Metagenomic analysis of bacterial and archaeal assemblages in the soil-mousse surrounding a geothermal spring

Bhatia, Sonu; Pathak, Ashish; Joshi, Amit; Souza, Leila Cristiane Virgens de; Almeida, Paulo Fernando de; Chauhan, Ashvini

doi:10.1016/j.gdata.2015.05.016

Cited by 9 publications

(3 citation statements)

References 6 publications

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“…() who reported a maximum of 30.7% unassigned sequences in their study and Bhatia et al. () who reported 31% unclassified sequences. To a large extent, occurrence of unclassified sequences have been attributed to lack of reference sequences or use of a strict Lowest Common Ancestor (LCA)‐taxonomic assignment algorithm (Badhai et al., ).…”

Section: Resultsmentioning

confidence: 70%

Thermophilic bacterial communities inhabiting the microbial mats of “indifferent” and chalybeate (iron‐rich) thermal springs: Diversity and biotechnological analysis

2017

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Microbial mats are occasionally reported in thermal springs and information on such mats is very scarce. In this study, microbial mats were collected from two hot springs (Brandvlei (BV) and Calitzdorp (CA)), South Africa and subjected to scanning electron microscopy (SEM) and targeted 16S rRNA gene amplicon analysis using Next Generation Sequencing (NGS). Spring water temperature was 55°C for Brandvlei and 58°C for Calitzdorp while the pH of both springs was slightly acidic, with an almost identical pH range (6.2–6.3). NGS analysis resulted in a total of 4943 reads, 517 and 736 OTUs for BV and CA at, respectively, a combined total of 14 different phyla in both samples, 88 genera in CA compared to 45 in BV and 37.64% unclassified sequences in CA compared to 27.32% recorded in BV. Dominant bacterial genera in CA microbial mat were Proteobacteria (29.19%), Bacteroidetes (9.41%), Firmicutes (9.01%), Cyanobacteria (6.89%), Actinobacteria (2.65%), Deinococcus‐Thermus (2.57%), and Planctomycetes (1.94%) while the BV microbial mat was dominated by Bacteroidetes (47.3%), Deinococcus‐Thermus (12.35%), Proteobacteria (7.98%), and Planctomycetes (2.97%). Scanning electron microscopy results showed the presence of microbial filaments possibly resembling cyanobacteria, coccids, rod‐shaped bacteria and diatoms in both microbial mats. Dominant genera that were detected in this study have been linked to different biotechnological applications including hydrocarbon degradation, glycerol fermentation, anoxic‐fermentation, dehalogenation, and biomining processes. Overall, the results of this study exhibited thermophilic bacterial community structures with high diversity in microbial mats, which have a potential for biotechnological exploitation.

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Section: Resultsmentioning

confidence: 70%

Thermophilic bacterial communities inhabiting the microbial mats of “indifferent” and chalybeate (iron‐rich) thermal springs: Diversity and biotechnological analysis

2017

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“…Additionally, Euryarchaeota and Crenarchaeota are the dominant archaeal groups in the rock and soil samples, which commonly inhabit geothermal environments [41]. In contrast, plant samples showed the abundance of Planctomycetes which is a rhizosphereassociated microbial phylum and was isolated from geothermal springs in previous studies [42,43]. These findings underscore the important role of fumaroles in shaping the adjacent ecosystem dynamics, enabling diverse microbes at the phylum level to be better adaptive in response to fumarolic influences.…”

Section: Discussionmentioning

confidence: 93%

Influence of Geothermal Fumaroles in Driving the Microbial Community Dynamics and Functions of Adjacent Ecosystems

Asif,

Chen,

Hsu

et al. 2024

J Basic Microbiol

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Growing evidence suggests that the hydrochemical properties of geothermal fumaroles may play a crucial role in shaping the diversity and functions of microbial communities in various environments. In the present study, the impact of geothermal furaneols on the microbial communities and their metabolic functions across the rock‐soil‐plant continuum was explored considering varying distances from the fumarole source. The results revealed that bacterial phylum Proteobacteria was predominant in all sample types, except in the 10 m rock sample, irrespective of the sampling distance. Archaeal phyla, such as Euryarchaeota and Crenarchaeota, were more prevalent in rock and soil samples, whereas bacterial phyla were more prevalent in plant samples. Thermoacidophilic archaeons, including Picrophilus, Ferroplasma, and Thermogymnomonas were dominant in rocks and soil samples of 1 and 5 m distances; acidophilic mesophiles, including Ferrimicrobium and Granulicella were abundant in the rhizoplane samples, whereas rhizosphere‐associated microbes including Pseudomonas, Pedobacter, Rhizobium, and Novosphingobium were found dominant in the rhizosphere samples. The functional analysis highlighted the higher expression of sulfur oxidative pathways in the rock and soil samples; dark iron oxidation and nitrate/nitrogen respiratory functions in the rhizosphere samples. The findings underscore microbial adaptations across the rock‐soil‐plant continuum, emphasizing the intricate relationship between geothermal fumaroles and microbial communities in adjacent ecosystems. These insights offer a crucial understanding of the evolution of microbial life and highlight their pivotal roles in shaping ecosystem dynamics and functions.

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“…16S rRNA analysis was carried out using the 16S rRNA pipeline from the EPI2ME database (Quick et al, 2015;. The raw reads were also processed in parallel using the microbial genomics module of CLC Genomics workbench version 11.0 (CLC Bio, Qiagen, Boston, MA, USA) for OTU table generation and further downstream statistical analysis (Bhatia et al, 2015;Suzuki et al, 2017). The Alpha diversity parameters of the four contrasting climatic zones like Shannon-Weiner diversity index (H'), Simpson's diversity index (D), Species richness (Margalef) and Species evenness (Pielou) were calculated using the data analysis package of MS-excel software.…”

Section: Read Processing and Data Analysismentioning

confidence: 99%

Insights into the diversity of grassland soil bacterial communities associated with four contrasting Köppen climatic zones of India

Nair, G. R.,

Raja, S. S. S.

2024

MJM

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Aims: This study investigates the community structure and diversity of terrestrial soil bacterial communities thriving in four contrasting Köppen climatic zones of India using high-throughput sequencing. Methodology and results: Soil samples were collected for metagenomic DNA isolation and PCR amplification using primers targeting the 16S rRNA gene region. Amplicons were subjected to Oxford nanopore sequencing and data analysis. Bacterial species diversity, evenness and richness were highest in a humid sub-tropical climatic zone (HSCZ). Firmicutes were the most abundant phylum in the tropical wet climatic zone (TWCZ), arid climatic zone (ACZ) and humid sub-tropical climatic zone (HSCZ), while Proteobacteria in the mountain climatic zone (MCZ). The predominance of class Alphaproteobacteria, Actinobacteria with genera Bradyrhizobium, Chthoniobacter and Mycobacterium, was observed in MCZ in contrast to class Bacilli with genera Bacillus and Paenibacillus in the rest of the zones. OTU abundance was positively correlated with moisture, TOC (total organic carbon), K, MAP (mean annual precipitation) and negatively correlated with pH, Ca, N, B, Fe, P, Mg and MAT (mean annual temperature). A significant correlation was only observed with Fe against Shannon diversity (H') in multiple regression analysis. Conclusion, significance and impact of study:The multidirectional relationship between soil, its microbiota and climate is crucial in modulating bacterial community diversity and its survival in terrestrial ecosystems that significantly contribute to ecosystem function. This work mapped the occurrence and distribution of terrestrial soil bacterial communities in contrasting climatic zones for the first time, enabling us to assess the effect of climate in the mentioned Köppen climatic zones.

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Metagenomic analysis of bacterial and archaeal assemblages in the soil-mousse surrounding a geothermal spring

Cited by 9 publications

References 6 publications

Thermophilic bacterial communities inhabiting the microbial mats of “indifferent” and chalybeate (iron‐rich) thermal springs: Diversity and biotechnological analysis

Thermophilic bacterial communities inhabiting the microbial mats of “indifferent” and chalybeate (iron‐rich) thermal springs: Diversity and biotechnological analysis

Influence of Geothermal Fumaroles in Driving the Microbial Community Dynamics and Functions of Adjacent Ecosystems

Insights into the diversity of grassland soil bacterial communities associated with four contrasting Köppen climatic zones of India

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