Variations of Bacterial and Diazotrophic Community Assemblies throughout the Soil Profile in Distinct Paddy Soil Types and Their Contributions to Soil Functionality

Wang, Xiaomi; Teng, Ying; Ren, Wenjie; Li, Yuntao; Yang, Teng; Chen, Yan; Zhao, Ling; Zhang, Huimin; Kuramae, Eiko E.

doi:10.1128/msystems.01047-21

Cited by 13 publications

(9 citation statements)

References 71 publications

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“…Within the DIRB group, unclassified_f_ Xanthobacteraceae, , Geothrix, , Trichlorobacter, , and Fonticella are dissimilatory iron-reducing autotrophs. In general, the most genus-level abundance within this group was positively correlated with the influent Sb(V) concentration (ρ > 0.3, except Fonticella, detailed in Table S5).…”

Section: Resultsmentioning

confidence: 99%

Dissimilatory and Cytoplasmic Antimonate Reductions in a Hydrogen-Based Membrane Biofilm Reactor

Zhou

Pang

et al. 2022

Environ. Sci. Technol.

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A hydrogen-based membrane biofilm reactor (H2-MBfR) was operated to investigate the bioreduction of antimonate [Sb(V)] in terms of Sb(V) removal, the fate of Sb, and the pathways of reduction metabolism. The MBfR achieved up to 80% Sb(V) removal and an Sb(V) removal flux of 0.55 g/m2·day. Sb(V) was reduced to Sb(III), which mainly formed Sb2O3 precipitates in the biofilm matrix, although some Sb(III) was retained intracellularly. High Sb(V) loading caused stress that deteriorated performance that was not recovered when the high Sb(V) loading was removed. The biofilm community consisted of DSbRB (dissimilatory Sb-reduction bacteria), SbRB (Sb-resistant bacteria), and DIRB (dissimilatory iron-reducing bacteria). Dissimilatory antimonate reduction, mediated by the respiratory arsenate reductase ArrAB, was the main reduction route, but respiratory reduction coexisted with cytoplasmic Sb(V)-reduction mediated by arsenate reductase ArsC. Increasing Sb(V) loading caused stress that led to increases in the expression of arsC gene and intracellular accumulation of Sb(III). By illuminating the roles of the dissimilatory and cytoplasmic Sb(V) reduction mechanism in the biofilms of the H2-MBfR, this study reveals that the Sb(V) loading should be controlled to avoid stress that deteriorates Sb(V) reduction.

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Section: Resultsmentioning

confidence: 99%

Dissimilatory and Cytoplasmic Antimonate Reductions in a Hydrogen-Based Membrane Biofilm Reactor

Zhou

Pang

et al. 2022

Environ. Sci. Technol.

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“…The prevalence of diazotrophic Geobacteraceae has actually been reported in some of amplicon sequencing studies (Fan et al, 2019; Wang et al, 2022), but the dominance of Anaeromyxobacteraceae has been overlooked in these. This may be due to the high GC content of nitrogenase genes in Anaeromyxobacteraceae (65.6%-69.7%, Fig.…”

Section: Resultsmentioning

confidence: 99%

Global soil metagenomics reveals ubiquitous yet previously-hidden predominance ofDeltaproteobacteriain nitrogen-fixing microbiome

Masuda

Mise

et al. 2022

Preprint

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Biological nitrogen fixation is a fundamental process sustaining all life on earth. In the soil, Alphaproteobacteria, Betaproteobacteria, and Cyanobacteria are traditionally considered the major groups of nitrogen fixation population. This conventional knowledge has been accumulated by numerous PCR amplicon surveys for nitrogenase genes. However, this prevalent view appears to be inconsistent with results of recent PCR-free meta-omics investigations. Here, we show the global distribution and diversity of terrestrial diazotrophic microbiome, updated by fully leveraging the planetary collections of soil metagenomes along with recently expanded culture collections. After extensive analysis of 1,445 soil metagenomic samples, we proved that the previously-undervalued Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous and predominant groups of diazotrophic microbiome in the soils, spanning a broad spectrum of environments, with different geographic origins and land usage types, including aerobic (croplands, grasslands) and anaerobic ones (paddy soils, sediments). Our results delineate a revised scheme of soil nitrogen fixation, which is inclusive of both conventional diazotrophs and the so far undervalued Deltaproteobacteria.

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“…The prevalence of diazotrophic Geobacteraceae has actually been reported in some of PCR amplicon sequencing analyses of nif genes [15,16,58], but the dominance of Anaeromyxobacteraceae has been overlooked in such PCR-based analyses. We suspected that this discrepancy is due to PCR biases behind amplicon sequencing.…”

Section: Biases Behind Amplicon Sequencing Of Nitrogenase Genesmentioning

confidence: 99%

Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome

Masuda,

Mise,

et al. 2024

Microbiome

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Background Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N2-fixing soil microbes have been investigated by numerous PCR amplicon sequencing of nitrogenase genes, their comprehensive understanding has been hindered by lack of de facto standard protocols for amplicon surveys and possible PCR biases. Here, by fully leveraging the planetary collections of soil shotgun metagenomes along with recently expanded culture collections, we evaluated the global distribution and diversity of terrestrial diazotrophic microbiome. Results After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments). Conclusion Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling.

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Variations of Bacterial and Diazotrophic Community Assemblies throughout the Soil Profile in Distinct Paddy Soil Types and Their Contributions to Soil Functionality

Abstract: Rice paddy ecosystems support nearly half of the global population and harbor remarkably diverse microbiomes and functions in a variety of soil types. Diazotrophs provide significant bioavailable nitrogen in paddy soil, priming nitrogen transformation and other biogeochemical processes.

Cited by 13 publications

References 71 publications

Dissimilatory and Cytoplasmic Antimonate Reductions in a Hydrogen-Based Membrane Biofilm Reactor

Dissimilatory and Cytoplasmic Antimonate Reductions in a Hydrogen-Based Membrane Biofilm Reactor

Global soil metagenomics reveals ubiquitous yet previously-hidden predominance ofDeltaproteobacteriain nitrogen-fixing microbiome

Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome

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