High-throughput sequencing of 16S RNA genes of soil bacterial communities from a naturally occurring CO 2 gas vent

Miera, Luis E. Sáenz de; Arroyo, Paula; Calabuig, Estanislao de Luis; Falagán, Jorge; Ansola, Gemma

doi:10.1016/j.ijggc.2014.08.014

Cited by 47 publications

(42 citation statements)

References 42 publications

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“…Many of these studies have described Ktedonobacteria as being among the most abundant types of bacteria in such environments. For example, they predominate in the cinder deposits of the Kilauea volcano (38), in lava caves (25), in high-elevation mineral soils (20), in soil from CO 2 gas vents in the Calatrava volcanic field in Spain (29), in orthoquartzite caves in Venezuela (2), in the dark oligotrophic volcanic ice caves of Mt. Erebus in Antarctica (34), in soil from northern Victoria Land in Antarctica (17), and in geothermal soils on Pantelleria Island in Italy (12).…”

Section: Discussionmentioning

confidence: 99%

“…Previous studies based on clone libraries or next-generation sequencing of the 16S rRNA gene of bacteria showed that environmental clone sequences assigned to Ktedonobacteria are prominent in extreme environments such as volcanic, Antarctic, and cave ecosystems (2, 12, 14, 17, 25, 29, 34, 38). A few studies have also investigated the detection of these clone sequences at low abundances in non-extreme environments such as sandy soils (1) and soils of the Flooding Pampa of Argentina (24).…”

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confidence: 99%

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Diversity of <i>Ktedonobacteria</i> with Actinomycetes-Like Morphology in Terrestrial Environments

Yabe

Sakai

Abe

et al. 2017

Microbes and environments

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Bacteria with an actinomycetes-like morphology have recently been discovered, and the class Ktedonobacteria was created for these bacteria in the phylum Chloroflexi. They may prove to be a valuable resource with the potential to produce unprecedented secondary metabolites. However, our understanding of their diversity, richness, habitat, and ecological significance is very limited. We herein developed a 16S rRNA gene-targeted, Ktedonobacteria-specific primer and analyzed ktedonobacterial amplicons. We investigated abundance, diversity, and community structure in forest and garden soils, sand, bark, geothermal sediment, and compost. Forest soils had the highest diversity among the samples tested (1181–2934 operational taxonomic units [OTUs]; Chao 1 estimate, 2503–5613; Shannon index, 4.21–6.42). A phylogenetic analysis of representative OTUs revealed at least eight groups within unclassified Ktedonobacterales, expanding the known diversity of this order. Ktedonobacterial communities markedly varied among our samples. The common mesic environments (soil, sand, and bark) were dominated by diverse phylotypes within the eight groups. In contrast, compost and geothermal sediment samples were dominated by known ktedonobacterial families (Thermosporotrichaceae and Thermogemmatisporaceae, respectively). The relative abundance of Ktedonobacteria in the communities, based on universal primers, was ≤0.8%, but was 12.9% in the geothermal sediment. These results suggest that unknown diverse Ktedonobacteria inhabit common environments including forests, gardens, and sand at low abundances, as well as extreme environments such as geothermal areas.

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Diversity of <i>Ktedonobacteria</i> with Actinomycetes-Like Morphology in Terrestrial Environments

Yabe

Sakai

Abe

et al. 2017

Microbes and environments

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“…Figure 3 showed that the most abundant and largest phylum was Proteobacteria with 59.42 % of the sequences on average (minimum 50.4 % in XQ1 and maximum 85.1 % in XQ5). Previous studies have shown that Proteobacteria is the prominent phylum in sediment from a drinking water reservoir (Roeske et al 2012) and intertidal zones of Bohai Bay (Wang et al 2013a), industrial wastewaters from steel industrial (Ma et al 2015), pharmaceutical, petroleum refinery and sewage (Ibarbalz et al 2013), soils of livestock-cotton production (Acosta-Martinez et al 2010), and CO 2 gas vent (Saenz de Miera et al 2014). Moreover, the abundance of Proteobacteria was higher when environmental conditions were aggravated, such as an increasing abundance of Proteobacteria in drinking water after chlorine disinfection (Huang et al 2014) and river sediment after huge nitrate injection (Chen et al 2013).…”

Section: Abundance Profiles For Phylum and Classesmentioning

confidence: 99%

Bacterial community compositions in sediment polluted by perfluoroalkyl acids (PFAAs) using Illumina high-throughput sequencing

Yu-rong

Wang

Peng

et al. 2016

Environ Sci Pollut Res

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The characterization of bacterial community compositions and the change in perfluoroalkyl acids (PFAAs) along a natural river distribution system were explored in the present study. Illumina high-throughput sequencing was used to explore bacterial community diversity and structure in sediment polluted by PFAAs from the Xiaoqing River, the area with concentrated fluorochemical facilities in China. The concentration of PFAAs was in the range of 8.44-465.60 ng/g dry weight (dw) in sediment. Perfluorooctanoic acid (PFOA) was the dominant PFAA in all samples, which accounted for 94.2 % of total PFAAs. High-level PFOA could lead to an obvious increase in relative abundance of Proteobacteria, ε-Proteobacteria, Thiobacillus, and Sulfurimonas and the decrease in relative abundance of other bacteria. Redundancy analysis revealed that PFOA played an important role in the formation of bacterial community, and PFOA at higher concentration could reduce the diversity of bacterial community. When the concentration of PFOA was below 100 ng/g dw in sediment, no significant effect on microbial community structure was observed. Thiobacillus and Sulfurimonas were positively correlated with the concentration of PFOA, suggesting that both genera were resistant to PFOA contamination.

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“…Soil microbial studies have also been carried out at the Campo de Calatrava natural CO 2 site in Spain (Sáenz de Miera et al, 2014). As CO 2 flux increases the relative abundance of Chloroflexi increased, whereas the relative abundance of Acidobacteria, Verrucomicrobia and Gemmatiomonadetes phyla decreases.…”

Section: Natural Systemsmentioning

confidence: 99%

Developments since 2005 in understanding potential environmental impacts of CO2 leakage from geological storage

Jones

Beaubien

Blackford

et al. 2015

International Journal of Greenhouse Gas Control

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This paper reviews research into the potential environmental impacts of leakage from geological storage of CO 2 since the publication of the IPCC Special Report on Carbon Dioxide Capture and Storage in 2005. Possible impacts are considered on onshore (including drinking water aquifers) and offshore ecosystems. The review does not consider direct impacts on man or other land animals from elevated atmospheric CO 2 levels. Improvements in our understanding of the potential impacts have come directly from CO 2 storage research but have also benefitted from studies of ocean acidification and other impacts on aquifers and onshore near surface ecosystems. Research has included observations at natural CO 2 sites, laboratory and field experiments and modelling. Studies to date suggest that the impacts from many lower level fault-or well-related leakage scenarios are likely to be limited spatially and temporarily and recovery may be rapid. The effects are often ameliorated by mixing and dispersion of the leakage and by buffering and other reactions; potentially harmful elements have rarely breached drinking water guidelines. Larger releases, with potentially higher impact, would be possible from open wells or major pipeline leaks but these are of lower probability and should be easier and quicker to detect and remediate.

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High-throughput sequencing of 16S RNA genes of soil bacterial communities from a naturally occurring CO 2 gas vent

Cited by 47 publications

References 42 publications

Diversity of <i>Ktedonobacteria</i> with Actinomycetes-Like Morphology in Terrestrial Environments

Diversity of <i>Ktedonobacteria</i> with Actinomycetes-Like Morphology in Terrestrial Environments

Bacterial community compositions in sediment polluted by perfluoroalkyl acids (PFAAs) using Illumina high-throughput sequencing

Developments since 2005 in understanding potential environmental impacts of CO2 leakage from geological storage

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