Changes in nitrogen-cycling microbial communities with depth in temperate and subtropical forest soils

Tang, Yue-Hua; Yu, Guirui; Zhang, Xinyu; Wang, Qiufeng; Ge, Jianping; Liu, Shuang

doi:10.1016/j.apsoil.2017.10.029

Cited by 71 publications

(40 citation statements)

References 70 publications

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“…Within one‐meter soil profiles, the species richness (OTU number) decreased significantly with increasing soil depth (Figure ). This trend of decreasing microbial alpha diversity is consistent with many other previous studies (Deng et al, 2015; Feng et al, 2019; Tang et al, 2018), which have shown that the richness, abundance, and composition of the soil microbiome displayed layer specificity and distinct differences across strata. The community distance showed clearly that community variability increased within sites from Upper layer to Substratum (Figure ), suggesting community heterogenization was occurring.…”

Section: Discussionsupporting

confidence: 92%

Steeper spatial scaling patterns of subsoil microbiota are shaped by deterministic assembly process

Deng

et al. 2020

Molecular Ecology

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Although many studies have investigated the spatial scaling of microbial communities living in surface soils, very little is known about the patterns within deeper strata, nor is the mechanism behind them. Here, we systematically assessed spatial scaling of prokaryotic biodiversity within three different strata (Upper: 0–20 cm, Middle: 20–40 cm, and Substratum: 40–100 cm) in a typical grassland by examining both distance–decay (DDRs) and species–area relationships (SARs), taxonomically and phylogenetically, as well as community assembly processes. Each layer exhibited significant biogeographic patterns in both DDR and SAR (p < .05), with taxonomic turnover rates higher than phylogenetic ones. Specifically, the spatial turnover rates, β and z values, respectively, ranged from 0.016 ± 0.005 to 0.023 ± 0.005 and 0.065 ± 0.002 to 0.077 ± 0.004 across soil strata, and both increased with depth. Moreover, the prokaryotic community in grassland soils assembled mainly according to deterministic rather than stochastic mechanisms. By using normalized stochasticity ratio (NST) based on null model, the relative importance of deterministic ratios increased from 48.0 to 63.3% from Upper to Substratum, meanwhile a phylogenetic based method revealed average βNTI also increased with depth, from −5.29 to 19.5. Using variation partitioning and distance approaches, both geographic distance and soil properties were found to strongly affect biodiversity structure, the proportions increasing with depth, but spatial distance was always the main underlying factor. These indicated increasingly deterministic proportions in accelerating turnover rates for spatial assembly of prokaryotic biodiversity. Our study provided new insights on biogeography in different strata, revealing importance of assembly patterns and mechanisms of prokaryote communities in below‐surface soils.

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Section: Discussionsupporting

confidence: 92%

Steeper spatial scaling patterns of subsoil microbiota are shaped by deterministic assembly process

Deng

et al. 2020

Molecular Ecology

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“…8 a). Both orders are known to be involved in various processes related to nitrogen metabolism and were previously identified as abundant groups in rainforest soils [ 40 ]. With unclassified Acidobacteria , and unclassified bacteria being high in abundance as well, observed patterns broadly reflected the general community structure as described before.…”

Section: Resultsmentioning

confidence: 99%

“…For more detailed analyses, we picked marker genes and divided them into two categories regarding energy metabolism or motility. Genes selected for nitrogen metabolism were amoA (ammonia monooxygenase A; K10944) [65], nifH (nitrogenase protein; K02588) [40], nosZ (nitrousoxide reductase; KK00376) [66], nirK and nirS (both encoding a nitrite reductase; K00368 and K15864) [40] and narG (nitrate reductase alpha subunit; K00370) [66]. For methane related processes we used pmoA/amoA (methane/ammonia monooxygenase subunit A; K10944) [64], mxaF (methanol dehydrogenase; K14028) [67], mmoY (methane monooxygenase component A beta chain; K16158) and mmoX (methane monooxygenase component A alpha chain; K16157) [68] and mcrA (5-methylcytosinespecific restriction enzyme A; K07451) [69].…”

Section: Analysis Of Selected Functional Metabolisms and Respective Mmentioning

confidence: 99%

Unravelling the effects of tropical land use conversion on the soil microbiome

Hölscher

Schneider

Meryandini

et al. 2020

Environmental Microbiome

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Background: The consequences of deforestation and agricultural treatments are complex and affect all trophic levels. Changes of microbial community structure and composition associated with rainforest conversion to managed systems such as rubber and oil palm plantations have been shown by 16S rRNA gene analysis previously, but functional profile shifts have been rarely addressed. In this study, we analysed the effects of rainforest conversion to different converted land use systems, including agroforestry ("jungle rubber") and monoculture plantations comprising rubber and oil palm, on soilborne microbial communities by metagenomic shotgun sequencing in Sumatra, Indonesia.Results: The diversity of bacteria and archaea decreased whereas diversity of fungi increased in the converted land use systems. The soil microbiome was dominated by bacteria followed by fungi. We detected negative effects of land use conversion on the abundance of Proteobacteria (especially on Rhizobiales and Burkholderiales) and positive effects on the abundance of Acidobacteria and Actinobacteria. These abundance changes were mainly driven by pH, C:N ratio, and Fe, C and N content. With increasing land use intensity, the functional diversity decreased for bacteria, archaea and fungi. Gene abundances of specific metabolisms such as nitrogen metabolism and carbon fixation were affected by land use management practices. The abundance of genes related to denitrification and nitrogen fixation increased in plantations while abundance of genes involved in nitrification and methane oxidation showed no significant difference. Linking taxonomic and functional assignment per read indicated that nitrogen metabolism-related genes were mostly assigned to members of the Rhizobiales and Burkholderiales. Abundances of carbon fixation genes increased also with increasing land use intensity. Motility-and interaction-related genes, especially genes involved in flagellar assembly and chemotaxis genes, decreased towards managed land use systems. This indicated a shift in mobility and interspecific interactions in bacterial communities within these soils. Conclusions: Rainforest conversion to managed land use systems drastically affects structure and functional potential of soil microbial communities. The decrease in motility-and interaction-related functions from rainforest to converted land use systems indicated not only a shift in nutrient cycling but also in community dynamics. Fertilizer application and correspondingly higher availability of nutrients in intensively managed plantations lead to an environment in which interspecific interactions are not favoured compared to rainforest soils. We could directly link effects of land management, microbial community structure and functional potential for several metabolic processes. As our study is the first study of this size and detail on soil microbial communities in tropical systems, we provide a basis for further analyses.

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“…The abundance, composition and N 2 -xing capacity of diazotrophs varied greatly across soil types, while only studied in the plough layer (0-15 cm), which processes are determined by soil properties, climate and geographical distance [3,24] . Previous studies presented that diazotrophic population was more abundant in surface soils due to larger organic matter contents and available N limitation [25,26] . However, the diversity and structure of diazotrophic community from deep soil horizons and their contribution to element biogeochemical cycles with depth remains unknown.…”

Section: Introductionmentioning

confidence: 99%

Multiple role of diazotrophs in coupling nitrogen and iron biogeochemical processes through vertical soil profiles of different paddy soil types

Wang¹,

Teng²,

Ren³

et al. 2020

Preprint

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Background: Soil microbiota exert fundamental functions in maintaining ecosystem functioning and services, including pedogenesis, biogeochemical processes and plant productivity, especially for agriculture system. Despite their ubiquitousness from the epipedon to deep soil, the vertical characteristics of microbiomes (especially for functional microorganisms) and their contribution to soil element cycling when considering soil developmental features are poorly understood. Here, nine profiles (0~135 cm) of two canonical paddy soil types (Fe-accumuli- and Hapli-stagnic anthrosols; 111 samples in total) at a local scale were collected, which represented relative long- and short-term water flooding history, respectively. The vertical variations in edaphic characteristics and assemblies of soil bacterial and diazotrophic communities, and microbial contribution to element cycling were explored. Results: Across soil profiles, Hapli-stagnic anthrosol was characteristic of higher concentrations in free iron oxides and total iron in the epipedon, and contained higher amounts of ammonia along the subsurface layers, as compared with acidic Fe-accumuli-anthrosol. Community assemblies of bacteria and diazotrophs, as well as edaphic properties, were mainly shaped by soil depths, followed by soil types. Furthermore, random forest analysis revealed that, for Fe-accumuli-anthrosol, available Fe could best predict nitrogen cycling index and nitrogen status was significantly related to iron cycling index; while in Hapli-stagnic anthrosol, available sulfur was the most important variable in predicting nitrogen and iron cycling indices. Among the dominant genera, some distinctive biomarkers that varied remarkably between the two soil types were noticeable for their contributions to both nitrogen and iron transformation, including iron-reducing diazotroph Geobacter and iron-oxidizing bacterium Rhodanobacter that characterized Fe-accumuli type, and sulfur reducing diazotroph Desulfobacca as main discriminant clades for Hapli-stagnic type.Conclusions: A novel perspective was proposed on the vertical characteristics of edaphic properties and bacterial and diazotrophic communities in the two paddy soil types. The findings indicated the nitrogen-iron cycling processes for Fe-accumuli-anthrosol and nitrogen-iron-sulfur coupling interaction for Hapli-stagnic anthrosol, advancing our understanding of the significant multiple role played by soil microorganisms, especially for diazotrophs, in element biogeochemical cycles.

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Changes in nitrogen-cycling microbial communities with depth in temperate and subtropical forest soils

Cited by 71 publications

References 70 publications

Steeper spatial scaling patterns of subsoil microbiota are shaped by deterministic assembly process

Steeper spatial scaling patterns of subsoil microbiota are shaped by deterministic assembly process

Unravelling the effects of tropical land use conversion on the soil microbiome

Multiple role of diazotrophs in coupling nitrogen and iron biogeochemical processes through vertical soil profiles of different paddy soil types

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