scholarly journals Temporal Variation of Culture Independent Bacterial Diversity Based on Amplicon Sequencing of the North Sikkim Hot Spring Solfataric Soil Sediments

2021 ◽  
Author(s):  
Sayak Das ◽  
Mingma Thundu Sherpa ◽  
Ishfaq Nabi Najar ◽  
Ankita Kumari ◽  
Nagendra Thakur
Keyword(s):  
Seasonal Variation ◽  
16S Rrna ◽  
Soil Sample ◽  
Bacterial Diversity ◽  
Hot Springs ◽  
Hot Spring ◽  
Amplicon Sequencing ◽  
The North ◽  
Culture Independent ◽  
Soil Sediments

Abstract The solfataric soil sediments of the hot springs of Sikkim located at Yume Samdung and Lachen valley were studied for deciphering the uncultured bacterial diversity. The main aim here is to present a comparative study and generate a baseline data on the post-monsoon seasonal variation for the months of October and December, analysed through 16S rRNA V3-V4 amplicon sequencing. At phylum level, in the New Yume Samdung (NYS) hot spring soil sample, in the month of October it was dominated by Proteobacteria (21.03%) followed by Thermi (12.33%) and Bacteroidetes (9.95%) whereas in December it was dominated by Proteobacteria (23.61%) followed by Chloroflexi (19.15%) and Bacteroidetes (16.55%). For Old Yume Samdung (OYS) hot spring soil sample, in the month of October, it was dominated by Proteobacteria (25.22%) followed by Bacteroidetes (11.76%) and Thermi (8.11%) whereas in December it was dominated by Proteobacteria (20.58%) followed by Chloroflexi (18.88%) and Thermi (9.89%). And in the case of Tarum (TAR) hot spring soil sediments, in the month of October, it was dominated by Proteobacteria (27.51%) followed by Bacteroidetes (12.29%) and Actinobacteria (11.1%) whereas in December it was dominated by Proteobacteria (16.76%) followed by Bacteroidetes (16.54%) and Thermi (14.17%). At genus level, in NYS, in October it was dominated by Meiothermus (12.33%) and in December it was Roseiflexus (8.59%). For OYS, it was dominated by Meiothermus (8.11%) in October and by unclassified Chloroflexales (10.94%) in December. And in TAR, it was dominated by unclassified Bacteroidales (10.29%) in October and by Meiothermus (14.12%) in December.

scholarly journals Unraveling the bacterial diversity of Cangar Hot Spring, Indonesia by Next Generation Sequencing of 16S rRNA gene

2021 ◽  
Vol 22 (9) ◽  
Author(s):  
Almando Geraldi ◽  
Chia Chay Tay ◽  
Ni’matuzahroh Ni’matuzahroh ◽  
Fatimah FATIMAH ◽  
Wan Nurhayati Wan Hanafi
Keyword(s):  
Next Generation Sequencing ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Diversity ◽  
Hot Springs ◽  
Hot Spring ◽  
Rrna Gene ◽  
Next Generation ◽  
Acinetobacter Junii ◽  
Generation Sequencing

Abstract. Geraldi A, Tay CC, Ni’matuzahroh, Fatimah, Hanafi WNW. 2021. Unraveling the bacterial diversity of Cangar Hot Spring, Indonesia by Next Generation Sequencing of 16S rRNA gene. Biodiversitas 22: 4060-4066. This study is the first attempt at using the Next Generation Sequencing (NGS) method with 16S rRNA to understand the bacterial community structure in an Indonesian hot spring. This study aims to unravel the bacterial diversity of the Cangar Hot Spring as one of the most explored natural hot springs in East Java, Indonesia. We found Proteobacteria and Bacteroidetes as the two most abundant phyla. We discovered the first occurrence of genera Cloacibacterium and Methylobacillus in the hot spring ecosystem, which was the most dominant genera at Cangar Hot Spring. We also found several potential bacteria for bioindustry and bioremediation, such as Acinetobacter junii and Pseudomonas alcaligenes. Besides that, we also observed opportunistic pathogens from genera Comamonas and Vogesella. This study result will provide valuable information for further bioprospecting of bacteria with commercial potential and the development of health and safety measures in the Cangar Hot Spring, among others. Hopefully, this report would encourage the use of NGS technology for studying other hot springs in Indonesia.

scholarly journals First Cultivation and Ecological Investigation of a Bacterium Affiliated with the Candidate Phylum OP5 from Hot Springs

2008 ◽  
Vol 74 (20) ◽  
pp. 6223-6229 ◽  
Author(s):  
Koji Mori ◽  
Michinari Sunamura ◽  
Katsunori Yanagawa ◽  
Jun-ichiro Ishibashi ◽  
Youko Miyoshi ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Hot Springs ◽  
Hot Spring ◽  
Phylogenetic Analyses ◽  
Sulfur Cycle ◽  
Field Analysis ◽  
Rrna Gene ◽  
Culture Independent ◽  
The 16S Rrna Gene

ABSTRACT The phylogenetic group termed OP5 was originally discovered in the Yellowstone National Park hot spring and proposed as an uncultured phylum; the group was afterwards analyzed by applying culture-independent approaches. Recently, a novel thermophilic chemoheterotrophic filamentous bacterium was obtained from a hot spring in Japan that was enriched through various isolation procedures. Phylogenetic analyses of the isolate have revealed that it is closely related to the OP5 phylum that has mainly been constructed with the environmental clones retrieved from thermophilic and mesophilic anaerobic environments. It appears that the lineage is independent at the phylum level in the domain Bacteria. Therefore, we designed a primer set for the 16S rRNA gene to specifically target the OP5 phylum and performed quantitative field analysis by using the real-time PCR method. Thus, the 16S rRNA gene of the OP5 phylum was detected in some hot-spring samples with the relative abundance ranging from 0.2% to 1.4% of the prokaryotic organisms detected. The physiology of the above-mentioned isolate and the related environmental clones indicated that they are scavengers contributing to the sulfur cycle in nature.

Diversity and composition of the North Sikkim hot spring mycobiome using a culture-independent method

2021 ◽  
Author(s):  
Sayak Das ◽  
Goshaidas Roy ◽  
Ishfaq Nabi Najar ◽  
Mingma Thundu Sherpa ◽  
Nagendra Thakur
Keyword(s):  
Hot Spring ◽  
Independent Method ◽  
The North ◽  
Culture Independent

scholarly journals Microbial Diversity of Terrestrial Geothermal Springs in Armenia and Nagorno-Karabakh: A Review

2021 ◽  
Vol 9 (7) ◽  
pp. 1473
Author(s):  
Ani Saghatelyan ◽  
Armine Margaryan ◽  
Hovik Panosyan ◽  
Nils-Kåre Birkeland
Keyword(s):  
16S Rrna ◽  
Microbial Diversity ◽  
High Altitude ◽  
Hot Springs ◽  
Hot Spring ◽  
Abiotic Factors ◽  
Rrna Gene ◽  
Geothermal Springs ◽  
Bacterial Phyla ◽  
Terrestrial Hot Springs

The microbial diversity of high-altitude geothermal springs has been recently assessed to explore their biotechnological potential. However, little is known regarding the microbiota of similar ecosystems located on the Armenian Highland. This review summarizes the known information on the microbiota of nine high-altitude mineralized geothermal springs (temperature range 25.8–70 °C and pH range 6.0–7.5) in Armenia and Nagorno-Karabakh. All these geothermal springs are at altitudes ranging from 960–2090 m above sea level and are located on the Alpide (Alpine–Himalayan) orogenic belt, a seismically active region. A mixed-cation mixed-anion composition, with total mineralization of 0.5 mg/L, has been identified for these thermal springs. The taxonomic diversity of hot spring microbiomes has been examined using culture-independent approaches, including denaturing gradient gel electrophoresis (DGGE), 16S rRNA gene library construction, 454 pyrosequencing, and Illumina HiSeq. The bacterial phyla Proteobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes are the predominant life forms in the studied springs. Archaea mainly include the phyla Euryarchaeota, Crenarchaeota, and Thaumarchaeota, and comprise less than 1% of the prokaryotic community. Comparison of microbial diversity in springs from Karvachar with that described for other terrestrial hot springs revealed that Proteobacteria, Bacteroidetes, Actinobacteria, and Deinococcus–Thermus are the common bacterial groups in terrestrial hot springs. Contemporaneously, specific bacterial and archaeal taxa were observed in different springs. Evaluation of the carbon, sulfur, and nitrogen metabolism in these hot spring communities has revealed diversity in terms of metabolic activity. Temperature seems to be an important factor in shaping the microbial communities of these springs. Overall, the diversity and richness of the microbiota are negatively affected by increasing temperature. Other abiotic factors, including pH, mineralization, and geological history, also impact the structure and function of the microbial community. More than 130 bacterial and archaeal strains (Bacillus, Geobacillus, Parageobacillus, Anoxybacillus, Paenibacillus, Brevibacillus Aeribacillus, Ureibacillus, Thermoactinomyces, Sporosarcina, Thermus, Rhodobacter, Thiospirillum, Thiocapsa, Rhodopseudomonas, Methylocaldum, Desulfomicrobium, Desulfovibrio, Treponema, Arcobacter, Nitropspira, and Methanoculleus) have been reported, some of which may be representative of novel species (sharing 91–97% sequence identity with their closest matches in GenBank) and producers of thermozymes and biomolecules with potential biotechnological applications. Whole-genome shotgun sequencing of T. scotoductus K1, as well as of the potentially new Treponema sp. J25 and Anoxybacillus sp. K1, were performed. Most of the phyla identified by 16S rRNA were also identified using metagenomic approaches. Detailed characterization of thermophilic isolates indicate the potential of the studied springs as a source of biotechnologically valuable microbes and biomolecules.

scholarly journals Diversity analysis and metagenomic insights into the Antibiotic Resistance and Metal Resistances among Hot Spring Bacteriobiome-insinuating inherent environmental baseline levels of Antibiotic and Metal tolerance

2019 ◽  
Author(s):  
Ishfaq Nabi Najar ◽  
Mingma Thundu Sherpa ◽  
Sayak Das ◽  
Nagendra Thakur
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Hot Springs ◽  
Metal Tolerance ◽  
Hot Spring ◽  
Thermophilic Bacteria ◽  
Antibiotic Resistance Genes ◽  
Metal Resistance ◽  
Culture Independent ◽  
Maximum Similarity

AbstractMechanisms of occurrence and expressions of antibiotic resistance genes (ARGs) in thermophilic bacteria are still unknown owing to limited research and data. The evolution and proliferation of ARGs in the thermophilic bacteria is unclear and needs a comprehensive study. In this research, comparative profiling of antibiotic resistance genes and metal tolerance genes among the thermophilic bacteria has been done by culture-independent functional metagenomic methods. Metagenomic analysis showed the dominance of Proteobacteria, Actinobacteria. Firmicutes and Bacteroidetes in these hot springs. ARG analysis through shotgun gene sequencing was found to be negative in case of thermophilic bacteria. However, few of genes were detected but they were showing maximum similarity with mesophilic bacteria. Concurrently, metal resistance genes were also detected in the metagenome sequence of hot springs. Detection of metal resistance gene and absence of ARG’s investigated by whole genome sequencing, in the reference genome sequence of thermophilic Geobacillus also conveyed the same message. This evolutionary selection of metal resistance over antibiotic genes may have been necessary to survive in the geological craters which are full of different metals from earth sediments rather than antibiotics. Furthermore, the selection could be environment driven depending on the susceptibility of ARG’s in thermophilic environment as it reduces the chances of horizontal gene transfer. With these findings this article highlights many theories and culminates different scopes to study these aspects in thermophiles.

Taxonomic fidelity of silicified filamentous microbes from hot-spring systems in the Taupo Volcanic Zone, North Island, New Zealand

2003 ◽  
Vol 94 (4) ◽  
pp. 475-483 ◽  
Author(s):  
Brian Jones ◽  
Robin W. Renaut ◽  
Michael R. Rosen
Keyword(s):  
New Zealand ◽  
Hot Springs ◽  
Hot Spring ◽  
Morphological Characteristics ◽  
Colony Morphology ◽  
Taupo Volcanic Zone ◽  
Volcanic Zone ◽  
The North ◽  
Preservation Potential ◽  
Physical Changes

ABSTRACTModern, silica-precipitating hot springs, like those found in the Taupo Volcanic Zone (TVZ) on the North Island of New Zealand, are natural laboratories for assessing microbial silicification. Many of the silicified microbes found in the siliceous sinters of these spring systems seem to be life-like replicas of the original microbes. Such preservation reflects the fact that many of the microbes are replaced and encrusted by opal-A before they are destroyed by desiccation and decay. The taxonomic fidelity of these silicified microbes depends on the preservation potential of those features which are needed to identify them. For example, identification of extant cyanobacteria, relies on as many as 37 different features, most of which are not preserved by silicification.In the hot-spring systems of the TVZ, characterisation of cyanobacteria which have been replaced and encrusted by opal-A is typically restricted to colony morphology, the length, diameter and morphology of the filament, and the presence/absence of septa, branching or a sheath. In many cases, description is limited to a subset of these parameters. Such a limited set of morphological characteristics severely impedes identifications in terms of extant taxa. The physical changes which accompany the stepwise diagenetic progression from opal-A to opal-CT ± opal-C to microcrystalline quartz may lead to further degradation of the silicified microbes and the loss of more taxonomically important features. Clearly, considerable care must be taken when trying to name silicified microorganisms and make palaeoenvironmental inferences.

scholarly journals Sasso Pisano Geothermal Field Environment Harbours Diverse Ktedonobacteria Representatives and Illustrates Habitat-Specific Adaptations

2021 ◽  
Vol 9 (7) ◽  
pp. 1402
Author(s):  
Sania Arif ◽  
Corinna Willenberg ◽  
Annika Dreyer ◽  
Heiko Nacke ◽  
Michael Hoppert
Keyword(s):  
Hot Springs ◽  
Hot Spring ◽  
Amplicon Sequencing ◽  
Heavy Metal Resistance ◽  
18S Rrna Gene ◽  
Metal Resistance ◽  
Geothermal Field ◽  
Rrna Gene ◽  
Metabolic Potential ◽  
Eukaryotic Diversity

The hydrothermal steam environment of Sasso Pisano (Italy) was selected to investigate the associated microbial community and its metabolic potential. In this context, 16S and 18S rRNA gene partial sequences of thermophilic prokaryotes and eukaryotes inhabiting hot springs and fumaroles as well as mesophilic microbes colonising soil and water were analysed by high-throughput amplicon sequencing. The eukaryotic and prokaryotic communities from hot environments clearly differ from reference microbial communities of colder soil sites, though Ktedonobacteria showed high abundances in various hot spring samples and a few soil samples. This indicates that the hydrothermal steam environments of Sasso Pisano represent not only a vast reservoir of thermophilic but also mesophilic members of this Chloroflexi class. Metabolic functional profiling revealed that the hot spring microbiome exhibits a higher capability to utilise methane and aromatic compounds and is more diverse in its sulphur and nitrogen metabolism than the mesophilic soil microbial consortium. In addition, heavy metal resistance-conferring genes were significantly more abundant in the hot spring microbiome. The eukaryotic diversity at a fumarole indicated high abundances of primary producers (unicellular red algae: Cyanidiales), consumers (Arthropoda: Collembola sp.), and endoparasite Apicomplexa (Gregarina sp.), which helps to hypothesise a simplified food web at this hot and extremely nutrient-deprived acidic environment.

scholarly journals Distribution of Acetothermia-dominated microbial communities in alkaline hot springs of Baikal Rift Zone.

2017 ◽  
Author(s):  
Svetlana V. Zaitseva ◽  
Elena V. Lavrentieva ◽  
Aryuna A. Radnagurueva ◽  
Olga A. Baturina ◽  
Marsel R. Kabilov ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Hot Springs ◽  
Rift Zone ◽  
Hot Spring ◽  
Baikal Rift Zone ◽  
Rrna Gene ◽  
Acetyl Coa Pathway

Alkaline hot springs are unique extreme habitats resemble the early Earth and present a valuable resource for the discovery of procaryotic community diversity and isolation of the novel thermophilic Bacteria and Archaea. One of the model for the possible origin of biochemistry in alkaline hot springs revealed the acetyl-CoA pathway of CO2 fixation might be the most ancient form of carbon metabolism. Recent phylogenetic studies have suggested that the phylum Acetothermia is one of the deep branches of the Bacteria domain. Firstly Acetothermia (Candidate division OP1) was characterized in a culture independent molecular phylogenetic survey based on the 16S rRNA gene of the sulfide-rich hot spring, Obsidian Pool, a 75 to 95oC hot spring. Two nearly complete genomes of Acetothermia were established based on genome-resolved metagenomic analysis and its capability of implementing acetogenesis through the ancient reductive acetyl-CoA pathway by utilizing CO2 and H2 was revealed. Although genomic, proteomic and metagenomic approaches investigate basic metabolism and potentional energy conservation of uncultivated candidate phyla but ecological roles of these bacteria and general patterns of diversity and community structure stay unclear. General hydrochemical and geological characterization of alkaline thermal springs of the Baikal Rift zone with high silica concentrations and a nitrogen dominated gas phase is provided. Previous microbiogical studies based on culture-dependent methods recovered a large number of bacterial strains from thermal springs located in Baikal Rift zone. We combined microbial communities analysis by using high-throughput 16S rRNA gene sequencing, biogeochemical measurements, sediment mineralogy and physicochemical characteristics to investigate ecosystems of alkaline hot springs located in the Baikal Rift zone. Uncultivated bacteria belonging to the phylum Acetothermia, along with members of the phyla Firmicutes and Proteobacteria, were identified as the dominant group in hydrothermal sediments communities in the alkaline hot springs of Baikal Rift zone. In bottom sediments of the Alla hot spring, about 57% of all classified sequences represent this phylum. Geochemistry of fluids and sample type were strongly correlated with microbial community composition. The Acetothermia exhibited the highest relative abundance in sediment microbial community associated with alkaline thermal fluids enriched in Fe, Zn, Ni, Al and Cr.

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