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Viladomat Jasso M, García-Ulloa M, Zapata-Peñasco I, Eguiarte LE, Souza V. Metagenomic insight into taxonomic composition, environmental filtering and functional redundancy for shaping worldwide modern non-lithifying microbial mats. PeerJ 2024; 12:e17412. [PMID: 38827283 PMCID: PMC11144394 DOI: 10.7717/peerj.17412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 04/26/2024] [Indexed: 06/04/2024] Open
Abstract
Modern microbial mats are relictual communities mostly found in extreme environments worldwide. Despite their significance as representatives of the ancestral Earth and their important roles in biogeochemical cycling, research on microbial mats has largely been localized, focusing on site-specific descriptions and environmental change experiments. Here, we present a global comparative analysis of non-lithifying microbial mats, integrating environmental measurements with metagenomic data from 62 samples across eight sites, including two new samples from the recently discovered Archaean Domes from Cuatro Ciénegas, Mexico. Our results revealed a notable influence of environmental filtering on both taxonomic and functional compositions of microbial mats. Functional redundancy appears to confer resilience to mats, with essential metabolic pathways conserved across diverse and highly contrasting habitats. We identified six highly correlated clusters of taxa performing similar ecological functions, suggesting niche partitioning and functional specialization as key mechanisms shaping community structure. Our findings provide insights into the ecological principles governing microbial mats, and lay the foundation for future research elucidating the intricate interplay between environmental factors and microbial community dynamics.
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Affiliation(s)
- Mariette Viladomat Jasso
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | | | - Icoquih Zapata-Peñasco
- Dirección de Investigación en Transformación de Hidrocarburos, Instituto Mexicano del Petróleo, Ciudad de México, Mexico
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Estudios del Cuaternario de Fuego-Patagonia y Antártica (CEQUA), Punta Arenas, Chile
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2
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Gafarova E, Kuracji D, Sogomonyan K, Gorokhov I, Polev D, Zubova E, Golikova E, Granovitch A, Maltseva A. Gut Bacteriomes and Ecological Niche Divergence: An Example of Two Cryptic Gastropod Species. BIOLOGY 2023; 12:1521. [PMID: 38132347 PMCID: PMC10740740 DOI: 10.3390/biology12121521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023]
Abstract
Symbiotic microorganisms may provide their hosts with abilities critical to their occupation of microhabitats. Gut (intestinal) bacterial communities aid animals to digest substrates that are either innutritious or toxic, as well as support their development and physiology. The role of microbial communities associated with sibling species in the hosts' adaptation remains largely unexplored. In this study, we examined the composition and plasticity of the bacteriomes in two sibling intertidal gastropod species, Littorina fabalis and L. obtusata, which are sympatric but differ in microhabitats. We applied 16S rRNA gene metabarcoding and shotgun sequencing to describe associated microbial communities and their spatial and temporal variation. A significant drop in the intestinal bacteriome diversity was revealed during the cold season, which may reflect temperature-related metabolic shifts and changes in snail behavior. Importantly, there were significant interspecies differences in the gut bacteriome composition in summer but not in autumn. The genera Vibrio, Aliivibrio, Moritella and Planktotalea were found to be predominantly associated with L. fabalis, while Granulosicoccus, Octadecabacter, Colwellia, Pseudomonas, Pseudoalteromonas and Maribacter were found to be mostly associated with L. obtusata. Based on these preferential associations, we analyzed the metabolic pathways' enrichment. We hypothesized that the L. obtusata gut bacteriome contributes to decomposing algae and detoxifying polyphenols produced by fucoids. Thus, differences in the sets of associated bacteria may equip their closely phylogenetically related hosts with a unique ability to occupy specific micro-niches.
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Affiliation(s)
- Elizaveta Gafarova
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
| | - Dmitrii Kuracji
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
| | - Karina Sogomonyan
- Center for Bioinformatics and Algorithmic Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Ivan Gorokhov
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
| | - Dmitrii Polev
- Department of Epidemiology, St. Petersburg Pasteur Institute, Mira Street 14, 197101 St. Petersburg, Russia;
| | - Ekaterina Zubova
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
| | - Elena Golikova
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
| | - Andrey Granovitch
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
| | - Arina Maltseva
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
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Kurokawa M, Higashi K, Yoshida K, Sato T, Maruyama S, Mori H, Kurokawa K. Metagenomic Thermometer. DNA Res 2023; 30:dsad024. [PMID: 37940329 PMCID: PMC10660216 DOI: 10.1093/dnares/dsad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 10/06/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023] Open
Abstract
Various microorganisms exist in environments, and each of them has its optimal growth temperature (OGT). The relationship between genomic information and OGT of each species has long been studied, and one such study revealed that OGT of prokaryotes can be accurately predicted based on the fraction of seven amino acids (IVYWREL) among all encoded amino-acid sequences in its genome. Extending this discovery, we developed a 'Metagenomic Thermometer' as a means of predicting environmental temperature based on metagenomic sequences. Temperature prediction of diverse environments using publicly available metagenomic data revealed that the Metagenomic Thermometer can predict environmental temperatures with small temperature changes and little influx of microorganisms from other environments. The accuracy of the Metagenomic Thermometer was also confirmed by a demonstration experiment using an artificial hot water canal. The Metagenomic Thermometer was also applied to human gut metagenomic samples, yielding a reasonably accurate value for human body temperature. The result further suggests that deep body temperature determines the dominant lineage of the gut community. Metagenomic Thermometer provides a new insight into temperature-driven community assembly based on amino-acid composition rather than microbial taxa.
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Affiliation(s)
- Masaomi Kurokawa
- Genome Evolution Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Koichi Higashi
- Genome Evolution Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Biological Information, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Keisuke Yoshida
- Department of Biological Information, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Tomohiko Sato
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Shigenori Maruyama
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Hiroshi Mori
- Genome Evolution Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Genome Diversity Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Biological Information, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Ken Kurokawa
- Genome Evolution Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Biological Information, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
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Ishaq K, Shah AH, Fariq A, Rasheed S, Jannat S. Diversity of culturable thermophilic bacteria from Tata Pani hotspring of Kotli Azad Jammu and Kashmir. Biodivers Data J 2023; 11:e99224. [PMID: 38327337 PMCID: PMC10848829 DOI: 10.3897/bdj.11.e99224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/28/2023] [Indexed: 03/17/2023] Open
Abstract
Hot water springs are unique areas populated by mesophiles, thermotolerant and hyperthermophiles. They are the source of diversity of thermophiles, mainly belonging to archaea and bacteria domains. The diversity of thermophiles gives an outline of the huge biological potential that can be exploited for industrial applications.To this end, this study was aimed to isolate and characterise the unexplored thermophilic microorganisms from hot water spring in Tatapani, Tehsil & District Kotli AJK, Pakistan. Around 10 bacterial isolates were identified using morphological, biochemical, physiological and molecular attributes. Sequencing of the 16S rDNA gene of the isolates followed by BLAST search revealed that the strain MBT008 has 100% similarity with Anoxybacilluskamchatkensis. MBT012 showed 99.57% similarity with A.mongoliensis, MBT014 was affiliated with A.tengchongensis with 99.43% similarity, MBT009 showed 99.83% homology with A.gonensis and MBT018, 98.70% similarity with A.karvacharensis. The presence of all this microbial diversity in one common source is of immense importance related to envioronmental and industrial aspects in general and extraction of thermostable enzymes from these thermophiles specifically opens new horizons in the field of industrial biotechnology. These thermophiles are revealing new capabilities and are being manipulated by biotechnologists in utilizing them in different unique ways.
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Affiliation(s)
- Kazima Ishaq
- Department of Biotechnology, Faculty of Basic and Applied Sciences, University of Kotli Azad Jammu and Kashmir, Kotli, PakistanDepartment of Biotechnology, Faculty of Basic and Applied Sciences, University of Kotli Azad Jammu and KashmirKotliPakistan
| | - Asad Hussain Shah
- Senior Research Fellow, Faculty of Biology Medicine and Health The University of Manchester The Michael Smith Building Oxford Road Manchester M13 9PT, Manchester, United KingdomSenior Research Fellow, Faculty of Biology Medicine and Health The University of Manchester The Michael Smith Building Oxford Road Manchester M13 9PTManchesterUnited Kingdom
| | - Anila Fariq
- Department of Biotechnology, Faculty of Basic and Applied Sciences, University of Kotli Azad Jammu and Kashmir, Kotli, PakistanDepartment of Biotechnology, Faculty of Basic and Applied Sciences, University of Kotli Azad Jammu and KashmirKotliPakistan
| | - Sajida Rasheed
- Department of Biotechnology, Faculty of Basic and Applied Sciences, University of Kotli Azad Jammu and Kashmir, Kotli, PakistanDepartment of Biotechnology, Faculty of Basic and Applied Sciences, University of Kotli Azad Jammu and KashmirKotliPakistan
| | - Sammyia Jannat
- Department of Biotechnology, Faculty of Basic and Applied Sciences, University of Kotli Azad Jammu and Kashmir, Kotli, PakistanDepartment of Biotechnology, Faculty of Basic and Applied Sciences, University of Kotli Azad Jammu and KashmirKotliPakistan
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Wang X, Yin Y, Yu Z, Shen G, Cheng H, Tao S. Distinct distribution patterns of the abundant and rare bacteria in high plateau hot spring sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160832. [PMID: 36521602 DOI: 10.1016/j.scitotenv.2022.160832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
The diversity and distribution patterns of the abundant and rare microbial sub-communities in hot spring ecosystems and their assembly mechanisms are poorly understood. The present study investigated the diversity and distribution patterns of the total, abundant, conditionally rare, and always rare taxa in the low- and moderate-temperature hot spring sediments on the Tibetan Plateau based on high-throughput 16S rRNA gene sequencing, and explored their major environmental drivers. The diversity of these four bacterial taxa showed no significant change between the low-temperature and moderate-temperature hot spring sediments, whereas the bacterial compositions were obviously different. Stochasticity dominated the bacterial sub-community assemblages, while heterogeneous selection also played an important role in shaping the abundant and conditionally rare taxa between the low-temperature and moderate-temperature hot spring sediments. No significant difference in the topological properties of co-occurrence networks was found between the conditionally rare and abundant taxa, and the connections between the paired operational taxonomic units (OTUs) were almost positive. The diversity of the total, abundant, and conditionally rare taxa was governed by the salinity of hot spring sediments, while that of the always rare taxa was determined by the content of S element. In contrast, temperature had significant direct effect on the composition of the total, abundant, and conditionally rare taxa, but relatively weak influence on that of the always rare taxa. Besides, salinity was another major environmental factor driving the composition of the abundant and rare sub-communities in the hot spring sediments. These results reveal the assembly processes and major environmental drivers that shaped different bacterial sub-communities in the hot spring sediments on the Tibetan Plateau, and indicate the importance of conditionally rare taxa in constructing bacterial communities. These findings enhance the current understanding of the ecological mechanisms maintaining the ecosystem stability and services in extreme environment.
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Affiliation(s)
- Xiaojie Wang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100049, China; MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yue Yin
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Zhiqiang Yu
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Guofeng Shen
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Hefa Cheng
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China.
| | - Shu Tao
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
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6
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Cheng YI, Lin YC, Leu JY, Kuo CH, Chu HA. Comparative analysis reveals distinctive genomic features of Taiwan hot-spring cyanobacterium Thermosynechococcus sp. TA-1. Front Microbiol 2022; 13:932840. [PMID: 36033852 PMCID: PMC9403480 DOI: 10.3389/fmicb.2022.932840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Thermosynechococcus is a genus of thermophilic unicellular cyanobacteria that dominates microbial mats in Asian non-acidic hot springs. These cyanobacteria are the major primary producers in their ecological niches and are promising sources of thermostable enzymes for biotechnology applications. To improve our understanding of these organisms, we conducted whole-genome sequencing of a novel strain for comparative analysis with other representatives in the same genus. This newly characterized strain, Thermosynechococcus sp. TA-1, was isolated from the Taian hot springs in Taiwan. Analyses based on average nucleotide identity (ANI) and genome-scale phylogeny suggested that TA-1 and another Taiwanese strain CL-1 belong to a novel species-level taxon. Two metagenome-assembled genomes (MAGs) originated from India represent the sister group, and Thermosynechococcus elongatus PKUAC-SCTE542 from China is the next closest lineage. All cultivated strains and MAGs from Japan form a separate monophyletic clade and could be classified into two species-level taxa. Intriguingly, although TA-1 and CL-1 share 97.0% ANI, the genome alignment identified at least 16 synteny breakpoints that are mostly associated with transposase genes, which illustrates the dynamic nature of their chromosomal evolution. Gene content comparisons identified multiple features distinct at species- or strain-level among these Thermosynechococcus representatives. Examples include genes involved in bicarbonate transportation, nitric oxide protection, urea utilization, kanamycin resistance, restriction-modification system, and chemotaxis. Moreover, we observed the insertion of type II inteins in multiple genes of the two Taiwanese strains and inferred putative horizontal transfer of an asparagine synthase gene (asnB) associated with exopolysaccharides gene cluster. Taken together, while previous work suggested that strains in this genus share a highly conserved genomic core and no clear genetic differentiation could be linked to environmental factors, we found that the overall pattern of gene content divergence is largely congruent with core genome phylogeny. However, it is difficult to distinguish between the roles of phylogenetic relatedness and geographic proximity in shaping the genetic differentiation. In conclusion, knowledge of the genomic differentiation among these strains provides valuable resources for future functional characterization.
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Affiliation(s)
- Yen-I Cheng
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Chen Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Jyh-Yih Leu
- Department of Life Science, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- *Correspondence: Chih-Horng Kuo,
| | - Hsiu-An Chu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Hsiu-An Chu,
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Corniello A, Guida M, Stellato L, Trifuoggi M, Carraturo F, Del Gaudio E, Del Giudice C, Forte G, Giarra A, Iorio M, Marzaioli F, Toscanesi M. Hydrochemical, isotopic and microbiota characterization of telese mineral waters (Southern Italy). ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2022; 44:1949-1970. [PMID: 33438150 PMCID: PMC9177486 DOI: 10.1007/s10653-021-00806-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/02/2021] [Indexed: 05/06/2023]
Abstract
The study deals with the analyses of springs and wells at the base of Montepugliano Hill that represents the SE edge of the wide carbonate Matese massif (Campania, southern Italy). At the base of the hill, from west to east and for almost one kilometre, cold springs HCO3-Ca type (Grassano springs, ~ 4.5 m3/s; TDS: about 0.45 g/L) pass to hypothermal, HCO3-Ca type, sulphurous and CO2-rich springs (~ 1 m3/s with TDS > 1 g/L). Some of the latter are widely used in Telese Spa and Centro Relax Spa. Chemical and isotopic analyses carried out for this study support the hypothesis that all these waters (mineral and non-mineral) have the same catchment area, which is located in the Matese massif. As regards the sulphurous springs, they receive both meteoric waters infiltration and uprising of deeper waters rich in endogenous CO2 and H2S gases through important faults systems. Far from these faults, the chemistry of groundwater is scarcely (or not at all) affected by these deep fluid enrichment processes. This scheme is very significant; in fact, when very important groundwater resources are present, it is possible to use both mineral waters in Spa and, in areas far from the faults, those not yet mineralized. Finally, at Montepugliano Hill, in the final stage of the flow path, groundwater is also affected by change in the microbiome: this could provide a basis for comparison between various mineral waters.
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Affiliation(s)
- Alfonso Corniello
- Department of Civil, Architectural and Environmental Engineering, Univ. Federico II, P/le Tecchio 80, Napoli, Italy
| | - Marco Guida
- Department of Biology, Univ. Federico II, Via Cupa Nuova Cintia, 21, Napoli, Italy
| | - Luisa Stellato
- Department of Mathematics and Physics, Univ. Vanvitelli, Viale Lincoln, 5, Caserta, Italy
| | - Marco Trifuoggi
- Department of Chemical Sciences, Univ. Federico II, Via Cupa Nuova Cintia, 21, Napoli, Italy
| | - Federica Carraturo
- Department of Biology, Univ. Federico II, Via Cupa Nuova Cintia, 21, Napoli, Italy
| | - Elena Del Gaudio
- Department of Civil, Architectural and Environmental Engineering, Univ. Federico II, P/le Tecchio 80, Napoli, Italy
| | - Carmela Del Giudice
- Department of Biology, Univ. Federico II, Via Cupa Nuova Cintia, 21, Napoli, Italy
| | - Giovanni Forte
- Department of Civil, Architectural and Environmental Engineering, Univ. Federico II, P/le Tecchio 80, Napoli, Italy.
| | - Antonella Giarra
- Department of Chemical Sciences, Univ. Federico II, Via Cupa Nuova Cintia, 21, Napoli, Italy
| | - Marina Iorio
- Institute of Marine Sciences (CNR), Calata Porta di Massa, 80, Napoli, Italy
| | - Fabio Marzaioli
- Department of Mathematics and Physics, Univ. Vanvitelli, Viale Lincoln, 5, Caserta, Italy
| | - Maria Toscanesi
- Department of Chemical Sciences, Univ. Federico II, Via Cupa Nuova Cintia, 21, Napoli, Italy
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Muramatsu S, Hirose S, Iino T, Ohkuma M, Hanada S, Haruta S. Neotabrizicola shimadae gen. nov., sp. nov., an aerobic anoxygenic phototrophic bacterium harbouring photosynthetic genes in the family Rhodobacteraceae, isolated from a terrestrial hot spring. Antonie van Leeuwenhoek 2022; 115:731-740. [PMID: 35380297 DOI: 10.1007/s10482-022-01728-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 03/06/2022] [Indexed: 11/27/2022]
Abstract
A bacteriochlorophyll-containing bacterium, designated as strain N10T, was isolated from a terrestrial hot spring in Nagano Prefecture, Japan. Gram-stain-negative, oxidase- and catalase-positive and ovoid to rod-shaped cells showed the features of aerobic anoxygenic phototrophic bacteria, i.e., strain N10T synthesised bacteriochlorophylls under aerobic conditions and could not grow anaerobically even under illumination. Genome analysis found genes for bacteriochlorophyll and carotenoid biosynthesis, light-harvesting complexes and type-2 photosynthetic reaction centre in the chromosome. Phylogenetic analyses based on the 16S rRNA gene sequence and 92 core proteins revealed that strain N10T was located in a distinct lineage near the type species of the genera Tabrizicola and Xinfangfangia and some species in the genus Rhodobacter (e.g., Rhodobacter blasticus). Strain N10T shared < 97.1% 16S rRNA gene sequence identity with those species in the family Rhodobacteraceae. The digital DNA-DNA hybridisation, average nucleotide identity and average amino acid identity values with the relatives, Tabrizicola aquatica RCRI19T (an aerobic anoxygenic phototrophic bacterium), Xinfangfangia soli ZQBWT and R. blasticus ATCC 33485T were 19.9-20.7%, 78.2-79.1% and 69.1-70.1%, respectively. Based on the phenotypic features, major fatty acid and polar lipid compositions, genome sequence and phylogenetic position, a novel genus and species are proposed for strain N10T, to be named Neotabrizicola shimadae (= JCM 34381T = DSM 112087T). Strain N10T which is phylogenetically located among aerobic anoxygenic phototrophic bacteria (Tabrizicola), bacteriochlorophyll-deficient bacteria (Xinfangfangia) and anaerobic anoxygenic phototrophic bacteria (Rhodobacter) has great potential to promote studies on the evolution of photosynthesis in Rhodobacteraceae.
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Affiliation(s)
- So Muramatsu
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
| | - Setsuko Hirose
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
| | - Takao Iino
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Satoshi Hanada
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-0856, Japan
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan.
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Abstract
Microbial community diversity is often correlated with physical environmental stresses like acidity, salinity, and temperature. For example, species diversity usually declines with increasing temperature above 20°C. However, few studies have examined whether the genetic functional diversity of community metagenomes varies in a similar way as species diversity along stress gradients. Here, we investigated bacterial communities in thermal spring sediments ranging from 21 to 88°C, representing communities of 330 to 3,800 bacterial and archaeal species based on 16S rRNA gene amplicon analysis. Metagenomes were sequenced, and Pfam abundances were used as a proxy for metagenomic functional diversity. Significant decreases in both species diversity and Pfam diversity were observed with increasing temperatures. The relationship between Pfam diversity and species diversity followed a power function with the steepest slopes in the high-temperature, low-diversity region of the gradient. Species additions to simple thermophilic communities added many new Pfams, while species additions to complex mesophilic communities added relatively fewer new Pfams, indicating that species diversity does not approach saturation as rapidly as Pfam diversity does. Many Pfams appeared to have distinct temperature ceilings of 60 to 80°C. This study suggests that temperature stress limits both taxonomic and functional diversity of microbial communities, but in a quantitatively different manner. Lower functional diversity at higher temperatures is probably due to two factors, including (i) the absence of many enzymes not adapted to thermophilic conditions, and (ii) the fact that high-temperature communities are comprised of fewer species with smaller average genomes and, therefore, contain fewer rare functions. IMPORTANCE Only recently have microbial ecologists begun to assess quantitatively how microbial species diversity correlates with environmental factors like pH, temperature, and salinity. However, still, very few studies have examined how the number of distinct biochemical functions of microbial communities, termed functional diversity, varies with the same environmental factors. Our study examined 18 microbial communities sampled across a wide temperature gradient and found that increasing temperature reduced both species and functional diversity, but in different ways. Initially, functional diversity increased sharply with increasing species diversity but eventually plateaued, following a power function. This pattern has been previously predicted in theoretical models, but our study validates this predicted power function with field metagenomic data. This study also presents a unique overview of the distribution of metabolic functions along a temperature gradient, demonstrating that many functions have temperature "ceilings" above which they are no longer found.
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Sadeepa D, Sirisena K, Manage PM. Diversity of microbial communities in hot springs of Sri Lanka as revealed by 16S rRNA gene high-throughput sequencing analysis. Gene 2021; 812:146103. [PMID: 34896522 DOI: 10.1016/j.gene.2021.146103] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 11/01/2021] [Accepted: 11/16/2021] [Indexed: 01/16/2023]
Abstract
Characterization of hot spring microbiota is useful as an initial platform for exploring industrially important microbes. The present study focused on characterization of microbiota in four hot springs in Sri Lanka: Maha Oya; Wahava; Madunagala; and Kivlegama using high throughput 16S amplicon sequencing. Temperatures of the selected springs were ranged from 33.7 °C to 52.4 °C, whereas pH ranged from 7.2 to 8.2. Bacteria were found to be the dominant microbial group (>99%) compared to Archaea which represented less than 1% of microbiota. Four hot springs comprised of unique microbial community structures. Proteobacteria, Firmicutes, Bacteroidetes, Cloroflexi, Deinococcus and Actenobacteria were the major bacterial phyla. Moderately thermophilic genera such as Thermodesulfobacteria and Deinococcus-Thermus were detected as major genera that could be used in industrial applications operating at temperatures around 50 °C and alkaline reaction conditions.
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Affiliation(s)
- Dilini Sadeepa
- Centre for Water Quality and Algae Research, Department of Zoology, University of Sri Jayewardenepura, Gangodawila, Nugegoda 10250, Sri Lanka; Faculty of Graduate Studies, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka
| | - Kosala Sirisena
- Department of Environmental Technology, Faculty of Technology, University of Colombo, Sri Lanka
| | - Pathmalal M Manage
- Centre for Water Quality and Algae Research, Department of Zoology, University of Sri Jayewardenepura, Gangodawila, Nugegoda 10250, Sri Lanka; Faculty of Graduate Studies, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka.
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11
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Chen Y, Nishihara A, Iino T, Ohkuma M, Haruta S. Caldicellulosiruptor diazotrophicus sp. nov., a thermophilic, nitrogen-fixing fermentative bacterium isolated from a terrestrial hot spring in Japan. Int J Syst Evol Microbiol 2021; 71. [PMID: 34542397 DOI: 10.1099/ijsem.0.005014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel nitrogen-fixing fermentative bacterium, designated as YA01T, was isolated from Nakabusa hot springs in Japan. The short-rod cells of strain YA01T were Gram-positive and non-sporulating. Phylogenetic trees of the 16S rRNA gene sequence and concatenated sequences of 40 single-copy ribosomal genes revealed that strain YA01T belonged to the genus Caldicellulosiruptor and was closely related to Caldicellulosiruptor hydrothermalis 108T, Caldicellulosiruptor bescii DSM 6725T and Caldicellulosiruptor kronotskyensis 2002T. The 16S rRNA gene sequence of strain YA01T shares less than 98.1 % identity to the known Caldicellulosiruptor species. The G+C content of the genomic DNA was 34.8 mol%. Strain YA01T shares low genome-wide average nucleotide identity (90.31-91.10 %), average amino acid identity (91.45-92.10 %) and <70 % digital DNA-DNA hybridization value (41.8-44.2 %) with the three related species of the genus Caldicellulosiruptor. Strain YA01T grew at 50-78 °C (optimum, 70 °C) and at pH 5.0-9.5 (optimum, pH 6.5). Strain YA01T mainly produced acetate by consuming d(+)-glucose as a carbon source. The main cellular fatty acids were iso-C17 : 0 (35.7 %), C16 : 0 (33.3 %), DMA16 : 0 (6.6 %) and iso-C15 : 0 (5.9 %). Based on its distinct phylogenetic position, biochemical and physiological characteristics, and the major cellular fatty acids, strain YA01T is considered to represent a novel species of the genus Caldicellulosiruptor for which the name Caldicellulosiruptor diazotrophicus sp. nov. is proposed (type strain YA01T=DSM 112098T=JCM 34253T).
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Affiliation(s)
- Yuxin Chen
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Arisa Nishihara
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-0856, Japan
| | - Takao Iino
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan.,Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
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12
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Abstract
In recent years, natural thermal mineral waters have been gaining the special attention of the scientific community, namely in the prevention and treatment of some diseases, due to the microbial properties that exist in these habitats. The aim of this work was to characterize the physicochemical composition and the microbial taxonomic communities present in three thermal waters of the Galician region in Spain and two samples of the northern region in Portugal. These collected water samples were analyzed for physicochemical characterization and the respective hydrogenome of the waters using next generation sequencing together with 16S rRNA gene sequencing. The sequencing showed a high diversity of microorganisms in all analyzed waters; however, there is a clear bacterial predominance of Proteobacteria phylum, followed by Firmicutes, Deinococcus-Thermus, Aquificae and Nitrospira. The main physicochemical parameters responsible for the clustering within the Spanish waters were sulfur compounds (SO32− and S2−), CO32− and neutral pH, and in the Portuguese waters were Mg, Ca and Sr, nitrogen compounds (NO3− and NH4+), Na, Rb, conductivity and dry residue. This work will allow for a better understanding of the microbial community’s composition and how these microorganisms interfere in the physicochemical constitution of these waters often associated with medicinal properties. Furthermore, the hydrogenome may be used as an auxiliary tool in the practice of medical hydrology, increasing the likelihood of safe use of these unique water types.
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13
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Kawai S, Martinez JN, Lichtenberg M, Trampe E, Kühl M, Tank M, Haruta S, Nishihara A, Hanada S, Thiel V. In-Situ Metatranscriptomic Analyses Reveal the Metabolic Flexibility of the Thermophilic Anoxygenic Photosynthetic Bacterium Chloroflexus aggregans in a Hot Spring Cyanobacteria-Dominated Microbial Mat. Microorganisms 2021; 9:microorganisms9030652. [PMID: 33801086 PMCID: PMC8004040 DOI: 10.3390/microorganisms9030652] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/17/2021] [Accepted: 03/17/2021] [Indexed: 12/13/2022] Open
Abstract
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.
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Affiliation(s)
- Shigeru Kawai
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
- Correspondence: (S.K.); (V.T.)
| | - Joval N. Martinez
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- Department of Natural Sciences, College of Arts and Sciences, University of St. La Salle, Bacolod City, Negros Occidental 6100, Philippines
| | - Mads Lichtenberg
- Department of Biology, Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark; (M.L.); (E.T.); (M.K.)
| | - Erik Trampe
- Department of Biology, Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark; (M.L.); (E.T.); (M.K.)
| | - Michael Kühl
- Department of Biology, Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark; (M.L.); (E.T.); (M.K.)
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- DSMZ—German Culture Collection of Microorganisms and Cell Culture, GmbH Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
| | - Arisa Nishihara
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki 305-8566, Japan
| | - Satoshi Hanada
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- DSMZ—German Culture Collection of Microorganisms and Cell Culture, GmbH Inhoffenstraße 7B, 38124 Braunschweig, Germany
- Correspondence: (S.K.); (V.T.)
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14
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Izaki K, Haruta S. Aerobic Production of Bacteriochlorophylls in the Filamentous Anoxygenic Photosynthetic Bacterium, Chloroflexus aurantiacus in the Light. Microbes Environ 2020; 35. [PMID: 32418929 PMCID: PMC7308566 DOI: 10.1264/jsme2.me20015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Filamentous anoxygenic photosynthetic bacteria grow by photosynthesis and aerobic respiration. The present study investigated the effects of light and O2 on bacteriochlorophyll contents and the transcription levels of photosynthesis-related genes in Chloroflexus aurantiacus J-10-fl T. Under aerobic conditions, C. aurantiacus produced marked amounts of bacteriochlorophylls in the presence of light, although their production was strongly suppressed in the dark. The transcription levels of genes related to the synthesis of bacteriochlorophylls, photosystems, and chlorosomes: bchM, bchU, pufL, pufBA, and csmM, were markedly increased by illumination. These results suggest that C. aurantiacus continuously synthesizes ATP by photophosphorylation even in the presence of O2.
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Affiliation(s)
- Kazaha Izaki
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University
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15
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The Role of Thermal Water in Chronic Skin Diseases Management: A Review of the Literature. J Clin Med 2020; 9:jcm9093047. [PMID: 32971735 PMCID: PMC7563194 DOI: 10.3390/jcm9093047] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/08/2020] [Accepted: 09/14/2020] [Indexed: 01/06/2023] Open
Abstract
The benefits of thermal water in different diseases have been known since ancient times. Over the past decades, a re-assessment of the use of mineral water for the treatment of several pathologic conditions has taken place around the world. Today, water therapy is being practiced in many countries that have a variety of mineral springs considerably different in their hydrogeologic origin, temperature, and chemical composition. Thermal water and balneotherapy offer several advantages: this approach needs no chemicals or potentially harmful drugs; there are almost no side effects during and after treatment, and there is a low risk to the patient’s general health and well-being. However, it is difficult to evaluate the efficacy of this therapeutic approach in clinical practice due to the complexity of molecular mechanisms underlying its efficacy. Here we review the current knowledge of the chemical, immunological, and microbiological basis for therapeutic effects of thermal water with a specific focus on chronic inflammatory skin diseases. We also describe recent evidence of the major dermatologic diseases that are frequently treated by balneotherapy with a remarkable rate of success. Moreover, we discuss the potential role of balneotherapy either alone or as a complement to conventional medical treatments.
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16
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Kawai S, Nishihara A, Matsuura K, Haruta S. Hydrogen-dependent autotrophic growth in phototrophic and chemolithotrophic cultures of thermophilic bacteria, Chloroflexus aggregans and Chloroflexus aurantiacus, isolated from Nakabusa hot springs. FEMS Microbiol Lett 2020; 366:5510454. [PMID: 31158281 DOI: 10.1093/femsle/fnz122] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/01/2019] [Indexed: 11/14/2022] Open
Abstract
The genus Chloroflexus is a deeply branching group of thermophilic filamentous anoxygenic phototrophic bacteria. The bacteria in this genus have been shown to grow well heterotrophically under anaerobic photosynthetic and aerobic respiratory conditions. We examined autotrophic growth in new isolates of Chloroflexus strains from hot springs in Nakabusa, Japan. The isolates belonging to Chloroflexus aggregans (98.7% identity of 16S rRNA gene sequence to the respective type strain) and Chloroflexus aurantiacus (99.9% identity to the respective type strain) grew photoautotrophically under a 24% H2 atmosphere. We also observed chemolithotrophic growth of these isolates under 80% H2 and 5% O2 conditions in the dark. This is the first report showing that Chloroflexus grew under both photoautotrophic and chemolithotrophic conditions in addition to photoheterotrophic and aerobic chemoheterotrophic conditions.
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Affiliation(s)
- Shigeru Kawai
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Arisa Nishihara
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Katsumi Matsuura
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Shin Haruta
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
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17
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Microbiome and ecology of a hot spring-microbialite system on the Trans-Himalayan Plateau. Sci Rep 2020; 10:5917. [PMID: 32246033 PMCID: PMC7125080 DOI: 10.1038/s41598-020-62797-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 03/17/2020] [Indexed: 11/30/2022] Open
Abstract
Little is known about life in the boron-rich hot springs of Trans-Himalayas. Here, we explore the geomicrobiology of a 4438-m-high spring which emanates ~70 °C-water from a boratic microbialite called Shivlinga. Due to low atmospheric pressure, the vent-water is close to boiling point so can entropically destabilize biomacromolecular systems. Starting from the vent, Shivlinga’s geomicrobiology was revealed along the thermal gradients of an outflow-channel and a progressively-drying mineral matrix that has no running water; ecosystem constraints were then considered in relation to those of entropically comparable environments. The spring-water chemistry and sinter mineralogy were dominated by borates, sodium, thiosulfate, sulfate, sulfite, sulfide, bicarbonate, and other macromolecule-stabilizing (kosmotropic) substances. Microbial diversity was high along both of the hydrothermal gradients. Bacteria, Eukarya and Archaea constituted >98%, ~1% and <1% of Shivlinga’s microbiome, respectively. Temperature constrained the biodiversity at ~50 °C and ~60 °C, but not below 46 °C. Along each thermal gradient, in the vent-to-apron trajectory, communities were dominated by Aquificae/Deinococcus-Thermus, then Chlorobi/Chloroflexi/Cyanobacteria, and finally Bacteroidetes/Proteobacteria/Firmicutes. Interestingly, sites of >45 °C were inhabited by phylogenetic relatives of taxa for which laboratory growth is not known at >45 °C. Shivlinga’s geomicrobiology highlights the possibility that the system’s kosmotrope-dominated chemistry mitigates against the biomacromolecule-disordering effects of its thermal water.
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18
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Iino T, Kawai S, Yuki M, Dekio I, Ohkuma M, Haruta S. Thermaurantimonas aggregans gen. nov., sp. nov., a moderately thermophilic heterotrophic aggregating bacterium isolated from microbial mats at a terrestrial hot spring. Int J Syst Evol Microbiol 2020; 70:1117-1121. [DOI: 10.1099/ijsem.0.003888] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Takao Iino
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Shigeru Kawai
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Masahiro Yuki
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Itaru Dekio
- Skin Microbe Laboratory, Mildix Skin Clinic, 3rd Floor, 3-98 Senju, Adachi-ku, Tokyo 120-0034, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
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19
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Cheng YI, Chou L, Chiu YF, Hsueh HT, Kuo CH, Chu HA. Comparative Genomic Analysis of a Novel Strain of Taiwan Hot-Spring Cyanobacterium Thermosynechococcus sp. CL-1. Front Microbiol 2020; 11:82. [PMID: 32082292 PMCID: PMC7005997 DOI: 10.3389/fmicb.2020.00082] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 01/15/2020] [Indexed: 11/22/2022] Open
Abstract
Thermosynechococcus is a genus of thermophilic unicellular cyanobacteria that are dominant in microbial mats at about 50–65°C in alkaline hot springs of eastern Asia. We used PacBio SMRT Sequencing to sequence the complete genome of a novel strain of thermophilic cyanobacterium, Thermosynechococcus sp. CL-1, isolated from the Chin-Lun hot spring (pH 9.3, 62°C) in Taiwan. Genome-scale phylogenetic analysis and average nucleotide identity (ANI) results suggested that CL-1 is a new species in the genus Thermosynechococcus. Comparative genome analysis revealed divergent genome structures of Thermosynechococcus strains. In addition, the distinct genetic differences between CL-1 and the other Thermosynechococcus strains are related to photosynthesis, transporters, signal transduction, the chaperone/usher system, nitric oxide protection, antibiotic resistance, prokaryotic immunity systems, and other physiological processes. This study suggests that Thermosynechococcus strains have actively acquired many putative horizontally transferred genes from other bacteria that enabled them to adapt to different ecological niches and stressful conditions in hot springs.
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Affiliation(s)
- Yen-I Cheng
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Lin Chou
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Fang Chiu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Hsin-Ta Hsueh
- Sustainable Environment Research Laboratories, National Cheng Kung University, Tainan, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Hsiu-An Chu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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20
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Martinez JN, Nishihara A, Lichtenberg M, Trampe E, Kawai S, Tank M, Kühl M, Hanada S, Thiel V. Vertical Distribution and Diversity of Phototrophic Bacteria within a Hot Spring Microbial Mat (Nakabusa Hot Springs, Japan). Microbes Environ 2019; 34:374-387. [PMID: 31685759 PMCID: PMC6934398 DOI: 10.1264/jsme2.me19047] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Phototrophic microbial mats are assemblages of vertically layered microbial populations dominated by photosynthetic microorganisms. In order to elucidate the vertical distribution and diversity of phototrophic microorganisms in a hot spring-associated microbial mat in Nakabusa (Japan), we analyzed the 16S rRNA gene amplicon sequences of the microbial mat separated into five depth horizons, and correlated them with microsensor measurements of O2 and spectral scalar irradiance. A stable core community and high diversity of phototrophic organisms dominated by the filamentous anoxygenic phototrophs, Roseiflexus castenholzii and Chloroflexus aggregans were identified together with the spectral signatures of bacteriochlorophylls (BChls) a and c absorption in all mat layers. In the upper mat layers, a high abundance of cyanobacteria (Thermosynechococcus sp.) correlated with strong spectral signatures of chlorophyll a and phycobiliprotein absorption near the surface in a zone of high O2 concentrations during the day. Deeper mat layers were dominated by uncultured chemotrophic Chlorobi such as the novel putatively sulfate-reducing “Ca. Thermonerobacter sp.”, which showed increasing abundance with depth correlating with low O2 in these layers enabling anaerobic metabolism. Oxygen tolerance and requirements for the novel phototroph “Ca. Chloroanaerofilum sp.” and the uncultured chemotrophic Armatimonadetes member type OS-L detected in Nakabusa hot springs, Japan appeared to differ from previously suggested lifestyles for close relatives identified in hot springs in Yellowstone National Park, USA. The present study identified various microenvironmental gradients and niche differentiation enabling the co-existence of diverse chlorophototrophs in metabolically diverse communities in hot springs.
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Affiliation(s)
- Joval N Martinez
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University.,Department of Natural Sciences, College of Arts and Sciences, University of St. La Salle
| | - Arisa Nishihara
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Mads Lichtenberg
- Marine Biological Section, Department of Biology, University of Copenhagen
| | - Erik Trampe
- Marine Biological Section, Department of Biology, University of Copenhagen
| | - Shigeru Kawai
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University
| | - Marcus Tank
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen
| | - Satoshi Hanada
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University
| | - Vera Thiel
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University
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21
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Kanno N, Haruta S, Hanada S. Sulfide-dependent Photoautotrophy in the Filamentous Anoxygenic Phototrophic Bacterium, Chloroflexus aggregans. Microbes Environ 2019; 34:304-309. [PMID: 31391357 PMCID: PMC6759344 DOI: 10.1264/jsme2.me19008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Chloroflexus aggregans is a thermophilic filamentous anoxygenic phototrophic bacterium frequently found in microbial mats in natural hot springs. C. aggregans often thrives with cyanobacteria that engage in photosynthesis to provide it with an organic substrate; however, it sometimes appears as the dominant phototroph in microbial mats without cyanobacteria. This suggests that C. aggregans has the ability to grow photoautotrophically. However, photoautotrophic growth has not been observed in any cultured strains of C. aggregans. We herein attempted to isolate a photoautotrophic strain from C. aggregansdominated microbial mats in Nakabusa hot spring in Japan. Using an inorganic medium, we succeeded in isolating a new strain that we designated "ACA-12". A phylogenetic analysis based on 16S rRNA gene and 16S-23S rRNA gene internal transcribed spacer (ITS) region sequences revealed that strain ACA-12 was closely related to known C. aggregans strains. Strain ACA-12 showed sulfide consumption along with autotrophic growth under anaerobic light conditions. The deposited elemental sulfur particles observed by microscopy indicated that sulfide oxidation occurred, similar to that in photoautotrophic strains in the related species, C. aurantiacus. Moreover, we found that other strains of C. aggregans, including the type strain, also exhibited a slight photoautotrophic growing ability, whereas strain ACA-12 showed the fastest growth rate. This is the first demonstration of photoautotrophic growth with sulfide in C. aggregans. The present results strongly indicate that C. aggregans is associated with inorganic carbon incorporation using sulfide as an electron donor in hot spring microbial mats.
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Affiliation(s)
- Nanako Kanno
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University
| | - Shin Haruta
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University
| | - Satoshi Hanada
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University
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22
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Uribe-Lorío L, Brenes-Guillén L, Hernández-Ascencio W, Mora-Amador R, González G, Ramírez-Umaña CJ, Díez B, Pedrós-Alió C. The influence of temperature and pH on bacterial community composition of microbial mats in hot springs from Costa Rica. Microbiologyopen 2019; 8:e893. [PMID: 31271524 PMCID: PMC6813449 DOI: 10.1002/mbo3.893] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/01/2019] [Accepted: 05/20/2019] [Indexed: 11/27/2022] Open
Abstract
We used the 16S rRNA gene pyrosequencing approach to investigate the microbial diversity and community composition in several Costa Rican hot springs alongside the latitudinal axis of the country, with a range of temperatures (37–63°C), pH (6–7.5) and other geochemical conditions. A principal component analyses of the physicochemical parameters showed the samples were separated into three geochemically distinct habitats associated with the location (North, Central, and South). Cyanobacteria and Chloroflexi comprised 93% of the classified community, the former being the most abundant phylum in all samples except for Rocas Calientes 1, (63°C, pH 6), where Chloroflexi and Deinococcus‐Thermus represented 84% of the OTUs. Chloroflexi were more abundant as temperature increased. Proteobacteria, Bacteriodetes and Deinococcus‐Thermus comprised 5% of the OTUs represented. Other Phyla were present in very small percentages (<1%). A LINKTREE analysis showed that the community structure of the mats was shaped primarily by pH, separating samples with pH > 6.6 from samples with pH < 6.4. Thus, both pH and temperature were relevant for community composition even within the moderate ranges of variables studied. These results provide a basis for an understanding of the physicochemical influences in moderately thermophilic microbial mats.
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Affiliation(s)
- Lorena Uribe-Lorío
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, Ciudad Universitaria Rodrigo Facio, San José, Costa Rica
| | - Laura Brenes-Guillén
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, Ciudad Universitaria Rodrigo Facio, San José, Costa Rica
| | - Walter Hernández-Ascencio
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, Ciudad Universitaria Rodrigo Facio, San José, Costa Rica
| | - Raúl Mora-Amador
- Escuela Centroamericana de Geología, Universidad de Costa Rica, San José, Costa Rica
| | - Gino González
- Escuela Centroamericana de Geología, Universidad de Costa Rica, San José, Costa Rica
| | | | - Beatriz Díez
- Departamento de Microbiología y Genética, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carlos Pedrós-Alió
- Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
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23
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Kawai S, Kamiya N, Matsuura K, Haruta S. Symbiotic Growth of a Thermophilic Sulfide-Oxidizing Photoautotroph and an Elemental Sulfur-Disproportionating Chemolithoautotroph and Cooperative Dissimilatory Oxidation of Sulfide to Sulfate. Front Microbiol 2019; 10:1150. [PMID: 31178849 PMCID: PMC6543001 DOI: 10.3389/fmicb.2019.01150] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 05/06/2019] [Indexed: 11/13/2022] Open
Abstract
A thermophilic filamentous anoxygenic photosynthetic bacterium, Chloroflexus aggregans, is widely distributed in neutral to slightly alkaline hot springs. Sulfide has been suggested as an electron donor for autotrophic growth in microbial mats dominated with C. aggregans, but remarkable photoautotrophic growth of isolated C. aggregans has not been observed with sulfide as the sole electron source. From the idea that sulfide is oxidized to elemental sulfur by C. aggregans and the accumulation of elemental sulfur may have an inhibitory effect for the growth, the effects of an elemental sulfur-disproportionating bacterium that consumes elemental sulfur was examined on the autotrophic growth of C. aggregans, strain NA9-6, isolated from Nakabusa hot spring. A sulfur-disproportionating bacterium, Caldimicrobium thiodismutans strain TF1, also isolated from Nakabusa hot spring was co-cultured with C. aggregans. C. aggregans and C. thiodismutans were successfully co-cultured in a medium containing thiosulfate as the sole electron source and bicarbonate as the sole carbon source. Quantitative conversion of thiosulfate to sulfate and a small transient accumulation of sulfide was observed in the co-culture. Then the electron source of the established co-culture was changed from thiosulfate to sulfide, and the growth of C. aggregans and C. thiodismutans was successfully observed with sulfide as the sole electron donor for the autotrophic growth of the co-culture. During the cultivation in the light, simultaneous consumption and accumulation of sulfide and sulfate, respectively, were observed, accompanied with the increase of cellular DNAs of both species. C. thiodismutans likely works as an elemental sulfur scavenger for C. aggregans, and C. aggregans seems to work as a sulfide scavenger for C. thiodismutans. These results suggest that C. aggregans grows autotrophically with sulfide as the electron donor in the co-culture with C. thiodismutans, and the consumption of elemental sulfur by C. thiodismutans enabled the continuous growth of the C. aggregans in the symbiotic system. This study shows a novel symbiotic relationship between a sulfide-oxidizing photoautotroph and an elemental sulfur-disproportionating chemolithoautotroph via cooperative dissimilatory sulfide oxidation to sulfate.
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Affiliation(s)
- Shigeru Kawai
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Naoki Kamiya
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Katsumi Matsuura
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
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24
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Merino N, Aronson HS, Bojanova DP, Feyhl-Buska J, Wong ML, Zhang S, Giovannelli D. Living at the Extremes: Extremophiles and the Limits of Life in a Planetary Context. Front Microbiol 2019; 10:780. [PMID: 31037068 PMCID: PMC6476344 DOI: 10.3389/fmicb.2019.00780] [Citation(s) in RCA: 198] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/27/2019] [Indexed: 01/21/2023] Open
Abstract
Prokaryotic life has dominated most of the evolutionary history of our planet, evolving to occupy virtually all available environmental niches. Extremophiles, especially those thriving under multiple extremes, represent a key area of research for multiple disciplines, spanning from the study of adaptations to harsh conditions, to the biogeochemical cycling of elements. Extremophile research also has implications for origin of life studies and the search for life on other planetary and celestial bodies. In this article, we will review the current state of knowledge for the biospace in which life operates on Earth and will discuss it in a planetary context, highlighting knowledge gaps and areas of opportunity.
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Affiliation(s)
- Nancy Merino
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Lab, Livermore, CA, United States
| | - Heidi S Aronson
- Department of Biology, University of Southern California, Los Angeles, CA, United States
| | - Diana P Bojanova
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Jayme Feyhl-Buska
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Michael L Wong
- Department of Astronomy - Astrobiology Program, University of Washington, Seattle, WA, United States.,NASA Astrobiology Institute's Virtual Planetary Laboratory, University of Washington, Seattle, WA, United States
| | - Shu Zhang
- Section of Infection and Immunity, Herman Ostrow School of Dentistry of USC, University of Southern California, Los Angeles, CA, United States
| | - Donato Giovannelli
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Department of Biology, University of Naples "Federico II", Naples, Italy.,Department of Marine and Coastal Science, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States.,Institute for Biological Resources and Marine Biotechnology, National Research Council of Italy, Ancona, Italy
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25
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Nishihara A, Thiel V, Matsuura K, McGlynn SE, Haruta S. Phylogenetic Diversity of Nitrogenase Reductase Genes and Possible Nitrogen-Fixing Bacteria in Thermophilic Chemosynthetic Microbial Communities in Nakabusa Hot Springs. Microbes Environ 2018; 33:357-365. [PMID: 30404970 PMCID: PMC6307998 DOI: 10.1264/jsme2.me18030] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Chemosynthetic microbial communities develop and form dense cell aggregates in slightly alkaline sulfidic hot springs in the temperature range of 70–86°C at Nakabusa, Japan. Nitrogenase activity has recently been detected in the microbial communities collected. To identify possible members capable of nitrogen fixation, we examined the diversities of 16S rRNA and nitrogenase reductase (NifH) gene sequences in four types of chemosynthetic communities with visually different colors and thicknesses. The results of a 16S rRNA gene analysis indicated that all four microbial communities had similar bacterial constituents; the phylum Aquificae was the dominant member, followed in abundance by Thermodesulfobacteria, Firmicutes, and Thermotogae. Most of the NifH sequences were related to sequences reported in hydrothermal vents and terrestrial hot springs. The results of a phylogenetic analysis of NifH sequences revealed diversity in this gene among the communities collected, distributed within 7 phylogenetic groups. NifH sequences affiliated with Aquificae (Hydrogenobacter/Thermocrinis) and Firmicutes (Caldicellulosiruptor) were abundant. At least two different energy metabolic pathways appeared to be related to nitrogen fixation in the communities analyzed; aerobic sulfur/hydrogen-oxidizing bacteria in Aquificae and fermentative bacteria in Firmicutes. The metabolic characteristics of these two dominant phyla differed from those previously inferred from nitrogenase activity assays on chemosynthetic communities, which were associated with hydrogen-dependent autotrophic sulfate reduction. These assays may correspond to the observed NifH sequences that are distantly related to the known species of Thermodesulfovibrio sp. (Nitrospirae) detected in the present study. The activities of nitrogen-fixing organisms in communities may depend on redox states as well as the availability of electron donors, acceptors, and carbon sources.
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Affiliation(s)
- Arisa Nishihara
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Katsumi Matsuura
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Shawn E McGlynn
- Department of Biological Sciences, Tokyo Metropolitan University.,Earth-Life Science Institute, Tokyo Institute of Technology.,Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science.,Blue Marble Space Institute of Science
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University
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26
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Tang J, Liang Y, Jiang D, Li L, Luo Y, Shah MMR, Daroch M. Temperature-controlled thermophilic bacterial communities in hot springs of western Sichuan, China. BMC Microbiol 2018; 18:134. [PMID: 30332987 PMCID: PMC6191902 DOI: 10.1186/s12866-018-1271-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 09/27/2018] [Indexed: 12/13/2022] Open
Abstract
Background Ganzi Prefecture in Western China is situated geographically at the transition regions between Tibetan Plateau and Sichuan Basin in a highly tectonically active boundary area between the India and Eurasia plates. The region hosts various hot springs that span a wide range of temperature from 30 to 98 °C and are located at high altitude (up to 4200 m above sea level) in the region of large geothermal anomalies and active Xianshuihe slip-fault that has been active since Holocene. The site represents a biodiversity reservoir for thermophiles, yet their diversity and relationship to geochemical parameters are largely unknown. In the present work, bacterial diversity and community structure in 14 hot springs of Ganzi were investigated using Illumina MiSeq sequencing. Results Bacterial community compositions were evidently distinct among the 14 hot springs, and the bacterial communities in hot springs were majorly abundant in phyla Aquificae, Cyanobacteria and Proteobacteria. Both clustering and PCoA analysis suggested the existence of four bacterial community patterns in these hot springs. Temperature contributed to shaping bacterial community structure of hot springs as revealed by correlation analysis. Abundant unassigned-genus sequences detected in this study strongly implied the presence of novel genera or genetic resources in these hot springs. Conclusion The diversity of hot springs of Ganzi prefecture in Western Sichuan, China is evidently shaped by temperature. Interestingly disproportionally abundant unassigned-genus sequences detected in this study show indicate potential of novel genera or phylotypes. We hypothesize that frequent earthquakes and rapidly changing environment might have contributed to evolution of these potentially new lineages. Overall, this study provided first insight into the bacterial diversity of hot springs located in Western Sichuan, China and its comparison with other similar communities worldwide. Electronic supplementary material The online version of this article (10.1186/s12866-018-1271-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jie Tang
- School of Pharmacy and Bioengineering, Chengdu University, Chengdu, 610106, China
| | - Yuanmei Liang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Dong Jiang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Liheng Li
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Yifan Luo
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Md Mahfuzur R Shah
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
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27
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Lavrentyeva EV, Radnagurueva AA, Barkhutova DD, Belkova NL, Zaitseva SV, Namsaraev ZB, Gorlenko VM, Namsaraev BB. Bacterial Diversity and Functional Activity of Microbial Communities in Hot Springs of the Baikal Rift Zone. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718020078] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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28
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Nishihara A, Haruta S, McGlynn SE, Thiel V, Matsuura K. Nitrogen Fixation in Thermophilic Chemosynthetic Microbial Communities Depending on Hydrogen, Sulfate, and Carbon Dioxide. Microbes Environ 2018; 33:10-18. [PMID: 29367473 PMCID: PMC5877335 DOI: 10.1264/jsme2.me17134] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/28/2017] [Indexed: 12/20/2022] Open
Abstract
The activity of nitrogen fixation measured by acetylene reduction was examined in chemosynthetic microbial mats at 72-75°C in slightly-alkaline sulfidic hot springs in Nakabusa, Japan. Nitrogenase activity markedly varied from sampling to sampling. Nitrogenase activity did not correlate with methane production, but was detected in samples showing methane production levels less than the maximum amount, indicating a possible redox dependency of nitrogenase activity. Nitrogenase activity was not affected by 2-bromo-ethane sulfonate, an inhibitor of methanogenesis. However, it was inhibited by the addition of molybdate, an inhibitor of sulfate reduction and sulfur disproportionation, suggesting the involvement of sulfate-reducing or sulfur-disproportionating organisms. Nitrogenase activity was affected by different O2 concentrations in the gas phase, again supporting the hypothesis of a redox potential dependency, and was decreased by the dispersion of mats with a homogenizer. The loss of activity that occurred from dispersion was partially recovered by the addition of H2, sulfate, and carbon dioxide. These results suggested that the observed activity of nitrogen fixation was related to chemoautotrophic sulfate reducers, and fixation may be active in a limited range of ambient redox potential. Since thermophilic chemosynthetic communities may resemble ancient microbial communities before the appearance of photosynthesis, the present results may be useful when considering the ancient nitrogen cycle on earth.
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Affiliation(s)
- Arisa Nishihara
- Department of Biological Sciences, Tokyo Metropolitan UniversityMinami-Osawa, Hachioji, Tokyo 192–0397Japan
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan UniversityMinami-Osawa, Hachioji, Tokyo 192–0397Japan
| | - Shawn E. McGlynn
- Department of Biological Sciences, Tokyo Metropolitan UniversityMinami-Osawa, Hachioji, Tokyo 192–0397Japan
- Earth-Life Science Institute, Tokyo Institute of TechnologyOokayama, Meguro-ku, Tokyo 152–8551Japan
- Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource ScienceWako-shi 351–0198Japan
- Blue Marble Space Institute of ScienceSeattle, WA 98145–1561USA
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan UniversityMinami-Osawa, Hachioji, Tokyo 192–0397Japan
| | - Katsumi Matsuura
- Department of Biological Sciences, Tokyo Metropolitan UniversityMinami-Osawa, Hachioji, Tokyo 192–0397Japan
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29
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Ward LM, Hemp J, Shih PM, McGlynn SE, Fischer WW. Evolution of Phototrophy in the Chloroflexi Phylum Driven by Horizontal Gene Transfer. Front Microbiol 2018. [PMID: 29515543 PMCID: PMC5826079 DOI: 10.3389/fmicb.2018.00260] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The evolutionary mechanisms behind the extant distribution of photosynthesis is a point of substantial contention. Hypotheses range from the presence of phototrophy in the last universal common ancestor and massive gene loss in most lineages, to a later origin in Cyanobacteria followed by extensive horizontal gene transfer into the extant phototrophic clades, with intermediate scenarios that incorporate aspects of both end-members. Here, we report draft genomes of 11 Chloroflexi: the phototrophic Chloroflexia isolate Kouleothrix aurantiaca as well as 10 genome bins recovered from metagenomic sequencing of microbial mats found in Japanese hot springs. Two of these metagenome bins encode photrophic reaction centers and several of these bins form a metabolically diverse, monophyletic clade sister to the Anaerolineae class that we term Candidatus Thermofonsia. Comparisons of organismal (based on conserved ribosomal) and phototrophy (reaction center and bacteriochlorophyll synthesis) protein phylogenies throughout the Chloroflexi demonstrate that two new lineages acquired phototrophy independently via horizontal gene transfer (HGT) from different ancestral donors within the classically phototrophic Chloroflexia class. These results illustrate a complex history of phototrophy within this group, with metabolic innovation tied to HGT. These observations do not support simple hypotheses for the evolution of photosynthesis that require massive character loss from many clades; rather, HGT appears to be the defining mechanic for the distribution of phototrophy in many of the extant clades in which it appears.
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Affiliation(s)
- Lewis M Ward
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| | - James Hemp
- Department of Gastroenterology, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Patrick M Shih
- Department of Energy, Joint BioEnergy Institute, Emeryville, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Japan
| | - Woodward W Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
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30
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Effect of light wavelength on hot spring microbial mat biodiversity. PLoS One 2018; 13:e0191650. [PMID: 29381713 PMCID: PMC5790269 DOI: 10.1371/journal.pone.0191650] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 01/09/2018] [Indexed: 11/19/2022] Open
Abstract
Hot spring associated phototrophic microbial mats are purely microbial communities, in which phototrophic bacteria function as primary producers and thus shape the community. The microbial mats at Nakabusa hot springs in Japan harbor diverse photosynthetic bacteria, mainly Thermosynechococcus, Chloroflexus, and Roseiflexus, which use light of different wavelength for energy conversion. The aim of this study was to investigate the effect of the phototrophs on biodiversity and community composition in hot spring microbial mats. For this, we specifically activated the different phototrophs by irradiating the mats with different wavelengths in situ. We used 625, 730, and 890 nm wavelength LEDs alone or in combination and confirmed the hypothesized increase in relative abundance of different phototrophs by 16S rRNA gene sequencing. In addition to the increase of the targeted phototrophs, we studied the effect of the different treatments on chemotrophic members. The specific activation of Thermosynechococcus led to increased abundance of several other bacteria, whereas wavelengths specific to Chloroflexus and Roseiflexus induced a decrease in >50% of the community members as compared to the dark conditions. This suggests that the growth of Thermosynechococcus at the surface layer benefits many community members, whereas less benefit is obtained from an increase in filamentous anoxygenic phototrophs Chloroflexus and Roseiflexus. The increases in relative abundance of chemotrophs under different light conditions suggest a relationship between the two groups. Aerobic chemoheterotrophs such as Thermus sp. and Meiothermus sp. are thought to benefit from aerobic conditions and organic carbon in the form of photosynthates by Thermosynechococcus, while the oxidation of sulfide and production of elemental sulfur by filamentous anoxygenic phototrophs benefit the sulfur-disproportionating Caldimicrobium thiodismutans. In this study, we used an experimental approach under controlled environmental conditions for the analysis of natural microbial communities, which proved to be a powerful tool to study interspecies relationships in the microbiome.
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31
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Rozanov AS, Bryanskaya AV, Ivanisenko TV, Malup TK, Peltek SE. Biodiversity of the microbial mat of the Garga hot spring. BMC Evol Biol 2017; 17:254. [PMID: 29297382 PMCID: PMC5751763 DOI: 10.1186/s12862-017-1106-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Microbial mats are a good model system for ecological and evolutionary analysis of microbial communities. There are more than 20 alkaline hot springs on the banks of the Barguzin river inflows. Water temperature reaches 75 °C and pH is usually 8.0-9.0. The formation of microbial mats is observed in all hot springs. Microbial communities of hot springs of the Baikal rift zone are poorly studied. Garga is the biggest hot spring in this area. RESULTS In this study, we investigated bacterial and archaeal diversity of the Garga hot spring (Baikal rift zone, Russia) using 16S rRNA metagenomic sequencing. We studied two types of microbial communities: (i) small white biofilms on rocks in the points with the highest temperature (75 °C) and (ii) continuous thick phototrophic microbial mats observed at temperatures below 70 °C. Archaea (mainly Crenarchaeota; 19.8% of the total sequences) were detected only in the small biofilms. The high abundance of Archaea in the sample from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. In the microbial mats, primary products were formed by cyanobacteria of the genus Leptolyngbya. Heterotrophic microorganisms were mostly represented by Actinobacteria and Proteobacteria in all studied samples of the microbial mats. Planctomycetes, Chloroflexi, and Chlorobi were abundant in the middle layer of the microbial mats, while heterotrophic microorganisms represented mostly by Firmicutes (Clostridia, strict anaerobes) dominated in the bottom part. Besides prokaryotes, we detect some species of Algae with help of detection their chloroplasts 16 s rRNA. CONCLUSIONS High abundance of Archaea in samples from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. Metagenomic analysis of microbial communities of the microbial mat of Garga hot spring showed that the three studied points sampled at 70 °C, 55 °C, and 45 °C had similar species composition. Cyanobacteria of the genus Leptolyngbya dominated in the upper layer of the microbial mat. Chloroflexi and Chlorobi were less abundant and were mostly observed in the middle part of the microbial mat. We detected domains of heterotrophic organisms in high abundance (Proteobacteria, Firmicutes, Verrucomicrobia, Planctomicetes, Bacteroidetes, Actinobacteria, Thermi), according to metabolic properties of known relatives, which can form complete cycles of carbon, sulphur, and nitrogen in the microbial mat. The studied microbial mats evolved in early stages of biosphere formation. They can live autonomously, providing full cycles of substances and preventing live activity products poisoning.
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Affiliation(s)
- Alexey Sergeevich Rozanov
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
| | - Alla Victorovna Bryanskaya
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Timofey Vladimirovich Ivanisenko
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Tatyana Konstantinovna Malup
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergey Evgenievich Peltek
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Differences in Temperature and Water Chemistry Shape Distinct Diversity Patterns in Thermophilic Microbial Communities. Appl Environ Microbiol 2017; 83:AEM.01363-17. [PMID: 28821552 DOI: 10.1128/aem.01363-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/11/2017] [Indexed: 01/22/2023] Open
Abstract
This report describes the biodiversity and ecology of microbial mats developed in thermal gradients (20 to 65°C) in the surroundings of three drillings (Chiraleu [CH], Ciocaia [CI], and Mihai Bravu [MB]) tapping a hyperthermal aquifer in Romania. Using a metabarcoding approach, 16S rRNA genes were sequenced from both DNA and RNA transcripts (cDNA) and compared. The relationships between the microbial diversity and the physicochemical factors were explored. Additionally, the cDNA data were used for in silico functionality predictions, bringing new insights into the functional potential and dynamics of these communities. The results showed that each hot spring determined the formation of distinct microbial communities. In the CH mats (40 to 53°C), the abundance of Cyanobacteria decreased with temperature, opposite to those of Chloroflexi and ProteobacteriaEctothiorhodospira, Oscillatoria, and methanogenic archaea dominated the CI communities (20 to 65°C), while the MB microbial mats (53 to 65°C) were mainly composed of Chloroflexi, Hydrogenophilus, Thermi, and Aquificae Alpha-diversity was negatively correlated with the increase in water temperature, while beta-diversity was shaped in each hot spring by the unique combination of physicochemical parameters, regardless of the type of nucleic acid analyzed (DNA versus cDNA). The rank correlation analysis revealed a unique model that associated environmental data with community composition, consisting in the combined effect of Na+, K+, HCO3-, and PO43- concentrations, together with temperature and electrical conductivity. These factors seem to determine the grouping of samples according to location, rather than with the similarities in thermal regimes, showing that other parameters beside temperature are significant drivers of biodiversity.IMPORTANCE Hot spring microbial mats represent a remarkable manifestation of life on Earth and have been intensively studied for decades. Moreover, as hot spring areas are isolated and have a limited exchange of organisms, nutrients, and energy with the surrounding environments, hot spring microbial communities can be used in model studies to elucidate the colonizing potential within extreme settings. Thus, they are of great importance in evolutionary biology, microbial ecology, and exobiology. In spite of all the efforts that have been made, the current understanding of the influence of temperature and water chemistry on the microbial community composition, diversity, and abundance in microbial mats is limited. In this study, the composition and diversity of microbial communities developed in thermal gradients in the vicinity of three hot springs from Romania were investigated, each having particular physicochemical characteristics. Our results expose new factors that could determine the formation of these ecosystems, expanding the current knowledge in this regard.
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Ohkubo S, Miyashita H. A niche for cyanobacteria producing chlorophyll f within a microbial mat. THE ISME JOURNAL 2017; 11:2368-2378. [PMID: 28622287 PMCID: PMC5607378 DOI: 10.1038/ismej.2017.98] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 05/03/2017] [Accepted: 05/15/2017] [Indexed: 11/09/2022]
Abstract
Acquisition of additional photosynthetic pigments enables photosynthetic organisms to survive in particular niches. To reveal the ecological significance of chlorophyll (Chl) f, we investigated the distribution of Chl and cyanobacteria within two microbial mats. In a 7-mm-thick microbial mat beneath the running water of the Nakabusa hot spring, Japan, Chl f was only distributed 4.0-6.5 mm below the surface, where the intensity of far-red light (FR) was higher than that of photosynthetically active radiation (PAR). In the same mat, two ecotypes of Synechococcus and two ecotypes of Chl f-producing Leptolyngbya were detected in the upper and deeper layers, respectively. Only the Leptolyngbya strains could grow when FR was the sole light source. These results suggest that the deeper layer of the microbial mat was a habitat for Chl f-producing cyanobacteria, and Chl f enabled them to survive in a habitat with little PAR.
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Affiliation(s)
- Satoshi Ohkubo
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Hideaki Miyashita
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
- Graduate School of Global and Environmental Studies, Kyoto University, Kyoto, Japan
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34
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Poddar A, Das SK. Microbiological studies of hot springs in India: a review. Arch Microbiol 2017; 200:1-18. [PMID: 28887679 DOI: 10.1007/s00203-017-1429-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/22/2017] [Accepted: 08/31/2017] [Indexed: 10/18/2022]
Abstract
The earliest microbiological studies on hot springs in India date from 2003, a much later date compared to global attention in this striking field of study. As of today, 28 out of 400 geothermal springs have been explored following both culturable and non-culturable approaches. The temperatures and pH of the springs are 37-99 °C and 6.8-10, respectively. Several studies have been performed on the description of novel genera and species, characterization of different bio-resources, metagenomics of hot spring microbiome and whole genome analysis of few isolates. 17 strains representing novel species and many thermostable enzymes, including lipase, protease, chitinase, amylase, etc. with potential biotechnological applications have been reported by several authors. Influence of physico-chemical conditions, especially that of temperature, on shaping the hot spring microbiome has been established by metagenomic investigations. Bacteria are the predominant life forms in all the springs with an abundance of phyla Firmicutes, Proteobacteria, Actinobacteria, Thermi, Bacteroidetes, Deinococcus-Thermus and Chloroflexi. In this review, we have discussed the findings on all microbiological studies that have been carried out to date, on the 28 hot springs. Further, the possibilities of extrapolating these studies for practical applications and environmental impact assessment towards protection of natural ecosystem of hot springs have also been discussed.
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Affiliation(s)
- Abhijit Poddar
- Biosafety Support Unit, Regional Centre for Biotechnology, NPC Building, 5-6 Institutional Area, Lodhi Road, New Delhi, 110003, India.
| | - Subrata K Das
- Department of Biotechnology, Institute of Life Sciences, Bhubaneswar, 751023, India.
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Stoichiometric Network Analysis of Cyanobacterial Acclimation to Photosynthesis-Associated Stresses Identifies Heterotrophic Niches. Processes (Basel) 2017. [DOI: 10.3390/pr5020032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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36
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Thiel V, Hügler M, Ward DM, Bryant DA. The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. II. Metabolic Functions of Abundant Community Members Predicted from Metagenomic Analyses. Front Microbiol 2017. [PMID: 28634470 PMCID: PMC5459899 DOI: 10.3389/fmicb.2017.00943] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin of Yellowstone National Park have been extensively characterized. Previous studies have focused on the chlorophototrophic organisms of the phyla Cyanobacteria and Chloroflexi. However, the diversity and metabolic functions of the other portion of the community in the microoxic/anoxic region of the mat are poorly understood. We recently described the diverse but extremely uneven microbial assemblage in the undermat of Mushroom Spring based on 16S rRNA amplicon sequences, which was dominated by Roseiflexus members, filamentous anoxygenic chlorophototrophs. In this study, we analyzed the orange-colored undermat portion of the community of Mushroom Spring mats in a genome-centric approach and discuss the metabolic potentials of the major members. Metagenome binning recovered partial genomes of all abundant community members, ranging in completeness from ~28 to 96%, and allowed affiliation of function with taxonomic identity even for representatives of novel and Candidate phyla. Less complete metagenomic bins correlated with high microdiversity. The undermat portion of the community was found to be a mixture of phototrophic and chemotrophic organisms, which use bicarbonate as well as organic carbon sources derived from different cell components and fermentation products. The presence of rhodopsin genes in many taxa strengthens the hypothesis that light energy is of major importance. Evidence for the usage of all four bacterial carbon fixation pathways was found in the metagenome. Nitrogen fixation appears to be limited to Synechococcus spp. in the upper mat layer and Thermodesulfovibrio sp. in the undermat, and nitrate/nitrite metabolism was limited. A closed sulfur cycle is indicated by biological sulfate reduction combined with the presence of genes for sulfide oxidation mainly in phototrophs. Finally, a variety of undermat microorganisms have genes for hydrogen production and consumption, which leads to the observed diel hydrogen concentration patterns.
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Affiliation(s)
- Vera Thiel
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University ParkPA, United States
| | - Michael Hügler
- Department Microbiology and Molecular Biology, DVGW-Technologiezentrum WasserKarlsruhe, Germany
| | - David M Ward
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, United States
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University ParkPA, United States.,Department of Chemistry and Biochemistry, Montana State UniversityBozeman, MT, United States
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Impact of water heater temperature setting and water use frequency on the building plumbing microbiome. ISME JOURNAL 2017; 11:1318-1330. [PMID: 28282040 PMCID: PMC5437349 DOI: 10.1038/ismej.2017.14] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 11/28/2016] [Accepted: 01/22/2017] [Indexed: 01/06/2023]
Abstract
Hot water plumbing is an important conduit of microbes into the indoor environment and can increase risk of opportunistic pathogens (for example, Legionella pneumophila). We examined the combined effects of water heater temperature (39, 42, 48, 51 and 58 °C), pipe orientation (upward/downward), and water use frequency (21, 3 and 1 flush per week) on the microbial composition at the tap using a pilot-scale pipe rig. 16S rRNA gene amplicon sequencing indicated that bulk water and corresponding biofilm typically had distinct taxonomic compositions (R2Adonis=0.246, PAdonis=0.001), yet similar predicted functions based on PICRUSt analysis (R2Adonis=0.087, PAdonis=0.001). Although a prior study had identified 51 °C under low water use frequency to enrich Legionella at the tap, here we reveal that 51 °C is also a threshold above which there are marked effects of the combined influences of temperature, pipe orientation, and use frequency on taxonomic and functional composition. A positive association was noted between relative abundances of Legionella and mitochondrial DNA of Vermamoeba, a genus of amoebae that can enhance virulence and facilitate replication of some pathogens. This study takes a step towards intentional control of the plumbing microbiome and highlights the importance of microbial ecology in governing pathogen proliferation.
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Jiang X, Takacs-Vesbach CD. Microbial community analysis of pH 4 thermal springs in Yellowstone National Park. Extremophiles 2016; 21:135-152. [PMID: 27807621 DOI: 10.1007/s00792-016-0889-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 10/20/2016] [Indexed: 02/01/2023]
Abstract
The pH of the majority of thermal springs in Yellowstone National Park (YNP) is from 1 to 3 and 6 to 10; relatively few springs (~5%) have a pH range of 4-5. We used 16S rRNA gene pyrosequencing to investigate microbial communities sampled from four pH 4 thermal springs collected from four regions of YNP that differed in their fluid temperature and geochemistry. Our results revealed that the composition of bacterial communities varied among the sites, despite sharing similar pH values. The taxonomic composition and metabolic functional potential of the site with the lowest temperature (55 °C), a thermal spring from the Seven Mile Hole (SMH) area, were further investigated using shotgun metagenome sequencing. The taxonomic classification, based on 372 Mbp of unassembled metagenomic reads, indicated that this community included a high proportion of Chloroflexi, Bacteroidetes, Proteobacteria, and Firmicutes. Functional comparison with other YNP thermal spring metagenomes indicated that the SMH metagenome was enriched in genes related to energy production and conversion, transcription, and carbohydrate transport. Analysis of genes involved in nitrogen metabolism revealed assimilatory and dissimilatory nitrate reduction pathways, whereas the majority of genes involved in sulfur metabolism were related to the reduction of sulfate to adenylylsulfate, sulfite, and H2S. Given that pH 4 thermal springs are relatively less common in YNP and thermal areas worldwide, they may harbor novel microbiota and the communities that inhabit them deserve further investigation.
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Affiliation(s)
- Xiaoben Jiang
- Department of Biology, MSC03 2020 1UNM, University of New Mexico, Albuquerque, NM, 87131, USA
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Tamazawa S, Yamamoto K, Takasaki K, Mitani Y, Hanada S, Kamagata Y, Tamaki H. In Situ Gene Expression Responsible for Sulfide Oxidation and CO2 Fixation of an Uncultured Large Sausage-Shaped Aquificae Bacterium in a Sulfidic Hot Spring. Microbes Environ 2016; 31:194-8. [PMID: 27297893 PMCID: PMC4912159 DOI: 10.1264/jsme2.me16013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
We investigated the in situ gene expression profile of sulfur-turf microbial mats dominated by an uncultured large sausage-shaped Aquificae bacterium, a key metabolic player in sulfur-turfs in sulfidic hot springs. A reverse transcription-PCR analysis revealed that the genes responsible for sulfide, sulfite, and thiosulfate oxidation and carbon fixation via the reductive TCA cycle were continuously expressed in sulfur-turf mats taken at different sampling points, seasons, and years. These results suggest that the uncultured large sausage-shaped bacterium has the ability to grow chemolithoautotrophically and plays key roles as a primary producer in the sulfidic hot spring ecosystem in situ.
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Affiliation(s)
- Satoshi Tamazawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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Kojima H, Umezawa K, Fukui M. Caldimicrobium thiodismutans sp. nov., a sulfur-disproportionating bacterium isolated from a hot spring, and emended description of the genus Caldimicrobium. Int J Syst Evol Microbiol 2016; 66:1828-1831. [PMID: 26842785 DOI: 10.1099/ijsem.0.000947] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A novel autotrophic, thermophilic bacterium, strain TF1T, was isolated from a hot spring in Japan. Cells of strain TF1T were motile, Gram-stain-negative, rod-shaped, 1.0-2.0 μm in length and 0.5-0.6 μm in width. Major components in the cellular fatty acid profile were C16:0, C18:0 and anteiso-C17:0. The temperature range for growth was 40-77 °C, and optimum temperature was 75 °C. The pH range for growth was 5.9-9.5, and the optimum pH was 7.5-8.8. Strain TF1T grew chemolithoautotrophically by disproportionation of sulfur, thiosulfate and sulfite. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belongs to the family Thermodesulfobacteriaceae. The closest cultivated relative was Caldimicrobium rimae DST, with highest 16S rRNA gene sequence similarity of 96%. The genome of strain TF1T consists of one circular chromosome, with a size of 1.8 Mbp and G+C content of 38.30 mol%. On the basis of its phylogenetic and phenotypic properties, strain TF1T (=DSM 29380T=NBRC 110713T) is proposed as the type strain of a novel species, Caldimicrobium thiodismutans sp. nov.
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Affiliation(s)
- Hisaya Kojima
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan
| | - Kazuhiro Umezawa
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan
| | - Manabu Fukui
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan
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Gaisin VA, Grouzdev DS, Namsaraev ZB, Sukhacheva MV, Gorlenko VM, Kuznetsov BB. Biogeography of thermophilic phototrophic bacteria belonging toRoseiflexusgenus. FEMS Microbiol Ecol 2016; 92:fiw012. [DOI: 10.1093/femsec/fiw012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2016] [Indexed: 11/14/2022] Open
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Nozhevnikova AN, Botchkova EA, Plakunov VK. Multi-species biofilms in ecology, medicine, and biotechnology. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715060107] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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43
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Anda D, Makk J, Krett G, Jurecska L, Márialigeti K, Mádl-Szőnyi J, Borsodi AK. Thermophilic prokaryotic communities inhabiting the biofilm and well water of a thermal karst system located in Budapest (Hungary). Extremophiles 2015; 19:787-97. [PMID: 25952671 DOI: 10.1007/s00792-015-0754-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 04/26/2015] [Indexed: 11/29/2022]
Abstract
In this study, scanning electron microscopy (SEM) and 16S rRNA gene-based phylogenetic approach were applied to reveal the morphological structure and genetic diversity of thermophilic prokaryotic communities of a thermal karst well located in Budapest (Hungary). Bacterial and archaeal diversity of the well water (73.7 °C) and the biofilm developed on the inner surface of an outflow pipeline of the well were studied by molecular cloning method. According to the SEM images calcium carbonate minerals serve as a surface for colonization of bacterial aggregates. The vast majority of the bacterial and archaeal clones showed the highest sequence similarities to chemolithoautotrophic species. The bacterial clone libraries were dominated by sulfur oxidizer Thiobacillus (Betaproteobacteria) in the water and Sulfurihydrogenibium (Aquificae) in the biofilm. A relatively high proportion of molecular clones represented genera Thermus and Bellilinea in the biofilm library. The most abundant phylotypes both in water and biofilm archaeal clone libraries were closely related to thermophilic ammonia oxidizer Nitrosocaldus and Nitrososphaera but phylotypes belonging to methanogens were also detected. The results show that in addition to the bacterial sulfur and hydrogen oxidation, mainly archaeal ammonia oxidation may play a decisive role in the studied thermal karst system.
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Affiliation(s)
- Dóra Anda
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, Budapest, 1117, Hungary
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Greater temporal changes of sediment microbial community than its waterborne counterpart in Tengchong hot springs, Yunnan Province, China. Sci Rep 2014; 4:7479. [PMID: 25524763 PMCID: PMC5378992 DOI: 10.1038/srep07479] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 11/25/2014] [Indexed: 01/01/2023] Open
Abstract
Temporal variation in geochemistry can cause changes in microbial community structure and diversity. Here we studied temporal changes of microbial communities in Tengchong hot springs of Yunnan Province, China in response to geochemical variations by using microbial and geochemical data collected in January, June and August of 2011. Greater temporal variations were observed in individual taxa than at the whole community structure level. Water and sediment communities exhibited different temporal variation patterns. Water communities were largely stable across three sampling times and dominated by similar microbial lineages: Hydrogenobaculum in moderate-temperature acidic springs, Sulfolobus in high-temperature acidic springs, and Hydrogenobacter in high-temperature circumneutral to alkaline springs. Sediment communities were more diverse and responsive to changing physicochemical conditions. Most of the sediment communities in January and June were similar to those in waters. However, the August sediment community was more diverse and contained more anaerobic heterotrophs than the January and June: Desulfurella and Acidicaldus in moderate-temperature acidic springs, Ignisphaera and Desulfurococcus in high-temperature acidic springs, the candidate division OP1 and Fervidobacterium in alkaline springs, and Thermus and GAL35 in neutral springs. Temporal variations in physicochemical parameters including temperature, pH, and dissolved organic carbon may have triggered the observed microbial community shifts.
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45
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Morohoshi S, Matsuura K, Haruta S. Secreted protease mediates interspecies interaction and promotes cell aggregation of the photosynthetic bacterium Chloroflexus aggregans. FEMS Microbiol Lett 2014; 362:1-5. [PMID: 25673656 DOI: 10.1093/femsle/fnu046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Interspecies interactions were studied in hot spring microbial mats where diverse species of bacterial cells are densely packed. The anoxygenic photosynthetic bacterium, Chloroflexus aggregans, has been widely found in the microbial mats as a major component in terrestrial hot springs in Japan at the temperature from 50 to 70°C. C. aggregans shows cellular motility to form a microbial mat-like dense cell aggregate. The aggregating ability of C. aggregans was affected by another bacterial species, strain BL55a (related to Bacillus licheniformis) isolated from the microbial mats containing C. aggregans. Cell aggregation rate of C. aggregans was promoted by the addition of culture supernatants of strain BL55a. Similar effects were also detected from other bacterial isolates, specifically Geobacillus sp. and Aeribacillus sp. Protease activity was detected from the culture supernatants from all of these isolates. The promoting effect of strain BL55a was suppressed by a serine protease inhibitor, phenylmethylsulfonyl fluoride. A purified serine protease, subtilisin obtained from B. licheniformis, showed a promoting effect on the cell aggregation. These results suggest that an extracellular protease, secreted from co-existing bacterial species promoted the aggregating motility of C. aggregans. This is the first report that exogenous protease affects bacterial cellular motility.
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Affiliation(s)
- Sho Morohoshi
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Katsumi Matsuura
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Shin Haruta
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
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46
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Microbial diversity of the Soldhar hot spring, India, assessed by analyzing 16S rRNA and protein-coding genes. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0970-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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47
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Németh A, Szirányi B, Krett G, Janurik E, Kosáros T, Pekár F, Márialigeti K, Borsodi A. Prokaryotic phylogenetic diversity of Hungarian deep subsurface geothermal well waters. Acta Microbiol Immunol Hung 2014; 61:363-77. [PMID: 25261947 DOI: 10.1556/amicr.61.2014.3.9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Geothermal wells characterized by thermal waters warmer than 30°C can be found in more than 65% of the area of Hungary. The examined thermal wells located nearby Szarvas are used for heating industrial and agricultural facilities because of their relatively high hydrocarbon content. The aim of this study was to reveal the prokaryotic community structure of the water of SZR18, K87 and SZR21 geothermal wells using molecular cloning methods and Denaturing Gradient Gel Electrophoresis (DGGE). Water samples from the outflow pipes were collected in 2012 and 2013. The phylogenetic distribution of archaeal molecular clones was very similar in each sample, the most abundant groups belonged to the genera Methanosaeta, Methanothermobacter and Thermofilum. In contrast, the distribution of bacterial molecular clones was very diverse. Many of them showed the closest sequence similarities to uncultured clone sequences from similar thermal environments. From the water of the SZR18 well, phylotypes closely related to genera Fictibacillus and Alicyclobacillus (Firmicutes) were only revealed, while the bacterial diversity of the K87 well water was much higher. Here, the members of the phyla Thermodesulfobacteria, Proteobacteria, Nitrospira, Chlorobi, OP1 and OPB7 were also detected besides Firmicutes.
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Affiliation(s)
- Andrea Németh
- 1 Eötvös Loránd University Department of Microbiology Pázmány P. sétány 1/C H-1117 Budapest Hungary
| | - Barbara Szirányi
- 1 Eötvös Loránd University Department of Microbiology Pázmány P. sétány 1/C H-1117 Budapest Hungary
| | - Gergely Krett
- 1 Eötvös Loránd University Department of Microbiology Pázmány P. sétány 1/C H-1117 Budapest Hungary
| | - Endre Janurik
- 2 Research Institute for Fisheries, Aquaculture and Irrigation Anna-liget 8 H-5540 Szarvas Hungary
| | - Tünde Kosáros
- 2 Research Institute for Fisheries, Aquaculture and Irrigation Anna-liget 8 H-5540 Szarvas Hungary
| | - Ferenc Pekár
- 2 Research Institute for Fisheries, Aquaculture and Irrigation Anna-liget 8 H-5540 Szarvas Hungary
| | - Károly Márialigeti
- 1 Eötvös Loránd University Department of Microbiology Pázmány P. sétány 1/C H-1117 Budapest Hungary
| | - Andrea Borsodi
- 1 Eötvös Loránd University Department of Microbiology Pázmány P. sétány 1/C H-1117 Budapest Hungary
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Genome Sequence of the Thermophilic Cyanobacterium Thermosynechococcus sp. Strain NK55a. GENOME ANNOUNCEMENTS 2014; 2:2/1/e01060-13. [PMID: 24482507 PMCID: PMC3907722 DOI: 10.1128/genomea.01060-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The genome of the unicellular cyanobacterium Thermosynechococcus sp. strain NK55a, isolated from the Nakabusa hot spring, Nagano Prefecture, Japan, comprises a single, circular, 2.5-Mb chromosome. The genome is predicted to contain 2,358 protein-encoding genes, including genes for all typical cyanobacterial photosynthetic and metabolic functions. No genes encoding hydrogenases or nitrogenase were identified.
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Humboldt's spa: microbial diversity is controlled by temperature in geothermal environments. ISME JOURNAL 2014; 8:1166-74. [PMID: 24430481 DOI: 10.1038/ismej.2013.237] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 11/07/2013] [Accepted: 12/09/2013] [Indexed: 11/08/2022]
Abstract
Over 200 years ago Alexander von Humboldt (1808) observed that plant and animal diversity peaks at tropical latitudes and decreases toward the poles, a trend he attributed to more favorable temperatures in the tropics. Studies to date suggest that this temperature-diversity gradient is weak or nonexistent for Bacteria and Archaea. To test the impacts of temperature as well as pH on bacterial and archaeal diversity, we performed pyrotag sequencing of 16S rRNA genes retrieved from 165 soil, sediment and biomat samples of 36 geothermal areas in Canada and New Zealand, covering a temperature range of 7.5-99 °C and a pH range of 1.8-9.0. This represents the widest ranges of temperature and pH yet examined in a single microbial diversity study. Species richness and diversity indices were strongly correlated to temperature, with R(2) values up to 0.62 for neutral-alkaline springs. The distributions were unimodal, with peak diversity at 24 °C and decreasing diversity at higher and lower temperature extremes. There was also a significant pH effect on diversity; however, in contrast to previous studies of soil microbial diversity, pH explained less of the variability (13-20%) than temperature in the geothermal samples. No correlation was observed between diversity values and latitude from the equator, and we therefore infer a direct temperature effect in our data set. These results demonstrate that temperature exerts a strong control on microbial diversity when considered over most of the temperature range within which life is possible.
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50
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Affiliation(s)
- Shin Haruta
- Graduate School of Science and Engineering, Tokyo Metropolitan University
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