Archaeal Community Structures in the Solfataric Acidic Hot Springs with Different Temperatures and Elemental Compositions

Archaeal 16S rRNA gene compositions and environmental factors of four distinct solfataric acidic hot springs in Kirishima, Japan were compared. The four ponds were selected by differences of temperature and total dissolved elemental concentration as follows: (1) Pond-A: 93°C and 1679 mg L−1, (2) Pond-B: 66°C and 2248 mg L−1, (3) Pond-C: 88°C and 198 mg L−1, and (4) Pond-D: 67°C and 340 mg L−1. In total, 431 clones of 16S rRNA gene were classified into 26 phylotypes. In Pond-B, the archaeal diversity was the highest among the four, and the members of the order Sulfolobales were dominant. The Pond-D also showed relatively high diversity, and the most frequent group was uncultured thermoacidic spring clone group. In contrast to Pond-B and Pond-D, much less diverse archaeal clones were detected in Pond-A and Pond-C showing higher temperatures. However, dominant groups in these ponds were also different from each other. The members of the order Sulfolobales shared 89% of total clones in Pond-A, and the uncultured crenarchaeal groups shared 99% of total Pond-C clones. Therefore, species compositions and biodiversity were clearly different among the ponds showing different temperatures and dissolved elemental concentrations.

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Diversity of microbial communities in hot springs of Sri Lanka as revealed by 16S rRNA gene high-throughput sequencing analysis

Gene ◽

10.1016/j.gene.2021.146103 ◽

2021 ◽

pp. 146103

Author(s):

Dilini Sadeepa ◽

Kosala Sirisena ◽

Pathmalal M. Manage

Keyword(s):

Sri Lanka ◽

16S Rrna ◽

16S Rrna Gene ◽

Microbial Communities ◽

High Throughput ◽

High Throughput Sequencing ◽

Hot Springs ◽

Rrna Gene ◽

Sequencing Analysis

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Phylogenetically novel uncultured microbial cells dominate Earth microbiomes

10.1101/303602 ◽

2018 ◽

Cited By ~ 1

Author(s):

Karen G. Lloyd ◽

Joshua Ladau ◽

Andrew D. Steen ◽

Junqi Yin ◽

Lonnie Crosby

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Hydrothermal Vents ◽

Hot Springs ◽

Laboratory Culture ◽

Rrna Gene ◽

Gene Sequences ◽

16S Rrna Gene Sequences ◽

Microbial Cells ◽

Taxonomic Groups

AbstractTo unequivocally determine a microbe’s physiology, including its metabolism, environmental roles, and growth characteristics, it must be grown in a laboratory culture. Unfortunately, many phylogenetically-novel groups have never been cultured, so their physiologies have only been inferred from genomics and environmental characteristics. Although the diversity, or number of different taxonomic groups, of uncultured clades has been well-studied, their global abundances, or number of cells in any given environment, have not been assessed. We quantified the degree of similarity of 16S rRNA gene sequences from diverse environments in publicly-available metagenome and metatranscriptome databases, which we show are largely free of the culture-bias present in primer-amplified 16S rRNA gene surveys, to their nearest cultured relatives. Whether normalized to scaffold read depths or not, the highest abundance of metagenomic 16S rRNA gene sequences belong to phylogenetically novel uncultured groups in seawater, freshwater, terrestrial subsurface, soil, hypersaline environments, marine sediment, hot springs, hydrothermal vents, non-human hosts, snow and bioreactors (22-87% uncultured genera to classes and 0-64% uncultured phyla). The exceptions were human and human-associated environments which were dominated by cultured genera (45-97%). We estimate that uncultured genera and phyla could comprise 7.3 × 1029(81%) and 2.2 × 1029(25%) microbial cells, respectively. Uncultured phyla were over-represented in meta transcript omes relative to metagenomes (46-84% of sequences in a given environment), suggesting that they are viable, and possibly more active than cultured clades. Therefore, uncultured microbes, often from deeply phylogenetically divergent groups, dominate non-human environments on Earth, and their undiscovered physiologies may matter for Earth systems.

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

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.02790-0 ◽

2004 ◽

Vol 54 (1) ◽

pp. 33-39 ◽

Cited By ~ 73

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.

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Diversity and structure of the archaeal community in the leachate of a full-scale recirculating landfill as examined by direct 16S rRNA gene sequence retrieval

FEMS Microbiology Letters ◽

10.1111/j.1574-6968.2002.tb11353.x ◽

2002 ◽

Vol 214 (2) ◽

pp. 235-240 ◽

Cited By ~ 48

Author(s):

Li-Nan Huang ◽

Hui Zhou ◽

Yue-Qin Chen ◽

Shuo Luo ◽

Chong-Yu Lan ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequence ◽

Archaeal Community ◽

Full Scale ◽

16S Rrna Gene Sequence ◽

Rrna Gene ◽

Rrna Gene Sequence

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Phylogenetic Diversity of Archaea and the Archaeal Ammonia Monooxygenase Gene in Uranium Mining-Impacted Locations in Bulgaria

Archaea ◽

10.1155/2014/196140 ◽

2014 ◽

Vol 2014 ◽

pp. 1-10 ◽

Cited By ~ 4

Author(s):

Galina Radeva ◽

Anelia Kenarova ◽

Velina Bachvarova ◽

Katrin Flemming ◽

Ivan Popov ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Archaeal Community ◽

Uranium Mining ◽

Uranium Mine ◽

Rrna Gene ◽

Ammonia Monooxygenase ◽

Gene Sequences ◽

Monooxygenase Gene ◽

Archaeal Communities

Uranium mining and milling activities adversely affect the microbial populations of impacted sites. The negative effects of uranium on soil bacteria and fungi are well studied, but little is known about the effects of radionuclides and heavy metals on archaea. The composition and diversity of archaeal communities inhabiting the waste pile of the Sliven uranium mine and the soil of the Buhovo uranium mine were investigated using 16S rRNA gene retrieval. A total of 355 archaeal clones were selected, and their 16S rDNA inserts were analysed by restriction fragment length polymorphism (RFLP) discriminating 14 different RFLP types. All evaluated archaeal 16S rRNA gene sequences belong to the 1.1b/Nitrososphaeracluster of Crenarchaeota. The composition of the archaeal community is distinct for each site of interest and dependent on environmental characteristics, including pollution levels. Since the members of 1.1b/Nitrososphaeracluster have been implicated in the nitrogen cycle, the archaeal communities from these sites were probed for the presence of the ammonia monooxygenase gene (amoA). Our data indicate thatamoA gene sequences are distributed in a similar manner as in Crenarchaeota, suggesting that archaeal nitrification processes in uranium mining-impacted locations are under the control of the same key factors controlling archaeal diversity.

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Tepidisphaera mucosa gen. nov., sp. nov., a moderately thermophilic member of the class Phycisphaerae in the phylum Planctomycetes, and proposal of a new family, Tepidisphaeraceae fam. nov., and a new order, Tepidisphaerales ord. nov.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.070151-0 ◽

2015 ◽

Vol 65 (Pt_2) ◽

pp. 549-555 ◽

Cited By ~ 54

Author(s):

O. L. Kovaleva ◽

A. Yu. Merkel ◽

A. A. Novikov ◽

R. V. Baslerov ◽

S. V. Toshchakov ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Type Species ◽

Hot Springs ◽

Thermophilic Bacteria ◽

Physiological Data ◽

Rrna Gene ◽

Content Type ◽

Moderately Thermophilic ◽

Link Type

Three strains of facultatively aerobic, moderately thermophilic bacteria were isolated from terrestrial hot springs in Baikal Lake region and Kamchatka (Russia). Cells of the new isolates were cocci reproducing by binary fission. The temperature range for growth was between 20 and 56 °C and the pH range for growth from pH 4.5 to 8.5, with optimal growth at 47–50 °C and pH 7.0–7.5. The organisms were chemoheterotrophs preferring sugars and polysaccharides as growth substrates. 16S rRNA gene sequences of strains 2842, 2813 and 2918Kr were nearly identical (99.7–100 % similarity) and indicated that the strains belonged to the phylum Planctomycetes . The phylogenetically closest cultivated relatives were Algisphaera agarilytica 06SJR6-2T and Phycisphaera mikurensis FYK2301M01T with 16S rRNA gene sequence similarity values of 82.4 and 80.3 %, respectively. The novel strains differed from them by higher growth temperature, sensitivity to NaCl concentration above 3.0 % and by their cellular fatty acids profile. On the basis of phylogenetic and physiological data, strains 2842T, 2813 and 2918Kr represent a novel genus and species for which we propose the name Tepidisphaera mucosa sp. nov. The type strain is 2842T ( = VKM B-2832T = JCM 19875T). We also propose that Tepidisphaera gen. nov. is the type genus of a novel family, Tepidisphaeraceae fam. nov. and a novel order, Tepidisphaerales ord. nov.

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Archaeal diversity revealed in Antarctic sea ice

Antarctic Science ◽

10.1017/s0954102011000368 ◽

2011 ◽

Vol 23 (6) ◽

pp. 531-536 ◽

Cited By ~ 22

Author(s):

Rebecca O.M. Cowie ◽

Elizabeth W. Maas ◽

Ken G. Ryan

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Sea Ice ◽

Community Diversity ◽

Rrna Gene ◽

Archaeal Diversity ◽

Prokaryotic Community ◽

Antarctic Sea Ice ◽

Pcr Products ◽

Global Biogeochemical Cycles

AbstractArchaea, once thought to be only extremophiles, are now known to be abundant in most environments. They can predominate in microbial communities and be significantly involved in many global biogeochemical cycles. However, Archaea have not been reported in Antarctic sea ice. Our understanding of the ecology of Antarctic sea ice prokaryotes is still in its infancy but this information is important if we are to understand their diversity, adaptations and biogeochemical roles in Antarctic systems. We detected Archaea in sea ice at two sampling sites taken from three subsequent years using conserved 16S rRNA gene archaeal primers and PCR. Archaeal abundance was measured using quantitative PCR and community diversity was investigated by sequencing cloned 16S rRNA gene PCR products. Archaea in Antarctic sea ice were found to be in low abundance consisting of ≤ 6.6% of the prokaryotic community. The majority, 90.8% of the sequences, clustered with the recently described phylumThaumarchaeota, one group closely clustered with the ammonia-oxidizing CandidatusNitrosopumilus maritimus. The remainder of the clones grouped with theEuryarchaeota.

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Culture-Independent Characterization of Archaeal Biodiversity in Swine Confinement Building Bioaerosols

Applied and Environmental Microbiology ◽

10.1128/aem.00726-09 ◽

2009 ◽

Vol 75 (17) ◽

pp. 5445-5450 ◽

Cited By ~ 64

Author(s):

Benjamin Nehmï¿½ ◽

Yan Gilbert ◽

Valï¿½rie Lï¿½tourneau ◽

Robert J. Forster ◽

Marc Veillette ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Denaturing Gradient Gel Electrophoresis ◽

Molecular Ecology ◽

Pcr Amplification ◽

Methanogenic Archaea ◽

Archaeal Community ◽

Pig Manure ◽

Rrna Gene ◽

Swine Confinement

ABSTRACT It was previously demonstrated that microbial communities of pig manure were composed of both bacteria and archaea. Recent studies have shown that bacteria are aerosolized from pig manure, but none have ever focused on the airborne archaeal burden. We sought here to develop and apply molecular ecology approaches to thoroughly characterize airborne archaea from swine confinement buildings (SCBs). Eight swine operations were visited, twice in winter and once during summer. Institute of Occupational Medicine cassettes loaded with 25-mm gelatin filters were used to capture the inhalable microbial biomass. The total genomic DNA was extracted and used as a template for PCR amplification of the archaeal 16S rRNA gene. High concentrations of archaea were found in SCB bioaerosols, being as high as 108 16S rRNA gene copies per cubic meter of air. Construction and sequencing of 16S rRNA gene libraries revealed that all sequences were closely related to methanogenic archaea, such as Methanosphaera stadtmanae (94.7% of the archaeal biodiversity). Archaeal community profiles were compared by 16S rRNA gene denaturing gradient gel electrophoresis. This analysis showed similar fingerprints in each SCB and confirmed the predominance of methanogenic archaea in the bioaerosols. This study sheds new light on the nature of bioaerosols in SCBs and suggests that archaea are also aerosolized from pig manure.

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