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 Sulfurihydrogenibium azorense, sp. nov., a thermophilic hydrogen-oxidizing microaerophile from terrestrial hot springs in the Azores

2004 ◽  
Vol 54 (1) ◽  
pp. 33-39 ◽  
Author(s):  
P. Aguiar ◽  
T. J. Beveridge ◽  
A.-L. Reysenbach
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Elemental Sulfur ◽  
Hot Springs ◽  
Rrna Gene ◽  
Temperature Growth ◽  
Likelihood Analysis ◽  
Distinct Lineage ◽  
Terrestrial Hot Springs ◽  
Rrna Phylogeny

Five hydrogen-oxidizing, thermophilic, strictly chemolithoautotrophic, microaerophilic strains, with similar (99–100 %) 16S rRNA gene sequences were isolated from terrestrial hot springs at Furnas, São Miguel Island, Azores, Portugal. The strain, designated Az-Fu1T, was characterized. The motile, 0·9–2·0 μm rods were Gram-negative and non-sporulating. The temperature growth range was from 50 to 73 °C (optimum at 68 °C). The strains grew fastest in 0·1 % (w/v) NaCl and at pH 6, although growth was observed from pH 5·5 to 7·0. Az-Fu1T can use elemental sulfur, sulfite, thiosulfate, ferrous iron or hydrogen as electron donors, and oxygen (0·2–9·0 %, v/v) as electron acceptor. Az-Fu1T is also able to grow anaerobically, with elemental sulfur, arsenate and ferric iron as electron acceptors. The Az-Fu1T G+C content was 33·6 mol%. Maximum-likelihood analysis of the 16S rRNA phylogeny placed the isolate in a distinct lineage within the Aquificales, closely related to Sulfurihydrogenibium subterraneum (2·0 % distant). The 16S rRNA gene of Az-Fu1T is 7·7 % different from that of Persephonella marina and 6·8 % different from Hydrogenothermus marinus. Based on the phenotypic and phylogenetic characteristics presented here, it is proposed that Az-Fu1T belongs to the recently described genus Sulfurihydrogenibium. It is further proposed that Az-Fu1T represents a new species, Sulfurihydrogenibium azorense.

scholarly journals Advantage of Using Inosine at the 3′ Termini of 16S rRNA Gene Universal Primers for the Study of Microbial Diversity

2006 ◽  
Vol 72 (11) ◽  
pp. 6902-6906 ◽  
Author(s):  
Eitan Ben-Dov ◽  
Orr H. Shapiro ◽  
Nachshon Siboni ◽  
Ariel Kushmaro
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Environmental Samples ◽  
Annealing Temperature ◽  
Universal Primers ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Primer Sets

ABSTRACT To overcome the shortcomings of universal 16S rRNA gene primers 8F and 907R when studying the diversity of complex microbial communities, the 3′ termini of both primers were replaced with inosine. A comparison of the clone libraries derived using both primer sets showed seven bacterial phyla amplified by the altered primer set (8F-I/907R-I) whereas the original set amplified sequences belonging almost exclusively to Proteobacteria (95.8%). Sequences belonging to Firmicutes (42.6%) and Thermotogae (9.3%) were more abundant in a library obtained by using 8F-I/907R-I at a PCR annealing temperature of 54°C, while Proteobacteria sequences were more frequent (62.7%) in a library obtained at 50°C, somewhat resembling the result obtained using the original primer set. The increased diversity revealed by using primers 8F-I/907R-I confirms the usefulness of primers with inosine at the 3′ termini in studying the microbial diversity of environmental samples.

scholarly journals A Comprehensive Census of Microbial Diversity in Hot Springs of Tengchong, Yunnan Province China Using 16S rRNA Gene Pyrosequencing

PLoS ONE ◽  
2013 ◽  
Vol 8 (1) ◽  
pp. e53350 ◽  
Author(s):  
Weiguo Hou ◽  
Shang Wang ◽  
Hailiang Dong ◽  
Hongchen Jiang ◽  
Brandon R. Briggs ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Diversity ◽  
Yunnan Province ◽  
Hot Springs ◽  
Rrna Gene ◽  
16S Rrna Gene Pyrosequencing

scholarly journals Fervidicoccus fontis gen. nov., sp. nov., an anaerobic, thermophilic crenarchaeote from terrestrial hot springs, and proposal of Fervidicoccaceae fam. nov. and Fervidicoccales ord. nov.

2010 ◽  
Vol 60 (9) ◽  
pp. 2082-2088 ◽  
Author(s):  
Anna A. Perevalova ◽  
Salima Kh. Bidzhieva ◽  
Ilya V. Kublanov ◽  
Kai-Uwe Hinrichs ◽  
Xiaolei L. Liu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Hot Springs ◽  
Lipid Fraction ◽  
Kamchatka Peninsula ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Phenotypic Properties ◽  
Terrestrial Hot Springs

Two novel thermophilic and slightly acidophilic strains, Kam940T and Kam1507b, which shared 99 % 16S rRNA gene sequence identity, were isolated from terrestrial hot springs of the Uzon caldera on the Kamchatka peninsula. Cells of both strains were non-motile, regular cocci. Growth was observed between 55 and 85 °C, with an optimum at 65–70 °C (doubling time, 6.1 h), and at pH 4.5–7.5, with optimum growth at pH 5.5–6.0. The isolates were strictly anaerobic organotrophs and grew on a narrow spectrum of energy-rich substrates, such as beef extract, gelatin, peptone, pyruvate, sucrose and yeast extract, with yields above 107 cells ml−1. Sulfate, sulfite, thiosulfate and nitrate added as potential electron acceptors did not stimulate growth when tested with peptone. H2 at 100 % in the gas phase inhibited growth on peptone. Glycerol dibiphytanyl glycerol tetraethers (GDGTs) with zero to four cyclopentyl rings were present in the lipid fraction of isolate Kam940T. The G+C content of the genomic DNA of strain Kam940T was 37 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolates were archaea of the phylum Crenarchaeota, only distantly related to the cultured members of the class Thermoprotei (no more than 89 % identity), and formed an independent lineage adjacent to the orders Desulfurococcales and Acidilobales and clustering only with uncultured clones from hot springs of Yellowstone National Park and Iceland as the closest relatives. On the basis of their phylogenetic position and novel phenotypic features, isolates Kam940T and Kam1507b are proposed to be assigned to a new genus and species, Fervidicoccus fontis gen. nov., sp. nov. The type strain of Fervidicoccus fontis is strain Kam940T (=DSM 19380T =VKM B-2539T). The phylogenetic data as well as phenotypic properties suggest that the novel crenarchaeotes form the basis of a new family, Fervidicoccaceae fam. nov., and order, Fervidicoccales ord. nov., within the class Thermoprotei.

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.

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 Thermotoga profunda sp. nov. and Thermotoga caldifontis sp. nov., anaerobic thermophilic bacteria isolated from terrestrial hot springs

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 2128-2136 ◽  
Author(s):  
Koji Mori ◽  
Atsushi Yamazoe ◽  
Akira Hosoyama ◽  
Shoko Ohji ◽  
Nobuyuki Fujita ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Ribosomal Proteins ◽  
Type Strain ◽  
Type Species ◽  
Hot Springs ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Terrestrial Hot Springs

Two thermophilic, strictly anaerobic, Gram-negative bacteria, designated strains AZM34c06T and AZM44c09T, were isolated from terrestrial hot springs in Japan. The optimum growth conditions for strain AZM34c06T were 60 °C, pH 7.4 and 0 % additional NaCl, and those for strain AZM44c09T were 70 °C, pH 7.4 and 0 % additional NaCl. Complete genome sequencing was performed for both strains, revealing genome sizes of 2.19 Mbp (AZM34c06T) and 2.01 Mbp (AZM44c09T). Phylogenetic analyses based on 16S rRNA gene sequences and the concatenated predicted amino acid sequences of 33 ribosomal proteins showed that both strains belonged to the genus Thermotoga . The closest relatives of strains AZM34c06T and AZM44c09T were the type strains of Thermotoga lettingae (96.0 % similarity based on the 16S rRNA gene and 84.1 % similarity based on ribosomal proteins) and Thermotoga hypogea (98.6 and 92.7 % similarity), respectively. Using blast, the average nucleotide identity was 70.4–70.5 % when comparing strain AZM34c06T and T. lettingae TMOT and 76.6 % when comparing strain AZM44c09T and T. hypogea NBRC 106472T. Both values are far below the 95 % threshold value for species delineation. In view of these data, we propose the inclusion of the two isolates in the genus Thermotoga within two novel species, Thermotoga profunda sp. nov. (type strain AZM34c06T = NBRC 106115T = DSM 23275T) and Thermotoga caldifontis sp. nov. (type strain AZM44c09T = NBRC 106116T = DSM 23272T).

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.

scholarly journals Molecular Microbial Diversity Survey of Sponge Reproductive Stages and Mechanistic Insights into Vertical Transmission of Microbial Symbionts

2008 ◽  
Vol 74 (24) ◽  
pp. 7694-7708 ◽  
Author(s):  
Susanne Schmitt ◽  
Hilde Angermeier ◽  
Roswitha Schiller ◽  
Niels Lindquist ◽  
Ute Hentschel
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Diversity ◽  
Vertical Transmission ◽  
Microbial Consortia ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Bacterial Phyla ◽  
Symbiont Transmission

ABSTRACT Many marine sponges, hereafter termed high-microbial-abundance (HMA) sponges, harbor large and complex microbial consortia, including bacteria and archaea, within their mesohyl matrices. To investigate vertical microbial transmission as a strategy to maintain these complex associations, an extensive phylogenetic analysis was carried out with the 16S rRNA gene sequences of reproductive (n = 136) and adult (n = 88) material from five different Caribbean species, as well as all published 16S rRNA gene sequences from sponge offspring (n = 116). The overall microbial diversity, including members of at least 13 bacterial phyla and one archaeal phylum, in sponge reproductive stages is high. In total, 28 vertical-transmission clusters, defined as clusters of phylotypes that are found both in adult sponges and their offspring, were identified. They are distributed among at least 10 bacterial phyla and one archaeal phylum, demonstrating that the complex adult microbial community is collectively transmitted through reproductive stages. Indications of host-species specificity and cospeciation were not observed. Mechanistic insights were provided using a combined electron microscopy and fluorescence in situ hybridization analysis, and an indirect mechanism of vertical transmission via nurse cells is proposed for the oviparous sponge Ectyoplasia ferox. Based on these phylogenetic and mechanistic results, we suggest the following symbiont transmission model: entire microbial consortia are vertically transmitted in sponges. While vertical transmission is clearly present, additional environmental transfer between adult individuals of the same and even different species might obscure possible signals of cospeciation. We propose that associations of HMA sponges with highly sponge-specific microbial communities are maintained by this combination of vertical and horizontal symbiont transmission.

scholarly journals 16S amplicon sequencing of microbial communities in enriched and non-enriched sediments of non-volcanic hot spring with temperature gradients

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10995
Author(s):  
Muhammad Yasir ◽  
Arooj K. Qureshi ◽  
Esam I. Azhar
Keyword(s):  
Microbial Diversity ◽  
Hot Springs ◽  
Hot Spring ◽  
Amplicon Sequencing ◽  
Sequencing Data ◽  
Microbial Composition ◽  
Sediment Samples ◽  
Bacterial Phyla ◽  
16S Amplicon Sequencing ◽  
Culture Dependent

Microorganisms in geothermal springs can offer insights into the fundamental and applied study of extremophiles. However, low microbial abundance and culturing requirements limit the ability to analyze microbial diversity in these ecosystems. In this study, culture-dependent and culture-independent techniques were used to analyze sediment samples from the non-volcanic Tatta Pani hot springs in district Poonch of Azad Kashmir. Microbial composition, temperature gradient, and enrichment effects on rare taxa were evaluated. In total, 31 distinct bacterial phyla and 725 genera were identified from the non-enriched Tatta Pani hot spring sediment samples, and 33 distinct bacterial phyla and 890 genera from the enriched sediment samples. Unique phyla specimens from the enriched samples included Candidatus Cloacimonetes, Caldiserica, and Korarchaeota archaea. The enriched samples yielded specific microbiota including 805 bacteria and 42 archaea operational taxonomic units with 97% similarity, though decreased thermophilic microbiota were observed in the enriched samples. Microbial diversity increased as temperature decreased. Candidate novel species were isolated from the culture-dependent screening, along with several genera that were not found in the 16S amplicon sequencing data. Overall, the enriched sediments showed high microbial diversity but with adverse changes in the composition of relatively dominant bacteria. Metagenomic analyses are needed to study the diversity, phylogeny, and functional investigation of hot spring microbiota.

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