Soil Depth Determines the Composition and Diversity of Bacterial and Archaeal Communities in a Poplar Plantation

Feng, Huili; Guo, Jiahuan; Wang, Weifeng; Song, Xinzhang; Yu, Shen

doi:10.3390/f10070550

Cited by 43 publications

(44 citation statements)

References 57 publications

(61 reference statements)

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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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“…Our PCR analyses of soil samples (0–15 cm depth) failed to detect the presence of methanogens in the shallow soil, consistent with our measurements of methane uptake only at the soil surface (Fig. 4), and previous reports of minimal Euryarchaeota DNA in poplar forest soils (Feng et al ., 2019).…”

Section: Discussionmentioning

confidence: 99%

Multiple processes contribute to methane emission in a riparian cottonwood forest ecosystem

et al. 2020

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Methane emission from trees may partially or completely offset the methane sink in upland soils, the only process that has been regularly included in methane budgets for forest ecosystems. Our objective was to analyze multiple biogeochemical processes that influence the production, oxidation and transport of methane in a riparian cottonwood ecosystem and its adjacent river. We combined chamber flux measurements on tree stems, forest soil and the river surface with eddy covariance measurements of methane net ecosystem exchange. In addition, we tested whether methanogens were present in cottonwood stems, shallow soil layers and alluvial groundwater. Average midday peak in net methane emission measured by eddy covariance was c. 12 nmol m −2 s −1. The average uptake of methane by soils (0.87 nmol m −2 s −1) was largely offset by tree stem methane emission (0.75 nmol m −2 s −1). There was evidence of methanogens in tree stems but not in shallow soil. Growing season (May-September) cumulative net methane emission (17.4 mmol CH 4 m −2) included methane produced in cottonwood stems and methane input to the nocturnal boundary layer from the forest and the adjacent river. The multiple processes contributing to methane emission illustrated the linked nature of these adjacent terrestrial and aquatic ecosystems.

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“…For example, the bacterial and fungal communities differ depending on soil depth (topsoil versus subsoil) over long-term fertilization studies ( Gu et al, 2017 ). Many studies have shown that the microbial diversity typically decreases with soil depth, probably owing to the decreased exposure to fertilizers from topsoil to subsoil ( Li et al, 2014 ; Feng et al, 2019 ). Sampling of bulk soil can introduce high variability and, therefore, it is important to take into consideration sampling strategies to account for this variability ( Ogram et al, 2007 ).…”

Section: Limitations Of Microbial Community Experiments and Their Appmentioning

confidence: 99%

Tailoring plant-associated microbial inoculants in agriculture: a roadmap for successful application

Saad

Eida

Hirt

2020

Journal of Experimental Botany

126

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Plants are now recognized as metaorganisms which are composed of a host plant associated with a multitude of microbes that provide the host plant with a variety of essential functions to adapt to the local environment. Recent research showed the remarkable importance and range of microbial partners for enhancing the growth and health of plants. However, plant–microbe holobionts are influenced by many different factors, generating complex interactive systems. In this review, we summarize insights from this emerging field, highlighting the factors that contribute to the recruitment, selection, enrichment, and dynamic interactions of plant-associated microbiota. We then propose a roadmap for synthetic community application with the aim of establishing sustainable agricultural systems that use microbial communities to enhance the productivity and health of plants independently of chemical fertilizers and pesticides. Considering global warming and climate change, we suggest that desert plants can serve as a suitable pool of potentially beneficial microbes to maintain plant growth under abiotic stress conditions. Finally, we propose a framework for advancing the application of microbial inoculants in agriculture.

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Soil Depth Determines the Composition and Diversity of Bacterial and Archaeal Communities in a Poplar Plantation

Cited by 43 publications

References 57 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

Multiple processes contribute to methane emission in a riparian cottonwood forest ecosystem

Tailoring plant-associated microbial inoculants in agriculture: a roadmap for successful application

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