Phylogenetic analysis on the soil bacteria distributed in karst forest

Zhou, Junpei; Huang, Ying; Mo, Ming-He

doi:10.1590/s1517-83822009000400013

Cited by 16 publications

(10 citation statements)

References 8 publications

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“…Previous studies have documented how the dissolution of calcite can be enhanced in the presence of heterotrophic microorganisms (Jacobson and Wu, 2009). Our data revealed that the composition of Acidobacteria increased in the habitat of soil, which is consistent with that of a previous study (Zhou et al, 2009). We propose that light penetration plays a pivotal role in natural selection to promote the growth of weathering-associated bacteria, which in turn increase the nutrient level in situ and favor the development of microorganisms.…”

Section: Discussionsupporting

confidence: 92%

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Role of Microbial Communities in the Weathering and Stalactite Formation in Karst Topography

Huang

Hsu

Fan

et al. 2019

Preprint

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<p><strong>Abstract.</strong> This study investigated the long-term effect of environmental physical factors on the relative abundance of bacteria and the consequential landscape evolution in karst topography, focusing mainly on the effects of limestone weathering and calcite precipitation. The Narrow-Sky located in the upper part of Takangshan is a small gulch of Pleistocene coralline limestone formation in southern Taiwan. The landscapes were different in the karst walls between the opening and the inner of gulch due to the variation of physical parameters such as sunlight penetration, humidity, and temperature. A metagenomic approach was used out to determine the relationship of microbial community structures on the landscapes in various habitats around the gulch, namely on the inner and outer limestone wall, the water collected from speleothems surface, and the ground soil at the outer wall. The total organic carbon content was measured in solid samples to evaluate the biomass of the habitats. Our results showed that the biomass of habitats in the opening of the gulch was two times higher than the that inside where light penetration was lower. We also found that speleothems only occurred at the inner wall inside the gulch, where the environment exhibited water drips running through the surface of speleothems and less light penetration. The metagenomics in each habitat was surveyed to measure the sequence similarity of operational taxonomic units relative to urease-producing bacteria and weathering-associated bacteria available in the National Center for Biotechnology Information database. Our data revealed that the metagenomics of the inner wall and water samples exhibited more sequences that were similar to those of urease-producing bacteria, whereas the outer wall showed more sequences that were similar to those of weathering-associated bacteria, suggesting that bacteria facilitated the formation of limestone weathering and calcite precipitation for various habitats. This study revealed the pivotal roles of microorganisms in governing the geological evolution of the limestone landscape.</p>

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Section: Discussionsupporting

confidence: 92%

“…The bacterial communities from different geological areas exhibited regional difference. For example, the majority of bacterial phyla in karst soil in Guizhou China were Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes (Zhou et al, 2009).…”

Section: Discussionmentioning

confidence: 99%

Role of Microbial Communities in the Weathering and Stalactite Formation in Karst Topography

Huang

Hsu

Fan

et al. 2019

Preprint

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“…In the soils of karst forests, Proteobacteria, Acidobacteria, and Actinobacteria were described as dominant members of bacterial communities [3,5,7]. Proteobacteria and Actinobacteria were the most abundant phyla by both methods in this study as well.…”

Section: Discussionsupporting

confidence: 55%

“…Studying the soil quality changes in the karst area of southwest China, Zhang et al [2] found that microbial and biological parameters were more sensitive to land degradation or vegetation declining than nutrient pools. Zhou et al [3] reported on the soil bacterial diversity of a karst forest in China, and presented the first molecular microbiological data in such environment. In another study [4], the interactions among vegetation type, soil physical and chemical conditions, and soil microbial communities in a subtropical karst region were investigated.…”

Section: Introductionmentioning

confidence: 99%

Bacterial diversity in soils of different Hungarian karst areas

Knáb

Szili‐Kovács

Màrialigeti

et al. 2018

AMicr

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Karst areas have great environmental importance as sources of subsurface water and often maintain very sensitive ecosystems. In recent years, increasing number of microbiological studies focused on the bacterial communities of karst soils. In this study, diversity examinations on two distinct Hungarian karst areas, Aggtelek and Tapolca, were performed using parallel cultivation and molecular cloning methods. The phylogenetic affiliation of bacterial strains and molecular clones was determined based on their 16S rRNA gene sequences. Bacterial isolates were identified as members of the phyla Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. Besides the taxa identified by cultivation, members of the phyla Chloroflexi, Cyanobacteria, Acidobacteria, Verrucomicrobia, and Gemmatimonadetes were detected by the cloning. The difference in the composition of soil bacterial communities was related to geographic locations and soil types. Both the highest and the lowest bacterial diversities were detected in samples from Aggtelek National Park, characterized by Leptic Luvisol and Rendzic Leptosol soil types. The difference in the composition of bacterial communities between Rendzic Leptosol and Leptic Phaeozem soil types at Tapolca could be the result of human impacts.

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“…It is estimated that a metagenomic DNA sample obtained from an undisturbed soil could contain between 6,000 and 10,000 different microbial genomes (Torsvik and Øvreås 2002). Studies that involve analysis of the 16S rDNA have revealed that the most representative phyla in forest soils are Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes, Planctomycetes, Verrumicrobia and Bacteroidetes (Zhou et al 2009;DeAngelis et al 2010). However, the cloning and analysis of 16S rDNA has its limitations associated with PCR bias, instability of recombinant plasmids and the different number of copies of the gene per cell of each taxon.…”

Section: Introductionmentioning

confidence: 99%

Taxonomic and functional assignment of cloned sequences from high Andean forest soil metagenome

Montaña

Jiménez

Hernández

et al. 2011

Antonie van Leeuwenhoek

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Total metagenomic DNA was isolated from high Andean forest soil and subjected to taxonomical and functional composition analyses by means of clone library generation and sequencing. The obtained yield of 1.7 μg of DNA/g of soil was used to construct a metagenomic library of approximately 20,000 clones (in the plasmid p-Bluescript II SK+) with an average insert size of 4 Kb, covering 80 Mb of the total metagenomic DNA. Metagenomic sequences near the plasmid cloning site were sequenced and them trimmed and assembled, obtaining 299 reads and 31 contigs (0.3 Mb). Taxonomic assignment of total sequences was performed by BLASTX, resulting in 68.8, 44.8 and 24.5% classification into taxonomic groups using the metagenomic RAST server v2.0, WebCARMA v1.0 online system and MetaGenome Analyzer v3.8 software, respectively. Most clone sequences were classified as Bacteria belonging to phlya Actinobacteria, Proteobacteria and Acidobacteria. Among the most represented orders were Actinomycetales (34% average), Rhizobiales, Burkholderiales and Myxococcales and with a greater number of sequences in the genus Mycobacterium (7% average), Frankia, Streptomyces and Bradyrhizobium. The vast majority of sequences were associated with the metabolism of carbohydrates, proteins, lipids and catalytic functions, such as phosphatases, glycosyltransferases, dehydrogenases, methyltransferases, dehydratases and epoxide hydrolases. In this study we compared different methods of taxonomic and functional assignment of metagenomic clone sequences to evaluate microbial diversity in an unexplored soil ecosystem, searching for putative enzymes of biotechnological interest and generating important information for further functional screening of clone libraries.

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Phylogenetic analysis on the soil bacteria distributed in karst forest

Cited by 16 publications

References 8 publications

Role of Microbial Communities in the Weathering and Stalactite Formation in Karst Topography

Role of Microbial Communities in the Weathering and Stalactite Formation in Karst Topography

Bacterial diversity in soils of different Hungarian karst areas

Taxonomic and functional assignment of cloned sequences from high Andean forest soil metagenome

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