scholarly journals CandidatusNitrosocaldus cavascurensis, an ammonia oxidizing, extremely thermophilic archaeon with a highly mobile genome

2017 ◽  
Author(s):  
Sophie S. Abby ◽  
Michael Melcher ◽  
Melina Kerou ◽  
Mart Krupovic ◽  
Michaela Stieglmeier ◽  
...  
Keyword(s):  
Ribosomal Proteins ◽  
Alternative Energy ◽  
Carbon Fixation ◽  
Hot Springs ◽  
Hot Spring ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Gene Repertoire ◽  
Ammonia Oxidizing Archaea ◽  
Thermophilic Archaeon

AbstractAmmonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in moderate environments but their occurrence and activity has also been demonstrated in hot springs. Here we present the first cultivated thermophilic representative with a sequenced genome, which allows to search for adaptive strategies and for traits that shape the evolution of Thaumarchaeota.CandidatusNitrosocaldus cavascurensis has been cultivated from a hot spring in Ischia, Italy. It grows optimally at 68°C under chemolithoautotrophic conditions on ammonia or urea converting ammonia stoichiometrically into nitrite with a generation time of approximately 25h. Phylogenetic analyses based on ribosomal proteins place the organism as a sister group to all known mesophilic AOA. The 1.58 Mb genome ofCa.N. cavascurensis harbors an amoAXCB gene cluster encoding ammonia monooxygenase, genes for a 3-hydroxypropionate/4-hydroxybutyrate pathway for autotrophic carbon fixation, but also genes that indicate potential alternative energy metabolisms. Although a bona fide gene for nitrite reductase is missing, the organism is sensitive to NO-scavenging, underlining the importance of this compound for AOA metabolism.Ca.N. cavascurensis is distinct from all other AOA in its gene repertoire for replication, cell division and repair. Its genome has an impressive array of mobile genetic elements and other recently acquired gene sets, including conjugative systems, a provirus, transposons and cell appendages. Some of these elements indicate recent exchange with the environment, whereas others seem to have been domesticated and might convey crucial metabolic traits.

scholarly journals In-Situ Metatranscriptomic Analyses Reveal the Metabolic Flexibility of the Thermophilic Anoxygenic Photosynthetic Bacterium Chloroflexusaggregans in a Hot Spring Cyanobacteria-Dominated Microbial Mat

2021 ◽  
Vol 9 (3) ◽  
pp. 652
Author(s):  
Shigeru Kawai ◽  
Joval N. Martinez ◽  
Mads Lichtenberg ◽  
Erik Trampe ◽  
Michael Kühl ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Environmental Conditions ◽  
Microbial Mats ◽  
Carbon Fixation ◽  
Hot Springs ◽  
Hot Spring ◽  
Photosynthetic Bacterium ◽  
Early Morning ◽  
Metabolic Flexibility

Chloroflexus aggregans is a metabolically versatile, thermophilic, anoxygenic phototrophic member of the phylum Chloroflexota (formerly Chloroflexi), which can grow photoheterotrophically, photoautotrophically, chemoheterotrophically, and chemoautotrophically. In hot spring-associated microbial mats, C. aggregans co-exists with oxygenic cyanobacteria under dynamic micro-environmental conditions. To elucidate the predominant growth modes of C. aggregans, relative transcription levels of energy metabolism- and CO2 fixation-related genes were studied in Nakabusa Hot Springs microbial mats over a diel cycle and correlated with microscale in situ measurements of O2 and light. Metatranscriptomic analyses indicated two periods with different modes of energy metabolism of C. aggregans: (1) phototrophy around midday and (2) chemotrophy in the early morning hours. During midday, C. aggregans mainly employed photoheterotrophy when the microbial mats were hyperoxic (400–800 µmol L−1 O2). In the early morning hours, relative transcription peaks of genes encoding uptake hydrogenase, key enzymes for carbon fixation, respiratory complexes as well as enzymes for TCA cycle and acetate uptake suggest an aerobic chemomixotrophic lifestyle. This is the first in situ study of the versatile energy metabolism of C. aggregans based on gene transcription patterns. The results provide novel insights into the metabolic flexibility of these filamentous anoxygenic phototrophs that thrive under dynamic environmental conditions.

scholarly journals Short-Term Stable Isotope Probing of Proteins Reveals Taxa Incorporating Inorganic Carbon in a Hot Spring Microbial Mat

2020 ◽  
Vol 86 (7) ◽  
Author(s):  
Laurey Steinke ◽  
Gordon W. Slysz ◽  
Mary S. Lipton ◽  
Christian Klatt ◽  
James J. Moran ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Inorganic Carbon ◽  
Microbial Mats ◽  
Carbon Fixation ◽  
Hot Springs ◽  
Hot Spring ◽  
Stable Isotope Probing ◽  
Short Term ◽  
Low Light ◽  
Assembly Sequences

ABSTRACT The upper green layer of the chlorophototrophic microbial mats associated with the alkaline siliceous hot springs of Yellowstone National Park consists of oxygenic cyanobacteria (Synechococcus spp.), anoxygenic Roseiflexus spp., and several other anoxygenic chlorophototrophs. Synechococcus spp. are believed to be the main fixers of inorganic carbon (Ci), but some evidence suggests that Roseiflexus spp. also contribute to inorganic carbon fixation during low-light, anoxic morning periods. Contributions of other phototrophic taxa have not been investigated. In order to follow the pathway of Ci incorporation into different taxa, mat samples were incubated with [13C]bicarbonate for 3 h during the early-morning, low-light anoxic period. Extracted proteins were treated with trypsin and analyzed by mass spectrometry, leading to peptide identifications and peptide isotopic profile signatures containing evidence of 13C label incorporation. A total of 25,483 peptides, corresponding to 7,221 proteins, were identified from spectral features and associated with mat taxa by comparison to metagenomic assembly sequences. A total of 1,417 peptides, derived from 720 proteins, were detectably labeled with 13C. Most 13C-labeled peptides were derived from proteins of Synechococcus spp. and Roseiflexus spp. Chaperones and proteins of carbohydrate metabolism were most abundantly labeled. Proteins involved in photosynthesis, Ci fixation, and N2 fixation were also labeled in Synechococcus spp. Importantly, most proteins of the 3-hydroxypropionate bi-cycle for Ci fixation in Roseiflexus spp. were labeled, establishing that members of this taxocene contribute to Ci fixation. Other taxa showed much lower [13C]bicarbonate incorporation. IMPORTANCE Yellowstone hot spring mats have been studied as natural models for understanding microbial community ecology and as modern analogs of stromatolites, the earliest community fossils on Earth. Stable-isotope probing of proteins (Pro-SIP) permitted short-term interrogation of the taxa that are involved in the important process of light-driven Ci fixation in this highly active community and will be useful in linking other metabolic processes to mat taxa. Here, evidence is presented that Roseiflexus spp., which use the 3-hydroxypropionate bi-cycle, are active in Ci fixation. Because this pathway imparts a lower degree of selection of isotopically heavy Ci than does the Calvin-Benson-Bassham cycle, the results suggest a mechanism to explain why the natural abundance of 13C in mat biomass is greater than expected if only the latter pathway were involved. Understanding how mat community members influence the 13C/12C ratios of mat biomass will help geochemists interpret the 13C/12C ratios of organic carbon in the fossil record.

scholarly journals RNA-Based Investigation of Ammonia-Oxidizing Archaea in Hot Springs of Yunnan Province, China

2010 ◽  
Vol 76 (13) ◽  
pp. 4538-4541 ◽  
Author(s):  
Hongchen Jiang ◽  
Qiuyuan Huang ◽  
Hailiang Dong ◽  
Peng Wang ◽  
Fengping Wang ◽  
...  
Keyword(s):  
Yunnan Province ◽  
Hot Springs ◽  
Hot Spring ◽  
Ammonia Oxidizing Archaea

ABSTRACT Using RNA-based techniques and hot spring samples collected from Yunnan Province, China, we show that the amoA gene of aerobic ammonia-oxidizing archaea can be transcribed at temperatures higher than 74°C and up to 94°C, suggesting that archaeal nitrification can potentially occur at near boiling temperatures.

scholarly journals Thermal UAS survey of reactivated hot spring activity in Waiwera, New Zealand

2020 ◽  
Vol 54 ◽  
pp. 165-171
Author(s):  
Melissa Präg ◽  
Ivy Becker ◽  
Christoph Hilgers ◽  
Thomas R. Walter ◽  
Michael Kühn
Keyword(s):  
New Zealand ◽  
Alternative Energy ◽  
Hot Springs ◽  
Hot Spring ◽  
Water Reservoir ◽  
Surface Expression ◽  
Primary User ◽  
Unmanned Aircraft ◽  
Thermal Activity ◽  
1960S And 1970S

Abstract. The utilization of geothermal reservoirs as alternative energy source is becoming increasingly important worldwide. Through close-range aerial photogrammetry realized by unmanned aircraft systems (UAS), this study investigates the surface expression of a leaking warm water reservoir in Waiwera, New Zealand, that has been known for many centuries but remained little explored. Due to overproduction during the 1960s and 1970s the reservoir has suffered significant pressure reduction, which resulted in the loss of artesian conditions and led to the desiccation of the hot springs in close succession. However, shortly after the recent shutdown of the primary user (Waiwera Thermal Resort & Spa) renewed artesian activity was reported by locals but no hot spring activity has been observed so far. Therefore, this study was carried out in October 2019 to assess the actual conditions of thermal activity in the area of the former hot springs. UAS with coupled thermal infrared cameras were used for thermal mapping and the obtained data show renewed activity of the hot springs on the beachfront of Waiwera. Faults and fractures were identified as important fluid pathways, as well as individual fluid conducting lithologies.

scholarly journals Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Zheng-Shuang Hua ◽  
Yu-Lin Wang ◽  
Paul N. Evans ◽  
Yan-Ni Qu ◽  
Kian Mau Goh ◽  
...  
Keyword(s):  
Hot Springs ◽  
Ammonia Oxidation ◽  
Hot Spring ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Ancestral State ◽  
Coenzyme M ◽  
Key Enzyme ◽  
Vertical Evolution ◽  
Methyl Coenzyme M Reductase

Abstract Several recent studies have shown the presence of genes for the key enzyme associated with archaeal methane/alkane metabolism, methyl-coenzyme M reductase (Mcr), in metagenome-assembled genomes (MAGs) divergent to existing archaeal lineages. Here, we study the mcr-containing archaeal MAGs from several hot springs, which reveal further expansion in the diversity of archaeal organisms performing methane/alkane metabolism. Significantly, an MAG basal to organisms from the phylum Thaumarchaeota that contains mcr genes, but not those for ammonia oxidation or aerobic metabolism, is identified. Together, our phylogenetic analyses and ancestral state reconstructions suggest a mostly vertical evolution of mcrABG genes among methanogens and methanotrophs, along with frequent horizontal gene transfer of mcr genes between alkanotrophs. Analysis of all mcr-containing archaeal MAGs/genomes suggests a hydrothermal origin for these microorganisms based on optimal growth temperature predictions. These results also suggest methane/alkane oxidation or methanogenesis at high temperature likely existed in a common archaeal ancestor.

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 Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Valerie De Anda ◽  
Lin-Xing Chen ◽  
Nina Dombrowski ◽  
Zheng-Shuang Hua ◽  
Hong-Chen Jiang ◽  
...  
Keyword(s):  
Carbon Cycling ◽  
Hydrothermal Vent ◽  
Gulf Of California ◽  
Hydrothermal Vents ◽  
Hot Springs ◽  
Hot Spring ◽  
Phylogenetic Analyses ◽  
Distinct Group ◽  
Sequence Information ◽  
Metabolic Versatility

AbstractGeothermal environments, such as hot springs and hydrothermal vents, are hotspots for carbon cycling and contain many poorly described microbial taxa. Here, we reconstructed 15 archaeal metagenome-assembled genomes (MAGs) from terrestrial hot spring sediments in China and deep-sea hydrothermal vent sediments in Guaymas Basin, Gulf of California. Phylogenetic analyses of these MAGs indicate that they form a distinct group within the TACK superphylum, and thus we propose their classification as a new phylum, ‘Brockarchaeota’, named after Thomas Brock for his seminal research in hot springs. Based on the MAG sequence information, we infer that some Brockarchaeota are uniquely capable of mediating non-methanogenic anaerobic methylotrophy, via the tetrahydrofolate methyl branch of the Wood-Ljungdahl pathway and reductive glycine pathway. The hydrothermal vent genotypes appear to be obligate fermenters of plant-derived polysaccharides that rely mostly on substrate-level phosphorylation, as they seem to lack most respiratory complexes. In contrast, hot spring lineages have alternate pathways to increase their ATP yield, including anaerobic methylotrophy of methanol and trimethylamine, and potentially use geothermally derived mercury, arsenic, or hydrogen. Their broad distribution and their apparent anaerobic metabolic versatility indicate that Brockarchaeota may occupy previously overlooked roles in anaerobic carbon cycling.

Diversification of the North American Doellingeria-Eucephalus Clade (Astereae: Asteraceae) Inferred from Molecular and Morphological Evidence

2019 ◽  
Vol 44 (4) ◽  
pp. 930-942
Author(s):  
Geraldine A. Allen ◽  
Luc Brouillet ◽  
John C. Semple ◽  
Heidi J. Guest ◽  
Robert Underhill
Keyword(s):  
North American ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Morphological Evidence ◽  
South American ◽  
New Combinations ◽  
The North ◽  
Hybridization Event ◽  
Ancient Hybridization

Abstract—Doellingeria and Eucephalus form the earliest-diverging clade of the North American Astereae lineage. Phylogenetic analyses of both nuclear and plastid sequence data show that the Doellingeria-Eucephalus clade consists of two main subclades that differ from current circumscriptions of the two genera. Doellingeria is the sister group to E. elegans, and the Doellingeria + E. elegans subclade in turn is sister to the subclade containing all remaining species of Eucephalus. In the plastid phylogeny, the two subclades are deeply divergent, a pattern that is consistent with an ancient hybridization event involving ancestral species of the Doellingeria-Eucephalus clade and an ancestral taxon of a related North American or South American group. Divergence of the two Doellingeria-Eucephalus subclades may have occurred in association with northward migration from South American ancestors. We combine these two genera under the older of the two names, Doellingeria, and propose 12 new combinations (10 species and two varieties) for all species of Eucephalus.

scholarly journals Origin of the low-medium temperature hot springs around Nanjing, China

2021 ◽  
Vol 13 (1) ◽  
pp. 820-834
Author(s):  
Jun Ma ◽  
Zhifang Zhou
Keyword(s):  
Hot Springs ◽  
Hot Spring ◽  
Hot Water ◽  
Geothermal Water ◽  
Geological Condition ◽  
Medium Temperature ◽  
Rock Interaction ◽  
Karst Landform ◽  
Karst Landforms ◽  
Development And Management

Abstract The exploration of the origin of hot spring is the basis of its development and utilization. There are many low-medium temperature hot springs in Nanjing and its surrounding karst landform areas, such as the Tangshan, Tangquan, Lunshan, and Xiangquan hot springs. This article discusses the origin characters of the Lunshan hot spring with geological condition analysis, hydrogeochemical data, and isotope data. The results show that the hot water is SO4–Ca type in Lunshan area, and the cation content of SO4 is high, which are related to the deep hydrogeological conditions of the circulation in the limestone. Carbonate and anhydrite dissolutions occur in the groundwater circulation process, and they also dominate the water–rock interaction processes in the geothermal reservoir of Lunshan. The hot water rising channels are deeply affected by the NW and SN faults. Schematic diagrams of the conceptual model of the geothermal water circulation in Lunshan are plotted. The origin of Tangshan, Tangquan, and Xiangquan hot springs are similar to the Lunshan hot spring. In general, the geothermal water in karst landforms around Nanjing mainly runs through the carbonate rock area and is exposed near the core of the anticlinal structure of karst strata, forming SO4–Ca/SO4–Ca–Mg type hot spring with the water temperature less than 60°C. The characters of the hot springs around Nanjing are similar, which are helpful for the further research, development, and management of the geothermal water resources in this region.

scholarly journals Radon Activity Concentrations in Natural Hot Spring Water: Dose Assessment and Health Perspective

2021 ◽  
Vol 18 (3) ◽  
pp. 920
Author(s):  
Eka Djatnika Nugraha ◽  
Masahiro Hosoda ◽  
June Mellawati ◽  
Untara Untara ◽  
Ilsa Rosianna ◽  
...  
Keyword(s):  
Public Health ◽  
Effective Dose ◽  
Radiation Protection ◽  
Water Samples ◽  
Hot Springs ◽  
Hot Spring ◽  
Annual Effective Dose ◽  
Spring Water ◽  
Dose Assessment ◽  
West Java

The world community has long used natural hot springs for tourist and medicinal purposes. In Indonesia, the province of West Java, which is naturally surrounded by volcanoes, is the main destination for hot spring tourism. This paper is the first report on radon measurements in tourism natural hot spring water in Indonesia as part of radiation protection for public health. The purpose of this paper is to study the contribution of radon doses from natural hot spring water and thereby facilitate radiation protection for public health. A total of 18 water samples were measured with an electrostatic collection type radon monitor (RAD7, Durridge Co., USA). The concentration of radon in natural hot spring water samples in the West Java region, Indonesia ranges from 0.26 to 31 Bq L−1. An estimate of the annual effective dose in the natural hot spring water area ranges from 0.51 to 0.71 mSv with a mean of 0.60 mSv for workers. Meanwhile, the annual effective dose for the public ranges from 0.10 to 0.14 mSv with an average of 0.12 mSv. This value is within the range of the average committed effective dose from inhalation and terrestrial radiation for the general public, 1.7 mSv annually.

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