Dataset Information

Pyrosequencing analysis of a bacterial community associated with lava-formed soil from the Gotjawal forest in Jeju, Korea.

ABSTRACT: In this study, we analyzed the bacterial diversity in soils collected from Gyorae Gotjawal forest, where globally unique topography, geology, and ecological features support a forest grown on basalt flows from 110,000 to 120,000 years ago and 40,000 to 50,000 years ago. The soils at the site are fertile, with rocky areas, and are home to endangered species of plants and animals. Rainwater penetrates to the groundwater aquifer, which is composed of 34% organic matter containing rare types of soil and no soil profile. We determined the bacterial community composition using 116,475 reads from a 454-pyrosequencing analysis. This dataset included 12,621 operational taxonomic units at 3% dissimilarity, distributed among the following groups: Proteobacteria (56.2%) with 45.7% of ?-Proteobacteria, Actinobacteria (25%), Acidobacteria (10.9%), Chloroflexi (2.4%), and Bacteroidetes (0.9%). In addition, 16S rRNA gene sequences were amplified using polymerase chain reaction and domain-specific primers to construct a clone library based on 142 bacterial clones. These clones were affiliated with the following groups: Proteobacteria (56%) with 51% of ?-Proteobacteria, Acidobacteria (7.8%), Actinobacteria (17.6%), Chloroflexi (2.1%), Bacilli (1.4%), Cyanobacteria (2.8%), and Planctomycetes (1.4%). Within the phylum Proteobacteria, 56 of 80 clones were tentatively identified as 12 unclassified genera. Several new genera and a new family were discovered within the Actinobacteria clones. Results from 454-pyrosequencing revealed that 57% and 34% of the sequences belonged to undescribed genera and families, respectively. The characteristics of Gotjawal soil, which are determined by lava morphology, vegetation, and groundwater penetration, might be reflected in the bacterial community composition.

SUBMITTER: Kim JS

PROVIDER: S-EPMC4398510 | biostudies-literature | 2015 Apr

REPOSITORIES: biostudies-literature

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Pyrosequencing analysis of a bacterial community associated with lava-formed soil from the Gotjawal forest in Jeju, Korea.

Kim Jong-Shik JS Lee Keun Chul KC Kim Dae-Shin DS Ko Suk-Hyung SH Jung Man-Young MY Rhee Sung-Keun SK Lee Jung-Sook JS

MicrobiologyOpen 20150121 2

In this study, we analyzed the bacterial diversity in soils collected from Gyorae Gotjawal forest, where globally unique topography, geology, and ecological features support a forest grown on basalt flows from 110,000 to 120,000 years ago and 40,000 to 50,000 years ago. The soils at the site are fertile, with rocky areas, and are home to endangered species of plants and animals. Rainwater penetrates to the groundwater aquifer, which is composed of 34% organic matter containing rare types of soil ...[more]

PMID: 25604185

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Project description:The Gotjawal areas of Jeju Island, Korea, are comprised of unmanaged forests growing on volcanic soils. They support unique assemblages of vascular plants from both northern and southern hemispheres, but are threatened by human disturbance. The health and ecosystem function of these assemblages likely depends in part on the diversity and community structure of soil microbial communities, about which little is known. To assess the diversity of Gotjawal soil microbial communities, twenty samples were collected in November 2010 from 4 representatives of Gotjawal forests. While soil properties and microbial communities measured by 16S rRNA gene sequence data were marginally distinct among sites by PERMANOVA (p = 0.017-0.191), GeoChip data showed significant differences among sites (p <0.006). Gene composition overall, and the composition of 3 functional gene categories had similar structures themselves and similar associations with environmental factors. Among these communities, phosphorous cycling genes exhibited the most distinct patterns. 16S rRNA gene sequence data resulted in a mean 777 operational taxonomic units (OTUs), which included the following major phyla: Proteobacteria (27.9%), Actinobacteria (17.7%), Verrucomicrobia (14.3%), Acidobacteria (9.6%), Planctomycetes (9.8%), Bacteroidetes (8.9%), and Chloroflexi (2.2%). Indicator species analysis (ISA) was used to determine the taxa with high indicator value, which represented the following: uncultured Chlamydiaceae, Caulobacter, uncultured Sinobacteraceae, Paenibacillus, Arenimonas, Clostridium sensu.stricto, uncultured Burkholderiales incertae sedis, and Nocardioides in Aewol (AW), Aquicella, uncultured Planctomycetia, and Aciditerrimonas in Gujwa-Seongsan (GS), uncultured Acidobacteria Gp1, and Hamadaea in Hankyeong-Andeok (HA), and Bosea, Haliea, and Telmatocola in Jocheon-Hamdeok (JH) Gotjawal. Collectively, these results demonstrated the uniqueness of microbial communities within each Gotjawal region, likely reflecting different patterns of soil, plant assemblages and microclimates.

Project description:BACKGROUND: Soil bacteria are important drivers for nearly all biogeochemical cycles in terrestrial ecosystems and participate in most nutrient transformations in soil. In contrast to the importance of soil bacteria for ecosystem functioning, we understand little how different management types affect the soil bacterial community composition. METHODOLOGY/PRINCIPAL FINDINGS: We used pyrosequencing-based analysis of the V2-V3 16S rRNA gene region to identify changes in bacterial diversity and community structure in nine forest and nine grassland soils from the Schwäbische Alb that covered six different management types. The dataset comprised 598,962 sequences that were affiliated to the domain Bacteria. The number of classified sequences per sample ranged from 23,515 to 39,259. Bacterial diversity was more phylum rich in grassland soils than in forest soils. The dominant taxonomic groups across all samples (>1% of all sequences) were Acidobacteria, Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Firmicutes. Significant variations in relative abundances of bacterial phyla and proteobacterial classes, including Actinobacteria, Firmicutes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes and Alphaproteobacteria, between the land use types forest and grassland were observed. At the genus level, significant differences were also recorded for the dominant genera Phenylobacter, Bacillus, Kribbella, Streptomyces, Agromyces, and Defluviicoccus. In addition, soil bacterial community structure showed significant differences between beech and spruce forest soils. The relative abundances of bacterial groups at different taxonomic levels correlated with soil pH, but little or no relationships to management type and other soil properties were found. CONCLUSIONS/SIGNIFICANCE: Soil bacterial community composition and diversity of the six analyzed management types showed significant differences between the land use types grassland and forest. Furthermore, bacterial community structure was largely driven by tree species and soil pH.

Dataset Information

Pyrosequencing analysis of a bacterial community associated with lava-formed soil from the Gotjawal forest in Jeju, Korea.

Publications

Pyrosequencing analysis of a bacterial community associated with lava-formed soil from the Gotjawal forest in Jeju, Korea.

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