Spatial scale drives patterns in soil bacterial diversity

O’Brien, Sarah L.; Gibbons, Sean M.; Owens, Sarah M.; Hampton-Marcell, Jarrad; Johnston, Eric R.; Jastrow, Julie D.; Gilbert, Jack A.; Meyer, Folker; Antonopoulos, Dionysios A.

doi:10.1111/1462-2920.13231

Cited by 211 publications

(161 citation statements)

References 84 publications

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“…In contrast, a significant distance–decay slope of overall bacterial communities was observed only at the local scale (Figure b). The result was consistent with another study of grassland soil microbial communities showing that pronounced heterogeneity of microbial β‐diversity was significant only at centimetre scales (O'Brien et al, ). Such phenomena might be attributable to several causes.…”

Section: Discussionsupporting

confidence: 91%

The spatial scale dependence of diazotrophic and bacterial community assembly in paddy soil

Gao

Yang

Feng

et al. 2019

Global Ecol Biogeogr

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Aim The factors driving microbial community β‐diversity (variation in composition) at different spatial scales yield fundamental insights into the mechanisms that maintain ecosystem biodiversity, which as yet are uncertain. Here, we explore whether spatial scale‐dependent patterns of β‐diversity vary between microbial functional groups and bacterial taxa (i.e., diazotrophic and bacterial communities) across local to regional scales (from metres to hundreds of kilometres). Location Eastern China. Time period October and November 2015. Major taxa studied Diazotrophic and bacterial communities. MethodsWe use two complementary statistical tools to unveil biotic mechanisms (i.e., species association) underlying variation in β‐diversity of diazotrophic and bacterial communities. We examined distance–decay slopes of both communities at the local (1–113 m), meso‐ (3.4–39 km) and regional (103–668 km) scales. We used an environmentally constrained checkerboard score and topological features of association networks as indices of species association. We then calculated contributions of species association, abiotic factors and geographical distance to explain community β‐diversity. The scale‐dependent distance–decay relationships were also examined in ubiquitous (high occupancy across samples) and endemic communities of diazotrophs and bacteria. ResultsDiazotrophs displayed steeper distance–decay slopes than bacteria, suggesting that the β‐diversity of diazotrophic communities was more variable. The distance–decay slopes were dependent on spatial scales in both communities, owing to different contributions of geographical distance, abiotic factors and species association at three spatial scales. Intriguingly, species association was greater and contributed more to community β‐diversity than other forces at the local scale, implying that species association could greatly alter community structures. Main conclusionsDrivers of diazotrophic and bacterial community β‐diversity depended on spatial scales, resulting in different distance–decay patterns. Moreover, this was the first study to use two methods to demonstrate that species association played important, but as yet unrecognized, roles in driving spatial scale‐dependent β‐diversity.

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Section: Discussionsupporting

confidence: 91%

The spatial scale dependence of diazotrophic and bacterial community assembly in paddy soil

Gao

Yang

Feng

et al. 2019

Global Ecol Biogeogr

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“…), even though these communities were measured independently. To our knowledge, microbial community heterogeneity across spatial scales has not been explored within freshwater wetland soils, and the broad spatial similarity observed here contrasts with the high level of spatial heterogeneity observed within some dry soils (O'Brien et al ., ).…”

Section: Discussionmentioning

confidence: 97%

High‐resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils

Narrowe

Angle

Daly

et al. 2017

Environmental Microbiology

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Despite being key contributors to biogeochemical processes, archaea are frequently outnumbered by bacteria, and consequently are underrepresented in combined molecular surveys. Here, we demonstrate an approach to concurrently survey the archaea alongside the bacteria with high-resolution 16S rRNA gene sequencing, linking these community data to geochemical parameters. We applied this integrated analysis to hydric soils sampled across a model methane-emitting freshwater wetland. Geochemical profiles, archaeal communities, and bacterial communities were independently correlated with soil depth and water cover. Centimeters of soil depth and corresponding geochemical shifts consistently affected microbial community structure more than hundreds of meters of lateral distance. Methanogens with diverse metabolisms were detected across the wetland, but displayed surprising OTU-level partitioning by depth. Candidatus Methanoperedens spp. archaea thought to perform anaerobic oxidation of methane linked to iron reduction were abundant. Domain-specific sequencing also revealed unexpectedly diverse non-methane-cycling archaeal members. OTUs within the underexplored Woesearchaeota and Bathyarchaeota were prevalent across the wetland, with subgroups and individual OTUs exhibiting distinct occupancy and abundance distributions aligned with environmental gradients. This study adds to our understanding of ecological range for key archaeal taxa in a model freshwater wetland, and links these taxa and individual OTUs to hypotheses about processes governing biogeochemical cycling.

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“…In addition, the spatial heterogeneity of microbial communities in soils requires a sampling design that should cover all soil microhabitats (O'Brien et al . ).…”

Section: Introductionmentioning

confidence: 97%

Effect of the extraction and purification of soilDNAand pooling ofPCRamplification products on the description of bacterial and archaeal communities

et al. 2019

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Aims This study evaluated the effects of DNA extraction method, DNA purification and pooling of PCR amplification products on the description of bacterial and archaeal diversity. Methods and Results Soil DNA was extracted by the Power Soil DNA extraction kit and a customized Griffiths’ protocol. Both methods are based on cell disruption by bead beating. In total, we used three soils and six independent extractions from each soil obtained by each of the two methods. Then, three of the six extracts of each treatment were further purified by spin columns filled with Sepharose 2B and polyvinylpolypyrrolidone (PVPP). The V4 hypervariable region of the 16S rRNA gene was amplified from each extract using the 515F/806R primer pair in four independent reactions. Three amplification products were combined and sequenced as a pooled sample, while the additional amplification product was sequenced individually. The resulting 72 amplification products were sequenced by Illumina MiSeq platform. DNA extraction method had a statistically significant effect on the estimation of the composition of microbial communities that might overwhelm differences in microbial communities from distinct soils. On the other hand, a further DNA purification step or pooling of PCR amplification products had a minor effect on the description of bacterial and archaeal communities. Conclusions DNA extraction had the strongest effect on the description of bacterial and archaeal communities; low concentration of impurities, which allow PCR amplification, can still generate a minor additional bias, while PCR stochastic variability had the lowest effect. Significance and Impact of the Study Although it is well known that methodological factors affect the description of microbial communities, the relative importance of each step is still unknown. The present study determined that of the factors tested, the DNA extraction method had the strongest effects on the description of bacterial and archaeal communities.

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Spatial scale drives patterns in soil bacterial diversity

Cited by 211 publications

References 84 publications

The spatial scale dependence of diazotrophic and bacterial community assembly in paddy soil

The spatial scale dependence of diazotrophic and bacterial community assembly in paddy soil

High‐resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils

Effect of the extraction and purification of soilDNAand pooling ofPCRamplification products on the description of bacterial and archaeal communities

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