title: Plants of the fynbos biome harbour host species-specific bacterial communities.
abstract: The fynbos biome in South Africa is globally recognised as a plant biodiversity hotspot. However, very little is known about the bacterial communities associated with fynbos plants, despite interactions between primary producers and bacteria having an impact on the physiology of both partners and shaping ecosystem diversity. This study reports on the structure, phylogenetic composition and potential roles of the endophytic bacterial communities located in the stems of three fynbos plants (Erepsia anceps, Phaenocoma prolifera and Leucadendron laureolum). Using Illumina MiSeq 16S rRNA sequencing we found that different subpopulations of Deinococcus-Thermus, Alphaproteobacteria, Acidobacteria and Firmicutes dominated the endophytic bacterial communities. Alphaproteobacteria and Actinobacteria were prevalent in P. prolifera, whereas Deinococcus-Thermus dominated in L. laureolum, revealing species-specific host-bacteria associations. Although a high degree of variability in the endophytic bacterial communities within hosts was observed, we also detected a core microbiome across the stems of the three plant species, which accounted for 72% of the sequences. Altogether, it seems that both deterministic and stochastic processes shaped microbial communities. Endophytic bacterial communities harboured putative plant growth-promoting bacteria, thus having the potential to influence host health and growth.
authors.affiliation: Department of Genetics, Centre for Microbial Ecology and Genomics, Genomics Research Institute (GRI), University of Pretoria, Pretoria, South Africa.
authors.forename: Tsakani
authors.initials: T
authors.lastname: Miyambo
authors.affiliation: Department of Genetics, Centre for Microbial Ecology and Genomics, Genomics Research Institute (GRI), University of Pretoria, Pretoria, South Africa.
authors.forename: Thulani P
authors.initials: TP
authors.lastname: Makhalanyane
authors.affiliation: Department of Genetics, Centre for Microbial Ecology and Genomics, Genomics Research Institute (GRI), University of Pretoria, Pretoria, South Africa.
authors.forename: Don A
authors.initials: DA
authors.lastname: Cowan
authors.affiliation: Department of Genetics, Centre for Microbial Ecology and Genomics, Genomics Research Institute (GRI), University of Pretoria, Pretoria, South Africa avalverdeportal@gmail.com.
authors.forename: Angel
authors.initials: A
authors.lastname: Valverde
mesh_terms: D039903:Actinobacteria / Q000235:genetics; D020561:Alphaproteobacteria / Q000235:genetics; D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification; D018407:Bacterial Physiological Phenomena; D044822:Biodiversity; D004269:DNA, Bacterial / Q000235:genetics; D017753:Ecosystem; D060026:Endophytes / Q000145:classification / Q000235:genetics / Q000502:physiology*; D058507:Host Specificity; D059013:Microbial Consortia / Q000235:genetics / Q000502:physiology*; D010802:Phylogeny; D010944:Plants / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology; D013019:South Africa
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S
keywords: 16S rRNA amplicon sequencing; bacterial endophytes; community phylogenetics; core microbiome; diversity; fynbos