Variibacter gotjawalensis gen. nov., sp. nov., isolated from soil of a lava forest

Kim, Kwang Kyu; Lee, Keun Chul; Eom, Mi Kyung; Kim, Jong‐Shik; Kim, Dae-Shin; Ko, Suk-Hyung; Kim, Byung-Hyuk; Lee, Jung-Sook

doi:10.1007/s10482-014-0146-z

Cited by 25 publications

(10 citation statements)

References 31 publications

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“…At present, some areas of the Gotjawal are protected, but about 50% of the original forests have been replaced by secondary growth due to losses from deforestation, agricultural land use, and urbanization[ 3 ]. Gotjawal soils are considered highly fertile due to their high organic matter and low mineral content, but relatively little is known about their microbiology[ 2 , 4 ]. Previous cultivation-based studies of these soils have identified several new genera and species [ 2 , 4 – 8 ], but more comprehensive analyses are needed to understand patterns of microbial community structure and function, and interactions with Gotjawal plant assemblages.…”

Section: Introductionmentioning

confidence: 99%

Microbial community structure and functional potential of lava-formed Gotjawal soils in Jeju, Korea

Kim

Lee

et al. 2018

PLoS ONE

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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.

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Section: Introductionmentioning

confidence: 99%

Microbial community structure and functional potential of lava-formed Gotjawal soils in Jeju, Korea

Kim

Lee

et al. 2018

PLoS ONE

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“…nov., isolated from the soil of Aewol Gotjawal forest, one of four Gotjawal sites on Jeju Island (Kim et al. ); this isolate belongs to α ‐ Proteobacteria and shows high similarity with Bradyrhizobium oligotrophicum LMG 10732 (93.6%).…”

Section: Resultsmentioning

confidence: 99%

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

Kim

Lee

Kim³

et al. 2015

MicrobiologyOpen

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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 α-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 α-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.

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“…Bosea is a genus of bacteria in the bradyrhizobiaceae family, which has the ability to remove and degrade the pollutants arsenic, antinomy, and ciprofloxacin (Lu et al, 2018; Zhang et al, 2018). The genus Variibacter was first proposed by Kim et al (2014). One of its members, V. gotjawalensis GJW-30 T , was sequenced by Lee et al (2016), who found that various genes of strain GJW-30 T encode functional enzymes for nitrate reduction, ginsenoside biosynthesis and degradation, and gibberellin biosynthesis and inactivation.…”

Section: Discussionmentioning

confidence: 99%

Endophytic Communities of Transgenic Poplar Were Determined by the Environment and Niche Rather Than by Transgenic Events

et al. 2019

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Microbial communities associated with plants represent key determinants of plant health, survival, and growth. However, a good understanding of the structural composition of the bacterial and fungal microbiome present in different plant tissues and growing environments, especially in transgenic woody plants, is required. In the present study, we hypothesized that environmental conditions, ecological niches, and transgenic events could influence the community structure of plant-associated microorganisms (bacterial and fungal endophytes). We sampled the root and stem endospheres of field-grown transgenic and non-transgenic poplar trees ( Populus alba × P. berolinensis ) and applied 16S rRNA and internal transcribed spacer amplicon Illumina MiSeq sequencing to determine the bacterial and fungal communities associated with the different plant habitats and tissues. We found that actinobacteria, proteobacteria, bacteroidetes, and firmicutes were the dominant endophytic bacteria, and the fungal community was dominated by dothideomycetes, agaricomycetes, leotiomycetes, and sordariomycetes. In conclusion, transgenic events did not affect the endophytic bacterial and fungal diversity of poplar trees. The bacterial and fungal community structure depends on the pH and the soil organic matter content. Each plant tissue represents a unique ecological niche for the microbial communities. Finally, we identified the indicator operational taxonomic units (OTUs) and core microbiome associated with the different plant tissues of Populus and different environmental conditions. The results provide a basis for further study of host-microbial interactions with the identified abundant OTUs of Populus .

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Variibacter gotjawalensis gen. nov., sp. nov., isolated from soil of a lava forest

Cited by 25 publications

References 31 publications

Microbial community structure and functional potential of lava-formed Gotjawal soils in Jeju, Korea

Microbial community structure and functional potential of lava-formed Gotjawal soils in Jeju, Korea

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

Endophytic Communities of Transgenic Poplar Were Determined by the Environment and Niche Rather Than by Transgenic Events

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