Deterministic assembly processes govern bacterial community structure in the Fynbos, South Africa

Abstract

The Mediterranean Fynbos vegetation of South Africa is well known for its high levels of diversity, endemism, and the existence of very distinct plant communities on different soil types. Studies have documented the broad taxonomic classification and diversity patterns of soil microbial diversity, but none has focused on the community assembly processes. We hypothesised that bacterial phylogenetic community structure in the Fynbos is highly governed by deterministic processes. We sampled soils in four Fynbos vegetation types and examined bacterial communities using Illumina HiSeq platform with the 16S rRNA gene marker. UniFrac analysis showed that the community clustered strongly by vegetation type, suggesting a history of evolutionary specialisation in relation to habitats or plant communities. The standardised beta mean nearest taxon distance (ses. β NTD) index showed no association with vegetation type. However, the overall phylogenetic signal indicates that distantly related OTUs do tend to co-occur. Both NTI (nearest taxon index) and ses. β NTD deviated significantly from null models, indicating that deterministic processes were important in the assembly of bacterial communities. Furthermore, ses. β NTD was significantly higher than that of null expectations, indicating that co-occurrence of related bacterial lineages (over-dispersion in phylogenetic beta diversity) is determined by the differences in environmental conditions among the sites, even though the co-occurrence pattern did not correlate with any measured environmental parameter, except for a weak correlation with soil texture. We suggest that in the Fynbos, there are frequent shifts of niches by bacterial lineages, which then become constrained and evolutionary conserved in their new environments. Overall, this study sheds light on the relative roles of both deterministic and neutral processes in governing bacterial communities in the Fynbos. It seems that deterministic processes play a major role in assembling the bacterial community, with neutral processes playing a more minor role.

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Acknowledgments

The authors would like to thank the South African National Parks (SANParks) and Cape Nature for giving us access to the study sites (permit number 0028-AAA005-00161, 25/01/2010: SBM Chimphango), as well as Dr. James C Stegen and Dr. Binu M Tribathi for providing invaluable advice with the analysis of the data. This work was supported by a grant from the National Research Foundation (NRF) funded by the Korean Government Ministry of Education, Science and Technology (MEST) (NRF2013-031400). Also, the authors would like to thank the Department of Biological Science, University of Cape Town for use of their laboratory facilities.

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Moroenyane, I., Chimphango, S.B.M., Wang, J. et al. Deterministic assembly processes govern bacterial community structure in the Fynbos, South Africa. Microb Ecol 72, 313–323 (2016). https://doi.org/10.1007/s00248-016-0761-5

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Keywords

  • Bacteria
  • Fynbos
  • 16S rRNA gene
  • Phylogenetic diversity
  • Community assembly