bacterial community composition and %MeHg, compared to the abundance of methylating gene (hgcA) and edaphic properties. More importantly, random forest models suggested a more important role of non-Hg methylators than Hg methylators in predicting variations of soil %MeHg.</p><p>Microbial demethylation was demonstrated by significantly more degradation of MeHg in the unsterilized soils than the sterilized controls, although more degradation was observed in water-saturated soils than the unsaturated soil. 16S rRNA Illumina sequencing and metatranscriptomic analyses consistently revealed that Catenulisporaceae, Frankiaceae, Mycobacteriaceae, and Thermomonosporaceae were among the most likely microbial taxa in influencing These findings provide new insights into microbial communities associated with MeHg accumulation in paddy soils, with important implications in mitigating the net production and bioaccumulation of MeHg in rice worldwide.</p>

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Unraveling the effects of spatial variability and relic DNA on the temporal dynamics of soil microbial communities

10.1101/402438 ◽

2018 ◽

Cited By ~ 3

Author(s):

Paul Carini ◽

Manuel Delgado-Baquerizo ◽

Eve-Lyn S. Hinckley ◽

Hannah Holland-Moritz ◽

Tess E Brewer ◽

...

Keyword(s):

Microbial Community ◽

Spatial Variability ◽

Spatial Heterogeneity ◽

Microbial Communities ◽

Temporal Variability ◽

Temporal Dynamics ◽

Microbial Community Composition ◽

Soil Microbial Communities ◽

Soil Microbial ◽

Over Time

AbstractFew studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from non-living cells) may dampen temporal signals. Here we disentangle the relationships among spatial, temporal, and relic DNA effects on bacterial, archaeal, and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over six months to discriminate between temporal variability, intra-plot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intra-plot spatial variability in microbial community composition was strong and independent of relic DNA effects with these spatial patterns persisting throughout the study. When controlling for intra-plot spatial variability, we identified significant temporal variability in both plots over the six-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes.ImportanceNearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling is required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from non-living microbial cells masks important temporal patterns. We identified groups of microbes that display correlated behavior over time and show that these patterns are predictable from soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.

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Patterns of local, intercontinental and interseasonal variation of soil bacterial and eukaryotic microbial communities

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa018 ◽

2020 ◽

Vol 96 (3) ◽

Cited By ~ 3

Author(s):

Johan De Gruyter ◽

James T Weedon ◽

Stéphane Bazot ◽

Steven Dauwe ◽

Pere-Roc Fernandez-Garberí ◽

...

Keyword(s):

Temporal Variation ◽

Microbial Communities ◽

Community Composition ◽

Temporal Dynamics ◽

Soil Microbial Communities ◽

Soil Microbiome ◽

Ongoing Research ◽

Soil Microbial ◽

Spatio Temporal ◽

Microbial Groups

ABSTRACT Although ongoing research has revealed some of the main drivers behind global spatial patterns of microbial communities, spatio-temporal dynamics of these communities still remain largely unexplored. Here, we investigate spatio-temporal variability of both bacterial and eukaryotic soil microbial communities at local and intercontinental scales. We compare how temporal variation in community composition scales with spatial variation in community composition, and explore the extent to which bacteria, protists, fungi and metazoa have similar patterns of temporal community dynamics. All soil microbial groups displayed a strong correlation between spatial distance and community dissimilarity, which was related to the ratio of organism to sample size. Temporal changes were variable, ranging from equal to local between-sample variation, to as large as that between communities several thousand kilometers apart. Moreover, significant correlations were found between bacterial and protist communities, as well as between protist and fungal communities, indicating that these microbial groups change in tandem, potentially driven by interactions between them. We conclude that temporal variation can be considerable in soil microbial communities, and that future studies need to consider temporal variation in order to reliably capture all drivers of soil microbiome changes.

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