1
|
Marks TJ, Rowland IR. The Diversity of Bacteriophages in Hot Springs. Methods Mol Biol 2024; 2738:73-88. [PMID: 37966592 DOI: 10.1007/978-1-0716-3549-0_4] [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] [Indexed: 11/16/2023]
Abstract
Bacteriophages are ubiquitous in all environments that support microbial life. This includes hot springs, which can range in temperatures between 40 and 98 °C and pH levels between 1 and 9. Bacteriophages that survive in the higher temperatures of hot springs are known as thermophages. Thermophages have developed distinct adaptations allowing for thermostability in these extreme environments, including increased G + C DNA percentages, reliance upon the pentose phosphate metabolic pathway to avoid oxidative stress, and a codon preference for those with a GNA sequence leading to increased hydrophobic interactions and disulfide bonds. In this review, we discuss the diversity of characterized thermophages in hot spring environments that span five viral families: Myoviridae, Siphoviridae, Tectiviridae, Sphaerolipoviridae, and Inoviridae. Potential industrial and medicinal applications of thermophages will also be addressed.
Collapse
Affiliation(s)
- Timothy J Marks
- Department of Pharmaceutical and Clinical Sciences, Campbell University, Buies Creek, NC, USA.
| | - Isabella R Rowland
- Department of Pharmaceutical and Clinical Sciences, Campbell University, Buies Creek, NC, USA
| |
Collapse
|
2
|
DeCastro ME, Escuder-Rodríguez JJ, Becerra M, Rodríguez-Belmonte E, González-Siso MI. Comparative Metagenomic Analysis of Two Hot Springs From Ourense (Northwestern Spain) and Others Worldwide. Front Microbiol 2021; 12:769065. [PMID: 34899652 PMCID: PMC8661477 DOI: 10.3389/fmicb.2021.769065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/26/2021] [Indexed: 01/12/2023] Open
Abstract
With their circumneutral pH and their moderate temperature (66 and 68°C, respectively), As Burgas and Muiño da Veiga are two important human-use hot springs, previously studied with traditional culture methods, but never explored with a metagenomic approach. In the present study, we have performed metagenomic sequence-based analyses to compare the taxonomic composition and functional potential of these hot springs. Proteobacteria, Deinococcus-Thermus, Firmicutes, Nitrospirae, and Aquificae are the dominant phyla in both geothermal springs, but there is a significant difference in the abundance of these phyla between As Burgas and Muiño da Veiga. Phylum Proteobacteria dominates As Burgas ecosystem while Aquificae is the most abundant phylum in Muiño da Veiga. Taxonomic and functional analyses reveal that the variability in water geochemistry might be shaping the differences in the microbial communities inhabiting these geothermal springs. The content in organic compounds of As Burgas water promotes the presence of heterotrophic populations of the genera Acidovorax and Thermus, whereas the sulfate-rich water of Muiño da Veiga favors the co-dominance of genera Sulfurihydrogenibium and Thermodesulfovibrio. Differences in ammonia concentration exert a selective pressure toward the growth of nitrogen-fixing bacteria such as Thermodesulfovibrio in Muiño da Veiga. Temperature and pH are two important factors shaping hot springs microbial communities as was determined by comparative analysis with other thermal springs.
Collapse
Affiliation(s)
| | | | | | | | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, A Coruña, Spain
| |
Collapse
|
3
|
Microbial Diversity of Terrestrial Geothermal Springs in Armenia and Nagorno-Karabakh: A Review. Microorganisms 2021; 9:microorganisms9071473. [PMID: 34361908 PMCID: PMC8307006 DOI: 10.3390/microorganisms9071473] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/24/2021] [Accepted: 07/07/2021] [Indexed: 12/25/2022] Open
Abstract
The microbial diversity of high-altitude geothermal springs has been recently assessed to explore their biotechnological potential. However, little is known regarding the microbiota of similar ecosystems located on the Armenian Highland. This review summarizes the known information on the microbiota of nine high-altitude mineralized geothermal springs (temperature range 25.8–70 °C and pH range 6.0–7.5) in Armenia and Nagorno-Karabakh. All these geothermal springs are at altitudes ranging from 960–2090 m above sea level and are located on the Alpide (Alpine–Himalayan) orogenic belt, a seismically active region. A mixed-cation mixed-anion composition, with total mineralization of 0.5 mg/L, has been identified for these thermal springs. The taxonomic diversity of hot spring microbiomes has been examined using culture-independent approaches, including denaturing gradient gel electrophoresis (DGGE), 16S rRNA gene library construction, 454 pyrosequencing, and Illumina HiSeq. The bacterial phyla Proteobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes are the predominant life forms in the studied springs. Archaea mainly include the phyla Euryarchaeota, Crenarchaeota, and Thaumarchaeota, and comprise less than 1% of the prokaryotic community. Comparison of microbial diversity in springs from Karvachar with that described for other terrestrial hot springs revealed that Proteobacteria, Bacteroidetes, Actinobacteria, and Deinococcus–Thermus are the common bacterial groups in terrestrial hot springs. Contemporaneously, specific bacterial and archaeal taxa were observed in different springs. Evaluation of the carbon, sulfur, and nitrogen metabolism in these hot spring communities has revealed diversity in terms of metabolic activity. Temperature seems to be an important factor in shaping the microbial communities of these springs. Overall, the diversity and richness of the microbiota are negatively affected by increasing temperature. Other abiotic factors, including pH, mineralization, and geological history, also impact the structure and function of the microbial community. More than 130 bacterial and archaeal strains (Bacillus, Geobacillus, Parageobacillus, Anoxybacillus, Paenibacillus, Brevibacillus Aeribacillus, Ureibacillus, Thermoactinomyces, Sporosarcina, Thermus, Rhodobacter, Thiospirillum, Thiocapsa, Rhodopseudomonas, Methylocaldum, Desulfomicrobium, Desulfovibrio, Treponema, Arcobacter, Nitropspira, and Methanoculleus) have been reported, some of which may be representative of novel species (sharing 91–97% sequence identity with their closest matches in GenBank) and producers of thermozymes and biomolecules with potential biotechnological applications. Whole-genome shotgun sequencing of T. scotoductus K1, as well as of the potentially new Treponema sp. J25 and Anoxybacillus sp. K1, were performed. Most of the phyla identified by 16S rRNA were also identified using metagenomic approaches. Detailed characterization of thermophilic isolates indicate the potential of the studied springs as a source of biotechnologically valuable microbes and biomolecules.
Collapse
|
4
|
DeCastro ME, Doane MP, Dinsdale EA, Rodríguez-Belmonte E, González-Siso MI. Exploring the taxonomical and functional profile of As Burgas hot spring focusing on thermostable β-galactosidases. Sci Rep 2021; 11:101. [PMID: 33420292 PMCID: PMC7794327 DOI: 10.1038/s41598-020-80489-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/17/2020] [Indexed: 01/29/2023] Open
Abstract
In the present study we investigate the microbial community inhabiting As Burgas geothermal spring, located in Ourense (Galicia, Spain). The approximately 23 Gbp of Illumina sequences generated for each replicate revealed a complex microbial community dominated by Bacteria in which Proteobacteria and Aquificae were the two prevalent phyla. An association between the two most prevalent genera, Thermus and Hydrogenobacter, was suggested by the relationship of their metabolism. The high relative abundance of sequences involved in the Calvin-Benson cycle and the reductive TCA cycle unveils the dominance of an autotrophic population. Important pathways from the nitrogen and sulfur cycle are potentially taking place in As Burgas hot spring. In the assembled reads, two complete ORFs matching GH2 beta-galactosidases were found. To assess their functional characterization, the two ORFs were cloned and overexpressed in E. coli. The pTsbg enzyme had activity towards o-Nitrophenyl-β-D-galactopyranoside (ONPG) and p-Nitrophenyl-β-D-fucopyranoside, with high thermal stability and showing maximal activity at 85 °C and pH 6, nevertheless the enzyme failed to hydrolyze lactose. The other enzyme, Tsbg, was unable to hydrolyze even ONPG or lactose. This finding highlights the challenge of finding novel active enzymes based only on their sequence.
Collapse
Affiliation(s)
- María-Eugenia DeCastro
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Facultade de Ciencias, Universidade da Coruña, A Coruña, Spain
| | - Michael P Doane
- Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
- Syndey Institute of Marine Science, 19 Chowder Bay Rd, Mosman, NSW, 2088, Australia
| | - Elizabeth Ann Dinsdale
- Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
- College of Science and Engineering, Flinders University, Sturt Rd, Bedford Park, SA, 5042, Australia
| | - Esther Rodríguez-Belmonte
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Facultade de Ciencias, Universidade da Coruña, A Coruña, Spain
| | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Facultade de Ciencias, Universidade da Coruña, A Coruña, Spain.
| |
Collapse
|
5
|
Talamantes-Becerra B, Carling J, Kilian A, Georges A. Discovery of thermophilic Bacillales using reduced-representation genotyping for identification. BMC Microbiol 2020; 20:114. [PMID: 32404118 PMCID: PMC7222431 DOI: 10.1186/s12866-020-01800-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 04/23/2020] [Indexed: 12/25/2022] Open
Abstract
Background This study demonstrates the use of reduced-representation genotyping to provide preliminary identifications for thermophilic bacterial isolates. The approach combines restriction enzyme digestion and PCR with next-generation sequencing to provide thousands of short-read sequences from across the bacterial genomes. Isolates were obtained from compost, hot water systems, and artesian bores of the Great Artesian Basin. Genomic DNA was double-digested with two combinations of restriction enzymes followed by PCR amplification, using a commercial provider of DArTseq™, Diversity Arrays Technology Pty Ltd. (Canberra, Australia). The resulting fragments which formed a reduced-representation of approximately 2.3% of the genome were sequenced. The sequence tags obtained were aligned against all available RefSeq bacterial genome assemblies by BLASTn to identify the nearest reference genome. Results Based on the preliminary identifications, a total of 99 bacterial isolates were identified to species level, from which 8 isolates were selected for whole-genome sequencing to assess the identification results. Novel species and strains were discovered within this set of isolates. The preliminary identifications obtained by reduced-representation genotyping, as well as identifications obtained by BLASTn alignment of the 16S rRNA gene sequence, were compared with those derived from the whole-genome sequence data, using the same RefSeq sequence database for the three methods. Identifications obtained with reduced-representation sequencing agreed with the identifications provided by whole-genome sequencing in 100% of cases. The identifications produced by BLASTn alignment of 16S rRNA gene sequence to the same database differed from those provided by whole-genome sequencing in 37.5% of cases, and produced ambiguous identifications in 50% of cases. Conclusions Previously, this method has been successfully demonstrated for use in bacterial identification for medical microbiology. This study demonstrates the first successful use of DArTseq™ for preliminary identification of thermophilic bacterial isolates, providing results in complete agreement with those obtained from whole-genome sequencing of the same isolates. The growing database of bacterial genome sequences provides an excellent resource for alignment of reduced-representation sequence data for identification purposes, and as the available sequenced genomes continue to grow, the technique will become more effective.
Collapse
Affiliation(s)
| | - Jason Carling
- Diversity Arrays Technology Pty Ltd, Canberra, ACT, 2617, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, Canberra, ACT, 2617, Australia
| | - Arthur Georges
- Institute of Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| |
Collapse
|
6
|
Brito EMS, Romero-Núñez VM, Caretta CA, Bertin P, Valerdi-Negreros JC, Guyoneaud R, Goñi-Urriza M. The bacterial diversity on steam vents from Paricutín and Sapichu volcanoes. Extremophiles 2019; 23:249-263. [PMID: 30712189 DOI: 10.1007/s00792-019-01078-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 01/22/2019] [Indexed: 01/30/2023]
Abstract
Vapor steam vents are prevailing structures on geothermal sites in which local geochemical conditions allow the development of extremophilic microorganisms. We describe the structure of the prokaryotic community able to grow on the walls and rocks of such microecosystems in two terrestrial Mexican volcanoes: Paricutín (PI and PII samples) and its satellite Sapichu (S sample). The investigated samples showed similar diversity indices, with few dominant OTUs (abundance > 1%): 21, 16 and 23, respectively for PI, PII and S. However, each steam vent showed a particular community profile: PI was dominated by photosynthetic bacteria (Cyanobacteria and Chloroflexia class), PII by Actinobacteria and Proteobacteria, and S by Ktedonobacteria class, Acidobacteria and Cyanobacteria phyla. Concerning the predicted metabolic potential, we found a dominance of cellular pathways, especially the ones for energy generation with metabolisms for sulfur respiration, nitrogen fixation, methanogenesis, carbon fixation, photosynthesis, and metals, among others. We suggest a different maturity stage for the three studied fumaroles, from the youngest (PI) to the oldest (S and PII), also influenced by the temperature and other geochemical parameters. Furthermore, four anaerobic strains were isolated, belonging to Clostridia class (Clostridium sphenoides, C. swellfunanium and Anaerocolumna cellulosilytica) and to Bacilli class (Paenibacillus azoreducens).
Collapse
Affiliation(s)
| | - Víctor Manuel Romero-Núñez
- Ingeniería Ambiental, División de Ingenierías (CGT), Universidad de Guanajuato, Guanajuato, Gto., Mexico
| | - César Augusto Caretta
- Departamento de Astronomía, División de Ciencias Naturales y Exactas (CGT), Universidad de Guanajuato, Guanajuato, Gto., Mexico
| | - Pierre Bertin
- Equipe Génomique, Structure et Traduction, Inst. Biologie Intégrative de la Cellule (I2BC) CNRS-UMR9198, Universitè Paris-Sud, 91405, Orsay Cedex, France
| | | | - Rémy Guyoneaud
- CNRS/Universitè de Pau et des Pays de l'Adour/E2S, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, Environmental Microbiology Group, UMR 5254, 64000, Pau, France
| | - Marisol Goñi-Urriza
- CNRS/Universitè de Pau et des Pays de l'Adour/E2S, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, Environmental Microbiology Group, UMR 5254, 64000, Pau, France
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Strunecký O, Kopejtka K, Goecke F, Tomasch J, Lukavský J, Neori A, Kahl S, Pieper DH, Pilarski P, Kaftan D, Koblížek M. High diversity of thermophilic cyanobacteria in Rupite hot spring identified by microscopy, cultivation, single-cell PCR and amplicon sequencing. Extremophiles 2018; 23:35-48. [PMID: 30284641 DOI: 10.1007/s00792-018-1058-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 09/24/2018] [Indexed: 10/28/2022]
Abstract
Genotypic and morphological diversity of cyanobacteria in the Rupite hot spring (Bulgaria) was investigated by means of optical microscopy, cultivation, single-cell PCR, and 16S rRNA gene amplicon sequencing. Altogether, 34 sites were investigated along the 71-39 °C temperature gradient. Analysis of samples from eight representative sites shown that Illumina, optical microscopy, and Roche 454 identified 72, 45 and 19% respective occurrences of all cumulatively present taxa. Optical microscopy failed to detect species of minor occurrence; whereas, amplicon sequencing technologies suffered from failed primer annealing and the presence of species with extensive extracellular polysaccharides production. Amplicon sequencing of the 16S rRNA gene V5-V6 region performed by Illumina identified the cyanobacteria most reliably to the generic level. Nevertheless, only the combined use of optical microscopy, cultivation and sequencing methods allowed for reliable estimate of the cyanobacterial diversity. Here, we show that Rupite hot-spring system hosts one of the richest cyanobacterial flora reported from a single site above 50 °C. Chlorogloeopsis sp. was the most abundant at the highest temperature (68 °C), followed by Leptolyngbya boryana, Thermoleptolyngbya albertanoae, Synechococcus bigranulatus, Oculatella sp., and Desertifilum sp. thriving above 60 °C, while Leptolyngbya geysericola, Geitlerinema splendidum, and Cyanobacterium aponinum were found above 50 °C.
Collapse
Affiliation(s)
- Otakar Strunecký
- Institute of Aquaculture, CENAKVA, Faculty of Fisheries and Protection of Waters, University of South Bohemia, 37005, České Budějovice, Czech Republic. .,Faculty of Science, University of South Bohemia, 37005, České Budějovice, Czech Republic.
| | - Karel Kopejtka
- Center Algatech, Institute of Microbiology CAS, 37981, Třeboň, Czech Republic
| | - Franz Goecke
- Center Algatech, Institute of Microbiology CAS, 37981, Třeboň, Czech Republic.,Department of Plant and Environmental Science, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Jürgen Tomasch
- Group Microbial Communication, Helmholtz Centre for Infection Research, 38124, Brunswick, Germany
| | - Jaromír Lukavský
- Department of Plant Ecology, Institute of Botany CAS, 37901, Třeboň, Czech Republic
| | - Amir Neori
- Israel Oceanographic and Limnological Research Ltd., National Center for Mariculture, 88112, Eilat, Israel
| | - Silke Kahl
- Group Microbial Interactions and Processes, Helmholtz Centre for Infection Research, 38124, Brunswick, Germany
| | - Dietmar H Pieper
- Group Microbial Interactions and Processes, Helmholtz Centre for Infection Research, 38124, Brunswick, Germany
| | - Plamen Pilarski
- Institute of Plant Physiology and Genetics BAS, 1113, Sofia, Bulgaria
| | - David Kaftan
- Center Algatech, Institute of Microbiology CAS, 37981, Třeboň, Czech Republic.,Faculty of Science, University of South Bohemia, 37005, České Budějovice, Czech Republic
| | - Michal Koblížek
- Center Algatech, Institute of Microbiology CAS, 37981, Třeboň, Czech Republic
| |
Collapse
|
9
|
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; 87:272-281. [DOI: 10.1134/s0026261718020078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Indexed: 07/26/2024] Open
|
10
|
Prieto-Barajas CM, Alfaro-Cuevas R, Valencia-Cantero E, Santoyo G. Effect of seasonality and physicochemical parameters on bacterial communities in two hot spring microbial mats from Araró, Mexico. REV MEX BIODIVERS 2017. [DOI: 10.1016/j.rmb.2017.07.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
11
|
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
|
12
|
Sahoo RK, Subudhi E, Kumar M. Investigation of bacterial diversity of hot springs of Odisha, India. GENOMICS DATA 2015; 6:188-90. [PMID: 26697369 PMCID: PMC4664759 DOI: 10.1016/j.gdata.2015.09.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 09/14/2015] [Accepted: 09/15/2015] [Indexed: 11/22/2022]
Abstract
16S rRNA deep sequencing analysis, targeting V3 region was performed using Illumina bar coded sequencing. Sediment samples from two hot springs (Atri and Taptapani) were collected. Atri and Taptapani metagenomes were classified into 50 and 51 bacterial phyla. Proteobacteria (45.17%) dominated the Taptapani sample metagenome followed by Bacteriodetes (23.43%) and Cyanobacteria (10.48%) while in the Atri sample, Chloroflexi (52.39%), Nitrospirae (10.93%) and Proteobacteria (9.98%) dominated. A large number of sequences remained taxonomically unresolved in both hot springs, indicating the presence of potentially novel microbes in these two unique habitats thus unraveling the importance of the current study. Metagenome sequence information is now available at NCBI, SRA database accession no. SRP057428.
Collapse
Affiliation(s)
- Rajesh Kumar Sahoo
- Centre Of Biotechnology, Siksha O Anusandhan University, Bhubaneswar, Odisha, India
| | - Enketeswara Subudhi
- Centre Of Biotechnology, Siksha O Anusandhan University, Bhubaneswar, Odisha, India
| | - Mohit Kumar
- Biotechnology and Bioinformatics, NIIT University, Neemrana, Rajasthan, India
| |
Collapse
|
13
|
Bacterial communities during the process of high-temperature Daqu production of roasted sesame-like flavour liquor. JOURNAL OF THE INSTITUTE OF BREWING 2015. [DOI: 10.1002/jib.235] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
14
|
Tomova I, Dimitrova D, Stoilova-Disheva M, Lyutskanova D, Kambourova M. Archaeal Diversity at Two Hot Springs, Rupi Basin, Bulgaria. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2011.0120] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
15
|
Atanassov I, Stefanova K, Tomova I, Kamburova M. Seamless GFP and GFP-Amylase Cloning in Gateway Shuttle Vector, Expression of the Recombinant Proteins inE. ColiandBacillus Megateriumand Assessment of the GFP-Amylase Thermostability. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2013.0079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
16
|
Brito EMS, Villegas-Negrete N, Sotelo-González IA, Caretta CA, Goñi-Urriza M, Gassie C, Hakil F, Colin Y, Duran R, Gutiérrez-Corona F, Piñón-Castillo HA, Cuevas-Rodríguez G, Malm O, Torres JPM, Fahy A, Reyna-López GE, Guyoneaud R. Microbial diversity in Los Azufres geothermal field (Michoacán, Mexico) and isolation of representative sulfate and sulfur reducers. Extremophiles 2014; 18:385-98. [DOI: 10.1007/s00792-013-0624-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Accepted: 12/29/2013] [Indexed: 11/28/2022]
|
17
|
Jiménez DJ, Andreote FD, Chaves D, Montaña JS, Osorio-Forero C, Junca H, Zambrano MM, Baena S. Structural and functional insights from the metagenome of an acidic hot spring microbial planktonic community in the Colombian Andes. PLoS One 2012; 7:e52069. [PMID: 23251687 PMCID: PMC3522619 DOI: 10.1371/journal.pone.0052069] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 11/15/2012] [Indexed: 12/11/2022] Open
Abstract
A taxonomic and annotated functional description of microbial life was deduced from 53 Mb of metagenomic sequence retrieved from a planktonic fraction of the Neotropical high Andean (3,973 meters above sea level) acidic hot spring El Coquito (EC). A classification of unassembled metagenomic reads using different databases showed a high proportion of Gammaproteobacteria and Alphaproteobacteria (in total read affiliation), and through taxonomic affiliation of 16S rRNA gene fragments we observed the presence of Proteobacteria, micro-algae chloroplast and Firmicutes. Reads mapped against the genomes Acidiphilium cryptum JF-5, Legionella pneumophila str. Corby and Acidithiobacillus caldus revealed the presence of transposase-like sequences, potentially involved in horizontal gene transfer. Functional annotation and hierarchical comparison with different datasets obtained by pyrosequencing in different ecosystems showed that the microbial community also contained extensive DNA repair systems, possibly to cope with ultraviolet radiation at such high altitudes. Analysis of genes involved in the nitrogen cycle indicated the presence of dissimilatory nitrate reduction to N2 (narGHI, nirS, norBCDQ and nosZ), associated with Proteobacteria-like sequences. Genes involved in the sulfur cycle (cysDN, cysNC and aprA) indicated adenylsulfate and sulfite production that were affiliated to several bacterial species. In summary, metagenomic sequence data provided insight regarding the structure and possible functions of this hot spring microbial community, describing some groups potentially involved in the nitrogen and sulfur cycling in this environment.
Collapse
Affiliation(s)
- Diego Javier Jiménez
- Colombian Center for Genomic and Bioinformatics from Extreme Environments (GeBiX), Bogotá, Colombia.
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Dunfield PF, Tamas I, Lee KC, Morgan XC, McDonald IR, Stott MB. Electing a candidate: a speculative history of the bacterial phylum OP10. Environ Microbiol 2012; 14:3069-80. [DOI: 10.1111/j.1462-2920.2012.02742.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
19
|
Huang Q, Dong CZ, Dong RM, Jiang H, Wang S, Wang G, Fang B, Ding X, Niu L, Li X, Zhang C, Dong H. Archaeal and bacterial diversity in hot springs on the Tibetan Plateau, China. Extremophiles 2011; 15:549-63. [PMID: 21695489 DOI: 10.1007/s00792-011-0386-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2010] [Accepted: 06/06/2011] [Indexed: 11/24/2022]
Abstract
The diversity of archaea and bacteria was investigated in ten hot springs (elevation >4600 m above sea level) in Central and Central-Eastern Tibet using 16S rRNA gene phylogenetic analysis. The temperature and pH of these hot springs were 26-81°C and close to neutral, respectively. A total of 959 (415 and 544 for bacteria and archaea, respectively) clone sequences were obtained. Phylogenetic analysis showed that bacteria were more diverse than archaea and that these clone sequences were classified into 82 bacterial and 41 archaeal operational taxonomic units (OTUs), respectively. The retrieved bacterial clones were mainly affiliated with four known groups (i.e., Firmicutes, Proteobacteria, Cyanobacteria, Chloroflexi), which were similar to those in other neutral-pH hot springs at low elevations. In contrast, most of the archaeal clones from the Tibetan hot springs were affiliated with Thaumarchaeota, a newly proposed archaeal phylum. The dominance of Thaumarchaeota in the archaeal community of the Tibetan hot springs appears to be unique, although the exact reasons are not yet known. Statistical analysis showed that diversity indices of both archaea and bacteria were not statistically correlated with temperature, which is consistent with previous studies.
Collapse
Affiliation(s)
- Qiuyuan Huang
- Department of Geology, Miami University, Oxford, OH 45056, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|