Microbial secondary succession in a chronosequence of chalk grasslands

Kuramae, Eiko E.; Gamper, Hannes A.; Yergeau, Étienne; Piceno, Yvette M.; Brodie, Eoin L.; DeSantis, Todd Z.; Andersen, Gary L.; Veen, Johannes A. van; Kowalchuk, George A.

doi:10.1038/ismej.2010.11

Cited by 72 publications

(54 citation statements)

References 18 publications

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“…In our study, moisture availability after incubation could be a potential clue for the structuring of the community by selecting for individual microbial species with relatively high moisture stress resistance. Other factors are also said to be key to the shaping of bacterial communities in soil (34)(35)(36)(37), but the relevance of these factors for the assemblage of the communities from various inocula, as in this study, is not known.…”

Section: Discussionmentioning

confidence: 68%

Revisiting the Dilution Procedure Used To Manipulate Microbial Biodiversity in Terrestrial Systems

Yan

Kuramae

Klinkhamer

et al. 2015

Appl Environ Microbiol

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bIt is hard to assess experimentally the importance of microbial diversity in soil for the functioning of terrestrial ecosystems. An approach that is often used to make such assessment is the so-called dilution method. This method is based on the assumption that the biodiversity of the microbial community is reduced after dilution of a soil suspension and that the reduced diversity persists after incubation of more or less diluted inocula in soil. However, little is known about how the communities develop in soil after inoculation. In this study, serial dilutions of a soil suspension were made and reinoculated into the original soil previously sterilized by gamma irradiation. We determined the structure of the microbial communities in the suspensions and in the inoculated soils using 454-pyrosequencing of 16S rRNA genes. Upon dilution, several diversity indices showed that, indeed, the diversity of the bacterial communities in the suspensions decreased dramatically, with Proteobacteria as the dominant phylum of bacteria detected in all dilutions. The structure of the microbial community was changed considerably in soil, with Proteobacteria, Bacteroidetes, and Verrucomicrobia as the dominant groups in most diluted samples, indicating the importance of soil-related mechanisms operating in the assembly of the communities. We found unique operational taxonomic units (OTUs) even in the highest dilution in both the suspensions and the incubated soil samples. We conclude that the dilution approach reduces the diversity of microbial communities in soil samples but that it does not allow accurate predictions of the community assemblage during incubation of (diluted) suspensions in soil.

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Section: Discussionmentioning

confidence: 68%

Revisiting the Dilution Procedure Used To Manipulate Microbial Biodiversity in Terrestrial Systems

Yan

Kuramae

Klinkhamer

et al. 2015

Appl Environ Microbiol

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“…In particular, it has been shown that the composition, and in some cases diversity, of soil bacterial community is correlated with soil pH (Sait et al ., ; Eichorst et al ., ; Hartman et al ., ; Jenkins et al ., ; Lauber et al ., ) and other soil factors than pH, such as Ca/Mg ratio, and Al and phosphorous content (Faoro et al ., ). This pattern holds both for overall bacterial community composition (Fierer & Jackson, ; Baker et al ., ; Lauber et al ., ; Kuramae et al ., ) and for the composition of individual bacterial groups (Nicol et al ., ; Davis et al ., ; Jenkins et al ., ; Jones et al ., ).…”

Section: Discussionmentioning

confidence: 99%

Acidobacterial community responses to agricultural management of soybean in Amazon forest soils

Navarrete¹,

Kuramae²,

Hollander

et al. 2012

FEMS Microbiol Ecol

219

157

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This study focused on the impact of land-use changes and agricultural management of soybean in Amazon forest soils on the abundance and composition of the acidobacterial community. Quantitative real-time PCR (q-PCR) assays and pyrosequencing of 16S rRNA gene were applied to study the acidobacterial community in bulk soil samples from soybean croplands and adjacent native forests, and mesocosm soil samples from soybean rhizosphere. Based on qPCR measurements, Acidobacteria accounted for 23% in forest soils, 18% in cropland soils, and 14% in soybean rhizosphere of the total bacterial signals. From the 16S rRNA gene sequences of Bacteria domain, the phylum Acidobacteria represented 28% of the sequences from forest soils, 16% from cropland soils, and 17% from soybean rhizosphere. Acidobacteria subgroups 1-8, 10, 11, 13, 17, 18, 22, and 25 were detected with subgroup 1 as dominant among them. Subgroups 4, 6, and 7 were significantly higher in cropland soils than in forest soils, which subgroups responded to decrease in soil aluminum. Subgroups 6 and 7 responded to high content of soil Ca, Mg, Mn, and B. These results showed a differential response of the Acidobacteria subgroups to abiotic soil factors, and open the possibilities to explore acidobacterial subgroups as early-warning bioindicators of agricultural soil management effects in the Amazon area.

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“…The few studies that so far have assessed the successional patterns of microbial communities along environmental chronosequences have focused on receding glacier forelands (Sigler and Zeyer, 2002;Nicol et al, 2005;Deiglmayr et al, 2006;Nemergut et al, 2007;Schmidt et al, 2008;Schü tte et al, 2009;Wu et al, 2012), abandoned agricultural fields (Elhottová et al, 2002;Kuramae et al, 2010) and post-mining areas (Hü ttl and Weber, 2001;Kozdró j and van Elsas, 2001). As an extension from what we know on successional dynamics of communities of larger organisms, we would expect microbial succession trajectories to present a continuing time series determined by orderly changes in environmental parameters, towards an increase of biological diversity and complexity (as observed for plant succession, Walker and del Moral, 2003).…”

Section: Introductionmentioning

confidence: 99%

Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning

et al. 2014

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The mechanisms underlying community assembly and promoting temporal succession are often overlooked in microbial ecology. Here, we studied an undisturbed salt marsh chronosequence, spanning over a century of ecosystem development, to understand bacterial succession in soil. We used 16S rRNA gene-based quantitative PCR to determine bacterial abundance and multitag 454 pyrosequencing for community composition and diversity analyses. Despite 10-fold lower 16S rRNA gene abundances, the initial stages of soil development held higher phylogenetic diversities than the soil at late succession. Temporal variations in phylogenetic b-diversity were greater at initial stages of soil development, possibly as a result of the great dynamism imposed by the daily influence of the tide, promoting high immigration rates. Allogenic succession of bacterial communities was mostly driven by shifts in the soil physical structure, as well as variations in pH and salinity, which collectively explained 84.5% of the variation concerning community assemblage. The community assembly data for each successional stage were integrated into a network co-occurrence analysis, revealing higher complexity at initial stages, coinciding with great dynamism in turnover and environmental variability. Contrary to a spatial niche-based perspective of bacterial community assembly, we suggest temporal niche partitioning as the dominant mechanism of assembly (promoting more phylotype co-occurrence) in the initial stages of succession, where continuous environmental change results in the existence of multiple niches over short periods of time.

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Microbial secondary succession in a chronosequence of chalk grasslands

Cited by 72 publications

References 18 publications

Revisiting the Dilution Procedure Used To Manipulate Microbial Biodiversity in Terrestrial Systems

Revisiting the Dilution Procedure Used To Manipulate Microbial Biodiversity in Terrestrial Systems

Acidobacterial community responses to agricultural management of soybean in Amazon forest soils

Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning

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