Characterizing mixed microbial population dynamics using time-series analysis

Trosvik, Pål; Rudi, Knut; Næs, Tormod; Köhler, Achim; Chan, Kung‐Sik; Jakobsen, Kjetill S.; Stenseth, Nils Chr.

doi:10.1038/ismej.2008.36

Cited by 38 publications

(40 citation statements)

References 33 publications

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“…The time-series data were analyzed using generalized additive models (GAM) implemented in R (Trosvik et al 2008). Differences among treatments were analyzed using one-way analysis of variance (ANOVA) and the least significant difference (LSD) in SPSS 19.0 for Windows (SPSS, Inc., Chicago, IL, USA).…”

Section: Discussionmentioning

confidence: 99%

Bacillus methylotrophicus isolated from the cucumber rhizosphere degrades ferulic acid in soil and affects antioxidant and rhizosphere enzyme activities

et al. 2015

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Aims Ferulic acid (FA) accumulates in soil and inhibits plant growth. We examined whether the FA-degrading bacterium Bacillus methylotrophicus degrades FA in soil. Methods B. methylotrophicus strain CSY-F1 was isolated and applied to unplanted soil and soil planted with Cucumis sativus (cucumber). We analyzed the effects of B. methylotrophicus on rhizosphere enzyme activities and antioxidant enzyme activities in cucumber and CSY-F1 exposed to FA. Results CSY-F1 degraded FA in culture medium and in soil, giving rise to 4-vinyl guaiacol, vanillin, vanillic acid, and protocatechuic acid. When cucumber seedlings were grown in soil treated with FA, the activities of some soil enzymes decreased, and the malonaldehyde content in cucumber leaves increased. The addition of CSY-F1 to FA-treated soil increased the activities of these soil enzymes, decreased the FA concentration in the soil, and elevated the activities of some antioxidant enzymes in seedlings. Moreover, the levels of superoxide radical, hydrogen peroxide, and malonaldehyde were reduced in cucumber leaves. FA treatment increased the activities of antioxidant enzymes, including superoxide dismutase, catalase, and monodehydroascorbate, in CSY-F1. Conclusion Bacillus methylotrophicus CSY-F1 has potential applications as an FA-degrading agent in soil, as it mitigates FA stress in cucumber seedlings by activating several antioxidant and soil enzymes.

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Section: Discussionmentioning

confidence: 99%

Bacillus methylotrophicus isolated from the cucumber rhizosphere degrades ferulic acid in soil and affects antioxidant and rhizosphere enzyme activities

et al. 2015

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“…Indeed, balance between populations was strictly governed by interaction among community members, each of them might be affected positively or negatively by each other (Trosvik et al, 2008). It should be the case for the most impacted fungi S. depressa, only present in CYP79A1 transgenic plants, that is a parasite of another fungi.…”

Section: Discussionmentioning

confidence: 99%

Exogenous glucosinolate produced by Arabidopsis thaliana has an impact on microbes in the rhizosphere and plant roots

et al. 2009

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A specificity of Brassicaceous plants is the production of sulphur secondary metabolites called glucosinolates that can be hydrolysed into glucose and biocidal products. Among them, isothiocyanates are toxic to a wide range of microorganisms and particularly soil-borne pathogens. The aim of this study was to investigate the role of glucosinolates and their breakdown products as a factor of selection on rhizosphere microbial community associated with living Brassicaceae. We used a DNA-stable isotope probing approach to focus on the active microbial populations involved in root exudates degradation in rhizosphere. A transgenic Arabidopsis thaliana line producing an exogenous glucosinolate and the associated wild-type plant associated were grown under an enriched 13 CO 2 atmosphere in natural soil. DNA from the rhizospheric soil was separated by density gradient centrifugation. Bacterial (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Acidobacteria), Archaea and fungal community structures were analysed by DGGE fingerprints of amplified 16S and 18S rRNA gene sequences. Specific populations were characterized by sequencing DGGE fragments. Roots of the transgenic plant line presented an altered profile of glucosinolates and other minor additional modifications. These modifications significantly influenced microbial community on roots and active populations in the rhizosphere. Alphaproteobacteria, particularly Rhizobiaceae, and fungal communities were mainly impacted by these Brassicaceous metabolites, in both structure and composition. Our results showed that even a minor modification in plant root could have important repercussions for soil microbial communities.

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“…Our study reports, for the first time, the application of GAM models to elucidate the microbial ecology of specific functional traits in mangrove sediments. These niche-based species distribution models [76] have been applied to a wide range of plants, macroorganisms and microorganisms [14,[77][78][79] and consist of observations of species over a gradient of environmental parameters (or "predictors") that can have a direct or indirect effect on the establishment or survival of the species at a limited time period. GAM models assume pseudo-equilibrium between the environmental parameters and the species spatial pattern underlying the realized niche for the species studied [76].…”

Section: Discussionmentioning

confidence: 99%

Phylogenetic Diversity of Diazotrophs along an Experimental Nutrient Gradient in Mangrove Sediments

Romero

Jacobson-Meyers

Fuhrman

et al. 2015

JMSE

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Abstract:The diversity of diazotrophs was studied in the sediment of mangrove forests (Twin Cays, Belize) subjected to a long-term fertilization with nitrogen and phosphorus. Terminal Restriction Fragment Length Polymorphism (TRFLP) and cloning of PCR-amplified nifH genes were combined via in silico analysis to assign clones to TRFLP-nifH phylotypes, as well as to characterize the occurrence of phylotypes in response to environmental conditions. Results indicated that mangrove sediments from Belize harbor a unique diazotrophic community with a low metabolic diversity dominated by sulfate reducers. The variability of potential nitrogen-fixing sulfate reducers was explained by several environmental parameters, primarily by the abundance of dead roots in the sediments, and the concentration of H2S in the pore-waters. This study describes the complexity of microbial communities within the mangrove sediments with specific functional groups varying along environmental gradients.

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Characterizing mixed microbial population dynamics using time-series analysis

Cited by 38 publications

References 33 publications

Bacillus methylotrophicus isolated from the cucumber rhizosphere degrades ferulic acid in soil and affects antioxidant and rhizosphere enzyme activities

Bacillus methylotrophicus isolated from the cucumber rhizosphere degrades ferulic acid in soil and affects antioxidant and rhizosphere enzyme activities

Exogenous glucosinolate produced by Arabidopsis thaliana has an impact on microbes in the rhizosphere and plant roots

Phylogenetic Diversity of Diazotrophs along an Experimental Nutrient Gradient in Mangrove Sediments

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