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. 2014;29(1):38-49.
doi: 10.1264/jsme2.me13142. Epub 2014 Jan 24.

Characterization of early microbial communities on volcanic deposits along a vegetation gradient on the island of Miyake, Japan

Yong Guo  1 , Reiko Fujimura, Yoshinori Sato, Wataru Suda, Seok-won Kim, Kenshiro Oshima, Masahira Hattori, Takashi Kamijo, Kazuhiko Narisawa, Hiroyuki Ohta
Affiliations

Characterization of early microbial communities on volcanic deposits along a vegetation gradient on the island of Miyake, Japan

Yong Guo et al. Microbes Environ. 2014.

Abstract

The 2000 eruption of Mount Oyama on the island of Miyake (Miyake-jima) created a unique opportunity to study the early ecosystem development on newly exposed terrestrial substrates. In this study, bacterial and fungal communities on 9- and 11-year-old volcanic deposits at poorly to fully vegetation-recovered sites in Miyake-jima, Japan, were characterized by conventional culture-based methods and pyrosequencing of 16S rRNA and 18S rRNA genes. Despite the differences in the vegetation cover, the upper volcanic deposit layer samples displayed low among-site variation for chemical properties (pH, total organic carbon, and total nitrogen) and microbial population densities (total direct count and culturable count). Statistical analyses of pyrosequencing data revealed that the microbial communities of volcanic deposit samples were phylogenetically diverse, in spite of very low-carbon environmental conditions, and their diversity was comparable to that in the lower soil layer (buried soil) samples. Comparing with the microbial communities in buried soil, the volcanic deposit communities were characterized by the presence of Betaproteobacteria and Gammaproteobacteria as the main bacterial class, Deinococcus- Thermus as the minor bacterial phyla, and Ascomycota as the major fungal phyla. Multivariate analysis revealed that several bacterial families and fungal classes correlated positively or negatively with plant species.

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Figures

Fig. 1
Fig. 1
Principal coordinate analysis (PCoA) plots of bacterial (A) and fungal (B) communities of the volcanic deposit (triangles and diamonds) and soil (circles and squares) samples by weighted UniFrac. Silva bacterial and eukaryotic trees were selected as the reference trees.
Fig. 2
Fig. 2
Heat map presentations of the 50 most abundant bacterial OTUs (A) and the 30 most abundant fungal OTUs (B) in each sample. The samples and OTUs were clustered on their Bray-Curtis similarities (group-average linkage). The key relates to the untransformed read counts.
Fig. 3
Fig. 3
Taxonomic classification of the pyrosequencing reads. Classification at the phylum and proteobacterial class level (α, Alphaproteobacteria; β, Betaproteobacteria; γ, Gammaproteobacteria; δ, Deltaproteobacteria; u, unclassified proteobacteria) for total bacterial OTUs (A), family-level classifications of the OTUs belonging to Alphaproteobacteria (B), Betaproteobacteria (C), and Gammaproteobacteria (D), and Actinobacteria (E), and classification of low-abundance OTUs (<1% of total bacterial OTUs in each sample) into bacterial phyla (F). Classification at the phylum level for total fungal reads (G), class-level classifications of the reads of Ascomycota (H) and Basidiomycota (I). △, IG1-VD-09; formula image, IG2-VD-09; ▲, IG3-VD-09; ⋄, IG1-VD-11; formula image, IG2-VD-11; ◆, IG3-VD-11; ○, IG1-S-09; formula image, IG2-S-09; ●, IG3-S-09; □, IG1-S-11; formula image, IG2-S-11; ■, IG3-S-11.
Fig. 4
Fig. 4
Canonical correspondence analysis (CCA) ordination plots of bacterial (A) and fungal (B) communities of six volcanic deposits (triangles and diamonds) and results of the analysis of environmental factors affecting bacterial and fungal distribution, showing significant effects of the colonizer plants. The direction of the arrows for individual plant species indicates an increasing coverage of that plant and the length of the arrows indicates the degree of correlation with the represented axes. The numbers correspond to the bacterial families (A) and fungal classes (B) in the keys on the right and are ranked according to abundance.
Fig. 5
Fig. 5
Relationship between TOC and respiration per unit amount of organic carbon (TOC).
See this image and copyright information in PMC

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