Land use driven change in soil pH affects microbial carbon cycling processes

Nature Communications, Journal Year: 2018, Volume and Issue: 9(1)

Published: Aug. 29, 2018

Abstract Soil microorganisms act as gatekeepers for soil–atmosphere carbon exchange by balancing the accumulation and release of soil organic matter. However, poor understanding mechanisms responsible hinders development effective land management strategies to enhance storage. Here we empirically test link between microbial ecophysiological traits topsoil content across geographically distributed soils use contrasts. We discovered distinct pH controls on accumulation. Land intensification in low-pH that increased above a threshold (~6.2) leads loss through decomposition, following alleviation acid retardation growth. with near-neutral was linked decreased biomass reduced growth efficiency was, turn, related trade-offs stress resource acquisition. Thus, less-intensive practices have more potential storage efficiency, whereas acidic soils, is bigger constraint decomposition rates.

Language: Английский

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Life and death in the soil microbiome: how ecological processes influence biogeochemistry

Nature Reviews Microbiology, Journal Year: 2022, Volume and Issue: 20(7), P. 415 - 430

Published: Feb. 28, 2022

Language: Английский

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Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem

Microbiome, Journal Year: 2018, Volume and Issue: 6(1)

Published: Feb. 26, 2018

The 16S ribosomal RNA gene is the most widely used marker in microbial ecology. Counts of sequence variants, often PCR amplicons, are to estimate proportions bacterial and archaeal taxa communities. Because different organisms contain copy numbers (GCNs), variant counts biased towards clades with greater GCNs. Several tools have recently been developed for predicting GCNs using phylogenetic methods based on sequenced genomes, order correct these biases. However, accuracy those predictions has not independently assessed. Here, we systematically evaluate predictability across clades, ∼ 6,800 public genomes several methods. Further, assess predicted by three published (PICRUSt, CopyRighter, PAPRICA) over a wide range 635 communities from varied environments. We find that regardless method tested, could only be accurately limited fraction taxa, namely closely moderately related representatives (≲15% divergence rRNA gene). Consistent this observation, all considered exhibit low predictive when evaluated against completely some cases explaining less than 10% variance. Substantial disagreement was also observed between (R2<0.5) majority tested nearest taxon index (NSTI) communities, i.e., average distance genome, strong predictor agreement GCN prediction non-animal-associated samples, but moderate animal-associated samples. recommend correcting microbiome surveys default, unless OTUs sufficiently or need true OTU warrants additional noise introduced, so community profiles remain interpretable comparable studies.

Language: Английский

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Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

Frontiers in Microbiology, Journal Year: 2016, Volume and Issue: 7

Published: Feb. 24, 2016

Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, relationship between community structure and ecosystem processes remains poorly understood. Here, we address a fundamental unanswered question ecology: 'When do need understand accurately predict function?' We present statistical analysis investigating value of data independently combination for explaining rates carbon nitrogen cycling within 82 global datasets. Environmental variables were strongest predictors process but left 44% variation unexplained on average, suggesting potential increase model accuracy. Although only 29% datasets significantly improved by adding information structure, observed improvement models mediated narrow phylogenetic guilds via functional gene data, conversely, facultative diversity metrics. Our results also suggest that can strengthen predictions respiration beyond biomass parameters, as 53% incorporating both sets compared 35% alone. represents first comprehensive research examining links function. Taken together, indicate greater understanding communities informed ecological principles may enhance relative assessments based physiology.

Language: Английский

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Bacterial Endophyte Colonization and Distribution within Plants

Microorganisms, Journal Year: 2017, Volume and Issue: 5(4), P. 77 - 77

Published: Nov. 25, 2017

The plant endosphere contains a diverse group of microbial communities. There is general consensus that these communities make significant contributions to health. Both recently adopted genomic approaches and classical microbiology techniques continue develop the science plant-microbe interactions. Endophytes are symbionts residing within for majority their life cycle without any detrimental impact host plant. use natural offers an opportunity maximize crop productivity while reducing environmental impacts agriculture. promote growth through nitrogen fixation, phytohormone production, nutrient acquisition, by conferring tolerance abiotic biotic stresses. Colonization endophytes crucial providing benefits Endophytic colonization refers entry, multiplication endophyte populations Lately, microbiome research has gained considerable attention but mechanism allowing plants recruit largely unknown. This review summarizes currently available knowledge about endophytic bacteria in various species, specifically discusses maize Populus endophytes.

Language: Английский

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Soil protists: a fertile frontier in soil biology research

FEMS Microbiology Reviews, Journal Year: 2018, Volume and Issue: 42(3), P. 293 - 323

Published: Feb. 12, 2018

Protists include all eukaryotes except plants, fungi and animals. They are an essential, yet often forgotten, component of the soil microbiome. Method developments have now furthered our understanding real taxonomic functional diversity protists. occupy key roles in microbial foodwebs as consumers bacteria, other small eukaryotes. As parasites animals even larger protists, they regulate populations shape communities. Pathogenic forms play a major role public health issues human parasites, or act agricultural pests. Predatory protists release nutrients enhancing plant growth. Soil importance for eukaryotic evolution biogeography. also useful applied research bioindicators quality, models ecotoxicology potential biofertilizers biocontrol agents. In this review, we provide overview enormous morphological, taxonomical discuss current challenges opportunities protistology. Research biology would clearly benefit from incorporating more protistology alongside study

Language: Английский

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Global biogeography of microbial nitrogen-cycling traits in soil

Proceedings of the National Academy of Sciences, Journal Year: 2016, Volume and Issue: 113(29), P. 8033 - 8040

Published: July 18, 2016

Microorganisms drive much of the Earth’s nitrogen (N) cycle, but we still lack a global overview abundance and composition microorganisms carrying out soil N processes. To address this gap, characterized biogeography microbial traits, defined as eight N-cycling pathways, using publically available metagenomes. The relative frequency pathways varied consistently across soils, such that frequencies individual were positively correlated samples. Habitat type, carbon, largely explained total pathway in sample. In contrast, could not identify major drivers taxonomic functional groups. Further, dominant genera encoding generally similar among habitat types. samples also revealed an unexpectedly high bacteria required for dissimilatory nitrate reduction to ammonium, little-studied process soil. Finally, phylogenetic analysis showed some groups seem be specialists or generalists. For instance, taxa within Deltaproteobacteria encoded all whereas those Cyanobacteria primarily three pathways. Overall, trait-based approach provides baseline investigating relationship between diversity cycling soils.

Language: Английский

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Unraveling the processes shaping mammalian gut microbiomes over evolutionary time

Nature Communications, Journal Year: 2017, Volume and Issue: 8(1)

Published: Feb. 23, 2017

Abstract Whether mammal–microbiome interactions are persistent and specific over evolutionary time is controversial. Here we show that host phylogeny major dietary shifts have affected the distribution of different gut bacterial lineages did so on vastly phylogenetic resolutions. Diet mostly influences acquisition ancient large microbial lineages. Conversely, correlation with seen among more recently diverged lineages, consistent processes operating at similar timescales to evolution. Considering microbiomes appropriate scales allows us model their evolution along mammalian tree infer diets from predicted ancestors. Phylogenetic analyses support co-speciation as having a significant role in microbiome compositions. Highly co-speciating genera also associated immune diseases humans, laying path for future studies probe these bacteria signs co-evolution.

Language: Английский

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Abundant fungi adapt to broader environmental gradients than rare fungi in agricultural fields

Global Change Biology, Journal Year: 2020, Volume and Issue: 26(8), P. 4506 - 4520

Published: April 23, 2020

Abstract Soil communities are intricately linked to ecosystem functioning, and a predictive understanding of how assemble in response environmental change is great ecological importance. Little known about the assembly processes governing abundant rare fungal across agro‐ecosystems, particularly with regard their adaptation. By considering taxa, we tested thresholds phylogenetic signals for preferences complex gradients reflect adaptation, explored factors influencing based on large‐scale soil survey agricultural fields eastern China. We found that taxa exhibited remarkably broader stronger compared taxa. Neutral played key role shaping subcommunity subcommunity. Null model analysis revealed was less clustered phylogenetically governed primarily by dispersal limitation, while homogeneous selection major process available sulfur factor mediating balance between stochastic deterministic both subcommunities, as indicated an increase stochasticity higher concentration. Based macroecological spatial scale datasets, our study potential adaptation identified distinct community fields. These results contribute mechanisms underlying generation maintenance diversity global change.

Language: Английский

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Diversity-triggered deterministic bacterial assembly constrains community functions

Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)

Published: Aug. 23, 2019

Abstract A growing body of evidence suggests that microbial α-diversity (local species richness) may have positive effects on ecosystem function. However, less attention has been paid to β-diversity (the variation among local assemblages). Here we studied the impact stochastic/deterministic community assembly processes, which are related β-diversity, and consequences for Bacterial communities differing in were generated their structures potential functional traits inferred from DNA sequencing. Phylogenetic null modeling analysis stochastic processes dominant high-diversity communities. low-diversity communities, deterministic dominant, associating with reduction specialized functions correlated specific bacterial taxa. Overall, suggest low-diversity-induced constrain functions, highlighting roles generating sustaining function soil ecosystems.

Language: Английский

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