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

Gruyter, Johan De; Weedon, James T.; Bazot, Stéphane; Dauwe, Steven; Fernandez-Garberí, Pere Roc; Geisen, Stefan; Motte, Louis Gourlez de la; Heinesch, Bernard; Janssens, Ivan A.; Leblans, Niki I. W.; Manise, Tanguy; Ogaya, Romà; Löfvenius, Mikaell Ottosson; Peñuelas, Josep; Sigurðsson, Bjarni D.; Vincent, Gaëlle; Verbruggen, Erik

doi:10.1093/femsec/fiaa018

Cited by 24 publications

(18 citation statements)

References 74 publications

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“…ΔpH), which may be different along different gradients such as pH and geography (Harrison et al ., 1992; Anderson et al ., 2011). Notably, as observed in previous studies (Monroy et al ., 2012; Jiao et al ., 2019; De Gruyter et al ., 2020), one group may have a higher variation of community structure but lower turnover along a specific gradient and vice versa.…”

Section: Methodsmentioning

confidence: 99%

Stochastic processes regulate belowground community assembly in alpine grasslands on the Tibetan Plateau

Liu

Chen

Zhang

et al. 2021

Environmental Microbiology

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Understanding biogeographical patterns and underlying processes of belowground community assembly is crucial for predicting soil functions and their responses to global environmental change. However, little is known about potential differences of belowground community assembly among bacteria, fungi, protists and soil animals, particularly for alpine ecosystems. Based on the combination of largescale field sampling, high-throughput marker-gene sequencing and multiple statistical analyses, we explored patterns and drivers of belowground community assembly in alpine grasslands on the Tibetan Plateau. Our results revealed that the distance-decay rates varied among trophic levels, with organisms of higher trophic level having weaker distance-decay pattern. The spatial and environmental variables explained limited variations of belowground communities. By contrast, the stochastic processes, mainly consisting of dispersal limitation and drift, played a primary role in regulating belowground community assembly. Moreover, the relative importance of stochastic processes varied among trophic levels, with the role of dispersal limitation weakening whereas that of drift enhancing in the order of bacteria, fungi, protists and soil animals. These findings advance our understanding of patterns and mechanisms driving belowground community assembly in alpine ecosystems and provide a reference basis for predicting the dynamics of ecosystem functions under changing environment.

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Section: Methodsmentioning

confidence: 99%

Stochastic processes regulate belowground community assembly in alpine grasslands on the Tibetan Plateau

Liu

Chen

Zhang

et al. 2021

Environmental Microbiology

View full text Add to dashboard Cite

show abstract

“…temperature, precipitation) and edaphic conditions (e.g. soil pH, moisture) are often seen as important determinants of microbial communities (Borowik & Wyszkowska, 2016;Singh et al, 2009;Wang et al, 2020) yet they cannot completely explain the full variation observed within microbial communities (De Gruyter et al, 2020). This suggests that biotic interactions also play an important role in shaping microbial communities (Geisen, 2020).…”

Section: Introductionmentioning

confidence: 99%

Predicting the structure and functions of peatland microbial communities from Sphagnum phylogeny, anatomical and morphological traits and metabolites

et al. 2021

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1. Sphagnum mosses are keystone species in northern peatlands. Notably, they play an important role in peatland carbon (C) cycling by regulating the composition and activity of microbial communities. However, it remains unclear whether information on Sphagnum phylogeny and/or traits-based composition (i.e. anatomical and morphological traits and metabolites) can be used to predict the structure of microbial communities and their functioning. Here we evaluated whether Sphagnum phylogeny and traits predict additional variation in peatland microbial community composition and functioning beyond what would be predicted from environmental characteristics (i.e. climatic and edaphic conditions).2. We collected Sphagnum and microbial data from five European peatlands distributed along a latitudinal gradient from northern Sweden to southern France. This allowed us to assess Sphagnum anatomical and morphological traits and metabolites at different sites along changing environmental conditions. Using structural equation modelling (SEM) and phylogenetic distance analyses, we investigated the role of Sphagnum traits in shaping microbial community composition and functioning along with environmental conditions. We show that microbial community composition and traits varied independently from bothSphagnum phylogeny and the latitudinal gradient. Specifically, the addition of Sphagnum traits to climatic and edaphic variables to the SEM allowed it to explain a larger proportion of the explained variance (R 2 ). This observation was most apparent for the biomass of decomposers (+42%) and phototrophs (+19%), as well as for growth yield microbial traits (+10%). As such, that Sphagnum metabolites were important drivers for microbial community structure and traits, while Sphagnum anatomical and morphological traits were poor predictors. 3 4. Synthesis. Our results highlight that Sphagnum metabolites are more to influence peatland microbial food web structure and functioning than Sphagnum anatomical and morphological traits. We provide further evidence that measurements of the plant metabolome, when combined with classical functional traits, improve our understanding of how the plants interact with their associated microbiomes.

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“…These primers also have the advantage to cover well the basal fungal groups (i.e., Blastocladiomycota, Chytridiomycota, Entomophthoromycotina, Glomeromycota, Kickxellomycotina, Mucoromycota and Zoopagomycotina) when ITS primers are biased toward Dikarya. Fungal diversity could also be assessed jointly with protists using general eukaryotic primers, particularly the one targeting the V4 18S rRNA gene (see next section, e.g., [119]). The last alternative is to target the 28S rRNA gene with the primer combination LROR and LR3, with the 100 nucleotide (nt) region before the reverse primer being the best discriminant region for fungi [120].…”

Section: Identification Of Fungi From Environmental Samplesmentioning

confidence: 99%

DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

et al. 2021

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Soil-borne microbes are major ecological players in terrestrial environments since they cycle organic matter, channel nutrients across trophic levels and influence plant growth and health. Therefore, the identification, taxonomic characterization and determination of the ecological role of members of soil microbial communities have become major topics of interest. The development and continuous improvement of high-throughput sequencing platforms have further stimulated the study of complex microbiota in soils and plants. The most frequently used approach to study microbiota composition, diversity and dynamics is polymerase chain reaction (PCR), amplifying specific taxonomically informative gene markers with the subsequent sequencing of the amplicons. This methodological approach is called DNA metabarcoding. Over the last decade, DNA metabarcoding has rapidly emerged as a powerful and cost-effective method for the description of microbiota in environmental samples. However, this approach involves several processing steps, each of which might introduce significant biases that can considerably compromise the reliability of the metabarcoding output. The aim of this review is to provide state-of-the-art background knowledge needed to make appropriate decisions at each step of a DNA metabarcoding workflow, highlighting crucial steps that, if considered, ensures an accurate and standardized characterization of microbiota in environmental studies.

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

Cited by 24 publications

References 74 publications

Stochastic processes regulate belowground community assembly in alpine grasslands on the Tibetan Plateau

Stochastic processes regulate belowground community assembly in alpine grasslands on the Tibetan Plateau

Predicting the structure and functions of peatland microbial communities from Sphagnum phylogeny, anatomical and morphological traits and metabolites

DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

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