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. 2015 May 11;10(5):e0126962.
doi: 10.1371/journal.pone.0126962. eCollection 2015.

Patterns in species persistence and biomass production in soil microcosms recovering from a disturbance reject a neutral hypothesis for bacterial community assembly

Fen-Guo Zhang  1 , Quan-Guo Zhang  1
Affiliations

Patterns in species persistence and biomass production in soil microcosms recovering from a disturbance reject a neutral hypothesis for bacterial community assembly

Fen-Guo Zhang et al. PLoS One. .

Abstract

The neutral theory of biodiversity has emerged as a major null hypothesis in community ecology. The neutral theory may sufficiently well explain the structuring of microbial communities as the extremely high microbial diversity has led to an expectation of high ecological equivalence among species. To address this possibility, we worked with microcosms of two soils; the microcosms were either exposed, or not, to a dilution disturbance which reduces community sizes and removes some very rare species. After incubation for recovery, changes in bacterial species composition in microcosms compared with the source soils were assessed by pyrosequencing of bacterial 16S rRNA genes. Our assays could detect species with a proportional abundance ≥ 0.0001 in each community, and changes in the abundances of these species should have occurred during the recovery growth, but not be caused by the disturbance per se. The undisturbed microcosms showed slight changes in bacterial species diversity and composition, with a small number of initially low-abundance species going extinct. In microcosms recovering from the disturbance, however, species diversity decreased dramatically (by > 50%); and in most cases there was not a positive relationship between species initial abundance and their chance of persistence. Furthermore, a positive relationship between species richness and community biomass was observed in microcosms of one soil, but not in those of the other soil. The results are not consistent with a neutral hypothesis that predicts a positive abundance-persistence relationship and a null effect of diversity on ecosystem functioning. Adaptation mechanisms, in particular those associated with species interactions including facilitation and predation, may provide better explanations.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Species (OTUs) richness, Pielou’s eveness and Shannon index of bacterial communities.
(a), (c) and (e), the sandy soil microcosms. (b), (d) and (f), the grassland soil microcosms. The horizontal lines represent the source soils. Asterisks indicate significant departure from the source soils (based on one-sample t test; single asterisk, p < 0.05; double, p < 0.01; triple, p < 0.001). Data show mean ± SE (n = 5).
Fig 2
Fig 2. Persistence of species in each sandy soil microcosm as a function of initial abundances.
Persistence score of 1 indicates survival, and 0 indicates extinction. Each panel is referred by its microcosm ID; e.g. ‘control-1’ indicate the No. 1 microcosm under the control treatment. Asterisks indicate significantly positive abundance-persistence relationships (single asterisk, p < 0.05; double, p < 0.01; triple, p < 0.001).
Fig 3
Fig 3. Persistence of species in each grassland soil microcosm as a function of initial abundances.
Symbols as in Fig 2.
Fig 4
Fig 4. Bacterial community biomass in experimental microcosms.
(a), the sandy soil microcosms. (b), the grassland soil microcosms. Asterisks indicate significant departure from the source soils (based on one-sample t test; single asterisk, p < 0.05; double, p < 0.01; triple, p < 0.001). Data show mean ± SE (n = 5).
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Grants and funding

This study was funded by the National Natural Science Foundation of China (31222010 and 31421063). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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