51
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Liu K, Liu Y, Jiao N, Zhu L, Wang J, Hu A, Liu X. Vertical variation of bacterial community in Nam Co, a large stratified lake in central Tibetan Plateau. Antonie van Leeuwenhoek 2016; 109:1323-35. [DOI: 10.1007/s10482-016-0731-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/02/2016] [Indexed: 11/28/2022]
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Zhang L, Gao G, Tang X, Shao K, Gong Y. Pyrosequencing analysis of bacterial communities in Lake Bosten, a large brackish inland lake in the arid northwest of China. Can J Microbiol 2016; 62:455-63. [DOI: 10.1139/cjm-2015-0494] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The bacteria inhabiting brackish lake environments are poorly known, and there are few studies on the microbial diversity of these environments. Lake Bosten, a large brackish inland lake, is the largest lake in Xinjiang Province in northwestern China. Because sediments record past limnic changes, the analysis of sedimentary bacteria in Lake Bosten may help elucidate bacterial responses to environmental change. We employed 454 pyrosequencing to investigate the diversity and bacterial community composition in Lake Bosten. A total of 48 230 high-quality sequence reads with 16 314 operational taxonomic units were successfully obtained from the 4 selected samples, and they were numerically dominated by members of the Deltaproteobacteria (17.1%), Chloroflexi (16.1%), Betaproteobacteria (12.6%), Bacteroidetes (6.6%), and Firmicutes (5.7%) groups, accounting for more than 58.1% of the bacterial sequences. The sediment bacterial communities and diversity were consistently different along the 2 geographic environmental gradients: (i) freshwater–brackish water gradient and (ii) oligotrophic–mesotrophic habitat gradient. Deltaproteobacteria, Chloroflexi, and Betaproteobacteria were amplified throughout all of the sampling sites. More Bacteroidetes and Firmicutes were found near the Kaidu River estuary (site 14). Our investigation showed that Proteobacteria did not display any systematic change along the salinity gradient, and numerous 16S rRNA sequences could not be identified at the genus level. Our data will provide a better understanding of the diversity and distribution of bacteria in arid region brackish lakes.
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Affiliation(s)
- Lei Zhang
- School of Biology and Food Engineering, Chuzhou University, Chuzhou 239000, People’s Republic of China
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, People’s Republic of China
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, People’s Republic of China
| | - Keqiang Shao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, People’s Republic of China
| | - Yi Gong
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, People’s Republic of China
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Baatar B, Chiang PW, Rogozin DY, Wu YT, Tseng CH, Yang CY, Chiu HH, Oyuntsetseg B, Degermendzhy AG, Tang SL. Bacterial Communities of Three Saline Meromictic Lakes in Central Asia. PLoS One 2016; 11:e0150847. [PMID: 26934492 PMCID: PMC4775032 DOI: 10.1371/journal.pone.0150847] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 02/19/2016] [Indexed: 12/20/2022] Open
Abstract
Meromictic lakes located in landlocked steppes of central Asia (~2500 km inland) have unique geophysiochemical characteristics compared to other meromictic lakes. To characterize their bacteria and elucidate relationships between those bacteria and surrounding environments, water samples were collected from three saline meromictic lakes (Lakes Shira, Shunet and Oigon) in the border between Siberia and the West Mongolia, near the center of Asia. Based on in-depth tag pyrosequencing, bacterial communities were highly variable and dissimilar among lakes and between oxic and anoxic layers within individual lakes. Proteobacteria, Bacteroidetes, Cyanobacteria, Actinobacteria and Firmicutes were the most abundant phyla, whereas three genera of purple sulfur bacteria (a novel genus, Thiocapsa and Halochromatium) were predominant bacterial components in the anoxic layer of Lake Shira (~20.6% of relative abundance), Lake Shunet (~27.1%) and Lake Oigon (~9.25%), respectively. However, few known green sulfur bacteria were detected. Notably, 3.94% of all sequencing reads were classified into 19 candidate divisions, which was especially high (23.12%) in the anoxic layer of Lake Shunet. Furthermore, several hydro-parameters (temperature, pH, dissolved oxygen, H2S and salinity) were associated (P< 0.05) with variations in dominant bacterial groups. In conclusion, based on highly variable bacterial composition in water layers or lakes, we inferred that the meromictic ecosystem was characterized by high diversity and heterogenous niches.
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Affiliation(s)
- Bayanmunkh Baatar
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Yu-Ting Wu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- National Pingtung University of Science and Technology, Pingtung, Taiwan
| | | | - Cheng-Yu Yang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsiu-Hui Chiu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Bolormaa Oyuntsetseg
- School of Art and Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia
| | | | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan
- * E-mail:
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54
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Sanyal SK, Mou TJ, Chakrabarty RP, Hoque S, Hossain MA, Sultana M. Diversity of arsenite oxidase gene and arsenotrophic bacteria in arsenic affected Bangladesh soils. AMB Express 2016; 6:21. [PMID: 26980601 PMCID: PMC4792827 DOI: 10.1186/s13568-016-0193-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/08/2016] [Indexed: 11/10/2022] Open
Abstract
Arsenic (As) contaminated soils are enriched with arsenotrophic bacteria. The present study analyzes the microbiome and arsenotrophic genes-from As affected soil samples of Bhanga, Charvadrason and Sadarpur of Faridpur district in Bangladesh in summer (SFDSL1, 2, 3) and in winter (WFDSL1, 2, 3). Total As content of the soils was within the range of 3.24-17.8 mg/kg as per atomic absorption spectroscopy. The aioA gene, conferring arsenite [As (III)] oxidation, was retrieved from the soil sample, WFDSL-2, reported with As concentration of 4.9 mg/kg. Phylogenetic analysis revealed that the aioA genes of soil WFDSL-2 were distributed among four major phylogenetic lineages comprised of α, β, γ Proteobacteria and Archaea with a dominance of β Proteobacteria (56.67 %). An attempt to enrich As (III) metabolizing bacteria resulted 53 isolates. ARDRA (amplified ribosomal DNA restriction analysis) followed by 16S rRNA gene sequencing of the 53 soil isolates revealed that they belong to six genera; Pseudomonas spp., Bacillus spp., Brevibacillus spp., Delftia spp., Wohlfahrtiimonas spp. and Dietzia spp. From five different genera, isolates Delftia sp. A2i, Pseudomonas sp. A3i, W. chitiniclastica H3f, Dietzia sp. H2f, Bacillus sp. H2k contained arsB gene and showed arsenite tolerance up-to 27 mM. Phenotypic As (III) oxidation potential was also confirmed with the isolates of each genus and isolate Brevibacillus sp. A1a showed significant As (III) transforming potential of 0.2425 mM per hour. The genetic information of bacterial arsenotrophy and arsenite oxidation added scientific information about the possible bioremediation potential of the soil isolates in Bangladesh.
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Vavourakis CD, Ghai R, Rodriguez-Valera F, Sorokin DY, Tringe SG, Hugenholtz P, Muyzer G. Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines. Front Microbiol 2016; 7:211. [PMID: 26941731 PMCID: PMC4766312 DOI: 10.3389/fmicb.2016.00211] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 02/08/2016] [Indexed: 11/13/2022] Open
Abstract
Soda lakes are salt lakes with a naturally alkaline pH due to evaporative concentration of sodium carbonates in the absence of major divalent cations. Hypersaline soda brines harbor microbial communities with a high species- and strain-level archaeal diversity and a large proportion of still uncultured poly-extremophiles compared to neutral brines of similar salinities. We present the first "metagenomic snapshots" of microbial communities thriving in the brines of four shallow soda lakes from the Kulunda Steppe (Altai, Russia) covering a salinity range from 170 to 400 g/L. Both amplicon sequencing of 16S rRNA fragments and direct metagenomic sequencing showed that the top-level taxa abundance was linked to the ambient salinity: Bacteroidetes, Alpha-, and Gamma-proteobacteria were dominant below a salinity of 250 g/L, Euryarchaeota at higher salinities. Within these taxa, amplicon sequences related to Halorubrum, Natrinema, Gracilimonas, purple non-sulfur bacteria (Rhizobiales, Rhodobacter, and Rhodobaca) and chemolithotrophic sulfur oxidizers (Thioalkalivibrio) were highly abundant. Twenty-four draft population genomes from novel members and ecotypes within the Nanohaloarchaea, Halobacteria, and Bacteroidetes were reconstructed to explore their metabolic features, environmental abundance and strategies for osmotic adaptation. The Halobacteria- and Bacteroidetes-related draft genomes belong to putative aerobic heterotrophs, likely with the capacity to ferment sugars in the absence of oxygen. Members from both taxonomic groups are likely involved in primary organic carbon degradation, since some of the reconstructed genomes encode the ability to hydrolyze recalcitrant substrates, such as cellulose and chitin. Putative sodium-pumping rhodopsins were found in both a Flavobacteriaceae- and a Chitinophagaceae-related draft genome. The predicted proteomes of both the latter and a Rhodothermaceae-related draft genome were indicative of a "salt-in" strategy of osmotic adaptation. The primary catabolic and respiratory pathways shared among all available reference genomes of Nanohaloarchaea and our novel genome reconstructions remain incomplete, but point to a primarily fermentative lifestyle. Encoded xenorhodopsins found in most drafts suggest that light plays an important role in the ecology of Nanohaloarchaea. Putative encoded halolysins and laccase-like oxidases might indicate the potential for extracellular degradation of proteins and peptides, and phenolic or aromatic compounds.
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Affiliation(s)
- Charlotte D. Vavourakis
- Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of AmsterdamAmsterdam, Netherlands
| | - Rohit Ghai
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel HernándezSan Juan de Alicante, Spain
- Department of Aquatic Microbial Ecology, Biology Centre of the Czech Academy of Sciences, Institute of HydrobiologyČeské Budějovice, Czech Republic
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel HernándezSan Juan de Alicante, Spain
| | - Dimitry Y. Sorokin
- Research Centre of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of SciencesMoscow, Russia
- Department of Biotechnology, Delft University of TechnologyDelft, Netherlands
| | | | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of QueenslandBrisbane, QLD, Australia
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of AmsterdamAmsterdam, Netherlands
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Matyugina E, Belkova N. Distribution and diversity of microbial communities in meromictic soda Lake Doroninskoe (Transbaikalia, Russia) during winter. CHINESE JOURNAL OF OCEANOLOGY AND LIMNOLOGY 2015; 33:1378-1390. [DOI: 10.1007/s00343-015-4355-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2024]
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57
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Farooqui SM, Wright MH, Greene AC. Aliidiomarina minuta sp. nov., a haloalkaliphilic bacterium that forms ultra-small cells under non-optimal conditions. Antonie van Leeuwenhoek 2015; 109:83-93. [DOI: 10.1007/s10482-015-0611-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 10/22/2015] [Indexed: 10/22/2022]
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58
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İnceoğlu Ö, Llirós M, Crowe SA, García-Armisen T, Morana C, Darchambeau F, Borges AV, Descy JP, Servais P. Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu. MICROBIAL ECOLOGY 2015; 70:596-611. [PMID: 25912922 DOI: 10.1007/s00248-015-0612-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/02/2015] [Indexed: 06/04/2023]
Abstract
The microbial community composition in meromictic Lake Kivu, with one of the largest CH4 reservoirs, was studied using 16S rDNA and ribosomal RNA (rRNA) pyrosequencing during the dry and rainy seasons. Highly abundant taxa were shared in a high percentage between bulk (DNA-based) and active (RNA-based) bacterial communities, whereas a high proportion of rare species was detected only in either an active or bulk community, indicating the existence of a potentially active rare biosphere and the possible underestimation of diversity detected when using only one nucleic acid pool. Most taxa identified as generalists were abundant, and those identified as specialists were more likely to be rare in the bulk community. The overall number of environmental parameters that could explain the variation was higher for abundant taxa in comparison to rare taxa. Clustering analysis based on operational taxonomic units (OTUs at 0.03 cutoff) level revealed significant and systematic microbial community composition shifts with depth. In the oxic zone, Actinobacteria were found highly dominant in the bulk community but not in the metabolically active community. In the oxic-anoxic transition zone, highly abundant potentially active Nitrospira and Methylococcales were observed. The co-occurrence of potentially active sulfur-oxidizing and sulfate-reducing bacteria in the anoxic zone may suggest the presence of an active yet cryptic sulfur cycle.
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Affiliation(s)
- Özgul İnceoğlu
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Brussel, Belgium.
| | - Marc Llirós
- Laboratory of Freshwater Ecology, Université de Namur, Namur, Belgium
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Sean A Crowe
- Departments of Microbiology and Immunology, and Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | | | - Cedric Morana
- Department of Earth and Environmental Sciences, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | | | - Jean-Pierre Descy
- Laboratory of Freshwater Ecology, Université de Namur, Namur, Belgium
| | - Pierre Servais
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Brussel, Belgium
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59
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Fang L, Chen L, Liu Y, Tao W, Zhang Z, Liu H, Tang Y. Planktonic and sedimentary bacterial diversity of Lake Sayram in summer. Microbiologyopen 2015; 4:814-25. [PMID: 26242906 PMCID: PMC4618613 DOI: 10.1002/mbo3.281] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 06/23/2015] [Accepted: 07/06/2015] [Indexed: 12/21/2022] Open
Abstract
Lake Sayram is an ancient cold water lake locating at a mountain basin in Xinjiang, China. The lake water is brackish, alkaline, unpolluted, and abundant in SO4(2-) and Mg(2+). The lacustrine ecosystem of Lake Sayram has been intensely investigated. However, profiles of the microbial communities in the lake remain largely unknown. In this study, taxonomic compositions of the planktonic and sedimentary bacterial communities in Lake Sayram were investigated using 16S rRNA metagenomics. The lacustrine bacterial communities were generally structured by environmental conditions, including the hydrological and physicochemical parameters. Proteobacteria was the dominating phylum. In the lake water, the genera Acinetobacter and Ilumatobacter held an absolute predominance, implying their metabolic significance. In the bottom sediment, biogeochemically significant bacteria and thermophilic or acidothermophilic extremophiles were recovered. In contrast to the planktonic bacteria, an appreciable portion of the sedimentary bacteria could not be classified into any known taxonomic unit, indicating the largely unknown bacteriosphere hiding in the bottom sediment of Lake Sayram.
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Affiliation(s)
- Lei Fang
- School of Marine Science and Environmental Engineering, Dalian Ocean University, Dalian, 116023, China
| | - Lei Chen
- School of Marine Science and Environmental Engineering, Dalian Ocean University, Dalian, 116023, China.,School of Life Sciences, Liaoning Normal University, Dalian, 116029, China
| | - Yuan Liu
- School of Marine Science and Environmental Engineering, Dalian Ocean University, Dalian, 116023, China
| | - Wei Tao
- School of Marine Science and Environmental Engineering, Dalian Ocean University, Dalian, 116023, China
| | - Zhongzhe Zhang
- School of Marine Science and Environmental Engineering, Dalian Ocean University, Dalian, 116023, China
| | - Haiying Liu
- School of Marine Science and Environmental Engineering, Dalian Ocean University, Dalian, 116023, China
| | - Yong Tang
- School of Marine Science and Environmental Engineering, Dalian Ocean University, Dalian, 116023, China
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60
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A snapshot of microbial communities from the Kutch: one of the largest salt deserts in the World. Extremophiles 2015; 19:973-87. [PMID: 26186976 DOI: 10.1007/s00792-015-0772-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 07/06/2015] [Indexed: 10/23/2022]
Abstract
Here we present the first report on the taxonomic diversity of the microbial communities of the saline desert of the Great Rann of Kutch, Gujarat, India, using a metagenomic approach. Seven samples, differing in salinity levels and covering different seasons, were analysed to investigate the dynamics of microbial communities in relation to salinity and season. Metagenomic data generated using whole metagenome sequencing revealed that despite its very high salinity (4.11-30.79 %), the saline desert's microbiota had a rich microbial diversity that included all major phyla. Notably, 67 archaeal genera, representing more than 60 % of all known archaeal genera, were present in this ecosystem. A strong positive correlation (0.85) was observed between the presence of the extremely halophilic bacterium Salinibacter and salinity level. Taxonomic and functional comparisons of the saline desert metagenome with those of other publicly available metagenomes (i.e. sea, hypersaline lagoon, solar saltern, brine, hot desert) was carried out. The microbial community of the Kutch was found to be unique yet more similar to the sea biomes followed by hypersaline lagoon.
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61
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Nolla-Ardèvol V, Strous M, Tegetmeyer HE. Anaerobic digestion of the microalga Spirulina at extreme alkaline conditions: biogas production, metagenome, and metatranscriptome. Front Microbiol 2015; 6:597. [PMID: 26157422 PMCID: PMC4475827 DOI: 10.3389/fmicb.2015.00597] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/31/2015] [Indexed: 12/02/2022] Open
Abstract
A haloalkaline anaerobic microbial community obtained from soda lake sediments was used to inoculate anaerobic reactors for the production of methane rich biogas. The microalga Spirulina was successfully digested by the haloalkaline microbial consortium at alkaline conditions (pH 10, 2.0 M Na+). Continuous biogas production was observed and the obtained biogas was rich in methane, up to 96%. Alkaline medium acted as a CO2 scrubber which resulted in low amounts of CO2 and no traces of H2S in the produced biogas. A hydraulic retention time (HRT) of 15 days and 0.25 g Spirulina L−1 day−1 organic loading rate (OLR) were identified as the optimal operational parameters. Metagenomic and metatranscriptomic analysis showed that the hydrolysis of the supplied substrate was mainly carried out by Bacteroidetes of the “ML635J-40 aquatic group” while the hydrogenotrophic pathway was the main producer of methane in a methanogenic community dominated by Methanocalculus.
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Affiliation(s)
- Vímac Nolla-Ardèvol
- Institute for Genome Research and Systems Biology, Center for Biotechnology, University of Bielefeld Bielefeld, Germany
| | - Marc Strous
- Institute for Genome Research and Systems Biology, Center for Biotechnology, University of Bielefeld Bielefeld, Germany ; Department of Geoscience, University of Calgary Calgary, AB, Canada ; Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Halina E Tegetmeyer
- Institute for Genome Research and Systems Biology, Center for Biotechnology, University of Bielefeld Bielefeld, Germany ; Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany ; HGF-MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research Bremerhaven, Germany
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62
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Preiss L, Hicks DB, Suzuki S, Meier T, Krulwich TA. Alkaliphilic Bacteria with Impact on Industrial Applications, Concepts of Early Life Forms, and Bioenergetics of ATP Synthesis. Front Bioeng Biotechnol 2015; 3:75. [PMID: 26090360 PMCID: PMC4453477 DOI: 10.3389/fbioe.2015.00075] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/10/2015] [Indexed: 12/28/2022] Open
Abstract
Alkaliphilic bacteria typically grow well at pH 9, with the most extremophilic strains growing up to pH values as high as pH 12–13. Interest in extreme alkaliphiles arises because they are sources of useful, stable enzymes, and the cells themselves can be used for biotechnological and other applications at high pH. In addition, alkaline hydrothermal vents represent an early evolutionary niche for alkaliphiles and novel extreme alkaliphiles have also recently been found in alkaline serpentinizing sites. A third focus of interest in alkaliphiles is the challenge raised by the use of proton-coupled ATP synthases for oxidative phosphorylation by non-fermentative alkaliphiles. This creates a problem with respect to tenets of the chemiosmotic model that remains the core model for the bioenergetics of oxidative phosphorylation. Each of these facets of alkaliphilic bacteria will be discussed with a focus on extremely alkaliphilic Bacillus strains. These alkaliphilic bacteria have provided a cogent experimental system to probe adaptations that enable their growth and oxidative phosphorylation at high pH. Adaptations are clearly needed to enable secreted or partially exposed enzymes or protein complexes to function at the high external pH. Also, alkaliphiles must maintain a cytoplasmic pH that is significantly lower than the pH of the outside medium. This protects cytoplasmic components from an external pH that is alkaline enough to impair their stability or function. However, the pH gradient across the cytoplasmic membrane, with its orientation of more acidic inside than outside, is in the reverse of the productive orientation for bioenergetic work. The reversed gradient reduces the trans-membrane proton-motive force available to energize ATP synthesis. Multiple strategies are hypothesized to be involved in enabling alkaliphiles to circumvent the challenge of a low bulk proton-motive force energizing proton-coupled ATP synthesis at high pH.
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Affiliation(s)
- Laura Preiss
- Department of Structural Biology, Max Planck Institute of Biophysics , Frankfurt , Germany
| | - David B Hicks
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai , New York, NY , USA
| | - Shino Suzuki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology , Nankoku , Japan ; Microbial and Environmental Genomics, J. Craig Venter Institutes , La Jolla, CA , USA
| | - Thomas Meier
- Department of Structural Biology, Max Planck Institute of Biophysics , Frankfurt , Germany
| | - Terry Ann Krulwich
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai , New York, NY , USA
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63
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Banciu HL, Muntyan MS. Adaptive strategies in the double-extremophilic prokaryotes inhabiting soda lakes. Curr Opin Microbiol 2015; 25:73-9. [PMID: 26025020 DOI: 10.1016/j.mib.2015.05.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 04/27/2015] [Accepted: 05/01/2015] [Indexed: 10/23/2022]
Abstract
Haloalkaliphiles are double extremophilic organisms thriving both at high salinity and alkaline pH. Although numerous haloalkaliphilic representatives have been identified among Archaea and Bacteria over the past 15 years, the adaptations underlying their prosperity at haloalkaline conditions are scarcely known. A multi-level adaptive strategy was proposed to occur in haloalkaliphilic organisms isolated from saline alkaline and soda environments including adjustments in the cell wall structure, plasma membrane lipid composition, membrane transport systems, bioenergetics, and osmoregulation. Isolation of chemolithoautotrophic sulfur-oxidizing γ-Proteobacteria from soda lakes allowed the elucidation of the structural and physiological differences between haloalkaliphilic (prefer NaCl) and natronophilic (prefer NaHCO3/Na2CO3, i.e. soda) microbes.
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Affiliation(s)
- Horia Leonard Banciu
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babeş-Bolyai University, 400271 Cluj-Napoca, Romania; Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, 400006 Cluj-Napoca, Romania.
| | - Maria S Muntyan
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Moscow 119991, Russia
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64
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Sorokin DY, Banciu HL, Muyzer G. Functional microbiology of soda lakes. Curr Opin Microbiol 2015; 25:88-96. [PMID: 26025021 DOI: 10.1016/j.mib.2015.05.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 04/30/2015] [Accepted: 05/01/2015] [Indexed: 10/23/2022]
Abstract
Soda lakes represent unique permanently haloalkaline system. Despite the harsh conditions, they are inhabited by abundant, mostly prokaryotic, microbial communities. This review summarizes results of studies of main functional groups of the soda lake prokaryotes responsible for carbon, nitrogen and sulfur cycling, including oxygenic and anoxygenic phototrophs, aerobic chemolithotrophs, fermenting and respiring anaerobes. The main conclusion from this work is that the soda lakes are very different from other high-salt systems in respect to microbial richness and activity. The reason for this difference is determined by the major physico-chemical features of two dominant salts - NaCl in neutral saline systems and sodium carbonates in soda lakes, that are influencing the amount of energy required for osmotic adaptation.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia; Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.
| | - Horia L Banciu
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Babeş-Bolyai University, Cluj-Napoca, Romania; Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2015; 2015:646820. [PMID: 26074731 PMCID: PMC4444560 DOI: 10.1155/2015/646820] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 04/15/2015] [Indexed: 11/17/2022]
Abstract
In this study the archaeal communities in extreme saline-alkaline soils of the former lake Texcoco, Mexico, with electrolytic conductivities (EC) ranging from 0.7 to 157.2 dS/m and pH from 8.5 to 10.5 were explored. Archaeal communities in the 0.7 dS/m pH 8.5 soil had the lowest alpha diversity values and were dominated by a limited number of phylotypes belonging to the mesophilic Candidatus Nitrososphaera. Diversity and species richness were higher in the soils with EC between 9.0 and 157.2 dS/m. The majority of OTUs detected in the hypersaline soil were members of the Halobacteriaceae family. Novel phylogenetic branches in the Halobacteriales class were detected in the soil, and more abundantly in soil with the higher pH (10.5), indicating that unknown and uncharacterized Archaea can be found in this soil. Thirteen different genera of the Halobacteriaceae family were identified and were distributed differently between the soils. Halobiforma, Halostagnicola, Haloterrigena, and Natronomonas were found in all soil samples. Methanogenic archaea were found only in soil with pH between 10.0 and 10.3. Retrieved methanogenic archaea belonged to the Methanosarcinales and Methanomicrobiales orders. The comparison of the archaeal community structures considering phylogenetic information (UniFrac distances) clearly clustered the communities by pH.
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66
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Andrei AŞ, Robeson MS, Baricz A, Coman C, Muntean V, Ionescu A, Etiope G, Alexe M, Sicora CI, Podar M, Banciu HL. Contrasting taxonomic stratification of microbial communities in two hypersaline meromictic lakes. ISME JOURNAL 2015; 9:2642-56. [PMID: 25932617 DOI: 10.1038/ismej.2015.60] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Revised: 02/14/2015] [Accepted: 03/18/2015] [Indexed: 11/09/2022]
Abstract
Hypersaline meromictic lakes are extreme environments in which water stratification is associated with powerful physicochemical gradients and high salt concentrations. Furthermore, their physical stability coupled with vertical water column partitioning makes them important research model systems in microbial niche differentiation and biogeochemical cycling. Here, we compare the prokaryotic assemblages from Ursu and Fara Fund hypersaline meromictic lakes (Transylvanian Basin, Romania) in relation to their limnological factors and infer their role in elemental cycling by matching taxa to known taxon-specific biogeochemical functions. To assess the composition and structure of prokaryotic communities and the environmental factors that structure them, deep-coverage small subunit (SSU) ribosomal RNA (rDNA) amplicon sequencing, community domain-specific quantitative PCR and physicochemical analyses were performed on samples collected along depth profiles. The analyses showed that the lakes harbored multiple and diverse prokaryotic communities whose distribution mirrored the water stratification patterns. Ursu Lake was found to be dominated by Bacteria and to have a greater prokaryotic diversity than Fara Fund Lake that harbored an increased cell density and was populated mostly by Archaea within oxic strata. In spite of their contrasting diversity, the microbial populations indigenous to each lake pointed to similar physiological functions within carbon degradation and sulfate reduction. Furthermore, the taxonomy results coupled with methane detection and its stable C isotope composition indicated the presence of a yet-undescribed methanogenic group in the lakes' hypersaline monimolimnion. In addition, ultrasmall uncultivated archaeal lineages were detected in the chemocline of Fara Fund Lake, where the recently proposed Nanohaloarchaeota phylum was found to thrive.
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Affiliation(s)
- Adrian-Ştefan Andrei
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babeş-Bolyai University, Cluj-Napoca, Romania.,Department of Molecular Biology and Biotechnology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Michael S Robeson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Fish, Wildlife and Conservation Biology, Colorado State University, Fort Collins, CO, USA
| | - Andreea Baricz
- Department of Molecular Biology and Biotechnology, Babeş-Bolyai University, Cluj-Napoca, Romania.,National Institute of Research and Development for Biological Sciences (NIRDBS), Institute of Biological Research, Cluj-Napoca, Romania
| | - Cristian Coman
- Department of Molecular Biology and Biotechnology, Babeş-Bolyai University, Cluj-Napoca, Romania.,National Institute of Research and Development for Biological Sciences (NIRDBS), Institute of Biological Research, Cluj-Napoca, Romania
| | - Vasile Muntean
- Department of Molecular Biology and Biotechnology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Artur Ionescu
- Faculty of Environmental Science and Engineering, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Giuseppe Etiope
- Faculty of Environmental Science and Engineering, Babeş-Bolyai University, Cluj-Napoca, Romania.,Istituto Nazionale di Geofisica e Vulcanologia, Rome, Italy
| | - Mircea Alexe
- Faculty of Geography, Babeş-Bolyai University, Cluj-Napoca, Romania
| | | | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Horia Leonard Banciu
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babeş-Bolyai University, Cluj-Napoca, Romania.,Department of Molecular Biology and Biotechnology, Babeş-Bolyai University, Cluj-Napoca, Romania
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67
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Glaring MA, Vester JK, Lylloff JE, Abu Al-Soud W, Sørensen SJ, Stougaard P. Microbial diversity in a permanently cold and alkaline environment in Greenland. PLoS One 2015; 10:e0124863. [PMID: 25915866 PMCID: PMC4411134 DOI: 10.1371/journal.pone.0124863] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 03/09/2015] [Indexed: 02/01/2023] Open
Abstract
The submarine ikaite columns located in the Ikka Fjord in Southern Greenland represent a unique, permanently cold (less than 6°C) and alkaline (above pH 10) environment and are home to a microbial community adapted to these extreme conditions. The bacterial and archaeal community inhabiting the ikaite columns and surrounding fjord was characterised by high-throughput pyrosequencing of 16S rRNA genes. Analysis of the ikaite community structure revealed the presence of a diverse bacterial community, both in the column interior and at the surface, and very few archaea. A clear difference in overall taxonomic composition was observed between column interior and surface. Whereas the surface, and in particular newly formed ikaite material, was primarily dominated by Cyanobacteria and phototrophic Proteobacteria, the column interior was dominated by Proteobacteria and putative anaerobic representatives of the Firmicutes and Bacteroidetes. The results suggest a stratification of the ikaite columns similar to that of classical soda lakes, with a light-exposed surface inhabited by primary producers and an anoxic subsurface. This was further supported by identification of major taxonomic groups with close relatives in soda lake environments, including members of the genera Rhodobaca, Dethiobacter, Thioalkalivibrio and Tindallia, as well as very abundant groups related to uncharacterised environmental sequences originally isolated from Mono Lake in California.
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Affiliation(s)
- Mikkel A. Glaring
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jan K. Vester
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jeanette E. Lylloff
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Søren J. Sørensen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Peter Stougaard
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
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68
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Anders H, Power JF, MacKenzie AD, Lagutin K, Vyssotski M, Hanssen E, Moreau JW, Stott MB. Limisphaera ngatamarikiensis gen. nov., sp. nov., a thermophilic, pink-pigmented coccus isolated from subaqueous mud of a geothermal hotspring. Int J Syst Evol Microbiol 2015; 65:1114-1121. [DOI: 10.1099/ijs.0.000063] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain, NGM72.4T, was isolated from a hot spring in the Ngatamariki geothermal field, New Zealand. Phylogenetic analysis based on 16S rRNA gene sequences grouped it into the phylum
Verrucomicrobia
and class level group 3 (also known as OPB35 soil group). NGM72.4T stained Gram-negative, and was catalase- and oxidase-positive. Cells were small cocci, 0.5–0.8 µm in diameter, which were motile by means of single flagella. Transmission electron micrograph (TEM) imaging showed an unusual pirellulosome-like intracytoplasmic membrane. The peptidoglycan content was very small with only trace levels of diaminopimelic acid detected. No peptidoglycan structure was visible in TEM imaging. The predominant isoprenoid quinone was MK-7 (92 %). The major fatty acids (>15 %) were C16 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Major phospholipids were phosphatidylethanolamine (PE), phosphatidylmonomethylethanolamine (PMME) and cardiolipin (CL), and a novel analogous series of phospholipids where diacylglycerol was replaced with diacylserinol (sPE, sPMME, sCL). The DNA G+C content was 65.6 mol%. Cells displayed an oxidative chemoheterotrophic metabolism. NGM72.4T is a strictly aerobic thermophile (growth optimum 60–65 °C), has a slightly alkaliphilic pH growth optimum (optimum pH 8.1–8.4) and has a NaCl tolerance of up to 8 g l−1. Colonies were small, circular and pigmented pale pink. The distinct phylogenetic position and phenotypic traits of strain NGM72.4T distinguish it from all other described species of the phylum
Verrucomicrobia
and, therefore, it is considered to represent a novel species in a new genus for which we propose the name Limisphaera ngatamarikiensis gen. nov., sp. nov. The type strain is NGM72.4T ( = ICMP 20182T = DSM 27329T).
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Affiliation(s)
- Heike Anders
- Lehrstuhl für Tierhygiene, Technische Universität München, Weihenstephaner Berg 3 0D-85354, Freising, Germany
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupō 3352, New Zealand
| | - Jean F. Power
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupō 3352, New Zealand
| | | | - Kirill Lagutin
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, New Zealand
| | | | - Eric Hanssen
- University of Melbourne, 30 Flemington Road, Victoria 3010, Australia
| | - John W. Moreau
- University of Melbourne, 30 Flemington Road, Victoria 3010, Australia
| | - Matthew B. Stott
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupō 3352, New Zealand
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69
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Lim HC, Chu CC, Seufferheld MJ, Cameron SA. Deep sequencing and ecological characterization of gut microbial communities of diverse bumble bee species. PLoS One 2015; 10:e0118566. [PMID: 25768110 PMCID: PMC4359114 DOI: 10.1371/journal.pone.0118566] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/17/2015] [Indexed: 11/19/2022] Open
Abstract
Gut bacterial communities of bumble bees are correlated with defense against pathogens. Further understanding this host-microbe association is vitally important as bumble bees are currently experiencing global population declines, potentially due in part to emergent diseases. In this study, we used pyrosequencing and community fingerprinting (ARISA) to characterize the gut microbial communities of nine bumble species from across the Bombus phylogeny. Overall, we delimited 74 bacterial taxa (operational taxonomic units or OTUs) belonging to Betaproteobacteria, Gammaproteobacteria, Bacilli, Actinobacteria, Flavobacteria and Alphaproteobacteria. Each bacterial community was taxonomically simple, containing an average of 1.9 common (relative abundance per sample > 5%) bacterial OTUs. The most abundant and prevalent (occurring in 92% of the samples) bacterial OTU, based on 16S rRNA sequences, closely matched that of the previously described Betaproteobacteria species Snodgrassella alvi. Bacteria that were first described in bee-related external environments dominated a number of gut bacterial communities, suggesting that they are not strictly dependent on the internal gut environment. The ARISA data showed a correlation between bacterial community structures and the geographic locations where the bees were sampled, suggesting that at least a subset of the bacterial species may be transmitted environmentally. Using light and fluorescent microscopy, we demonstrated that the gut bacteria form a biofilm on the internal epithelial surface of the ileum, corroborating results obtained from Apis mellifera.
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Affiliation(s)
- Haw Chuan Lim
- Department of Entomology, University of Illinois, Urbana, IL, 61801, United States of America
- * E-mail: (HCL); (MJS); (SAC)
| | - Chia-Ching Chu
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, United States of America
| | - Manfredo J. Seufferheld
- Department of Entomology, University of Illinois, Urbana, IL, 61801, United States of America
- * E-mail: (HCL); (MJS); (SAC)
| | - Sydney A. Cameron
- Department of Entomology, University of Illinois, Urbana, IL, 61801, United States of America
- * E-mail: (HCL); (MJS); (SAC)
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70
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Baldwin SA, Khoshnoodi M, Rezadehbashi M, Taupp M, Hallam S, Mattes A, Sanei H. The microbial community of a passive biochemical reactor treating arsenic, zinc, and sulfate-rich seepage. Front Bioeng Biotechnol 2015; 3:27. [PMID: 25798439 PMCID: PMC4351619 DOI: 10.3389/fbioe.2015.00027] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 02/19/2015] [Indexed: 11/13/2022] Open
Abstract
Sulfidogenic biochemical reactors (BCRs) for metal removal that use complex organic carbon have been shown to be effective in laboratory studies, but their performance in the field is highly variable. Successful operation depends on the types of microorganisms supported by the organic matrix, and factors affecting the community composition are unknown. A molecular survey of a field-based BCR that had been removing zinc and arsenic for over 6 years revealed that the microbial community was dominated by methanogens related to Methanocorpusculum sp. and Methanosarcina sp., which co-occurred with Bacteroidetes environmental groups, such as Vadin HA17, in places where the organic matter was more degraded. The metabolic potential for organic matter decomposition by Ruminococcaceae was prevalent in samples with more pyrolyzable carbon. Rhodobium- and Hyphomicrobium-related genera within the Rhizobiales order that have the metabolic potential for dark hydrogen fermentation and methylotrophy, and unclassified Comamonadaceae were the dominant Proteobacteria. The unclassified environmental group Sh765B-TzT-29 was an important Delta-Proteobacteria group in this BCR that co-occurred with the dominant Rhizobiales operational taxonomic units. Organic matter degradation is one driver for shifting the microbial community composition and therefore possibly the performance of these bioreactors over time.
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Affiliation(s)
- Susan Anne Baldwin
- Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Maryam Khoshnoodi
- Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Maryam Rezadehbashi
- Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Marcus Taupp
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Steven Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Al Mattes
- NatureWorks Remediation Corporation, Rossland, BC, Canada
| | - Hamed Sanei
- Geological Survey of Canada, Calgary, AB, Canada
- Center for Energy Technologies (CET), AU-Herning, Aarhus University, Herning, Denmark
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
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71
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Della Porta G. Carbonate build-ups in lacustrine, hydrothermal and fluvial settings: comparing depositional geometry, fabric types and geochemical signature. ACTA ACUST UNITED AC 2015. [DOI: 10.1144/sp418.4] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AbstractCarbonate build-ups in lakes, hydrothermal and fluvial settings are characterized by distinctive geometry, spatial distribution, fabrics and geochemical signature but also by some comparable features. Lake margin bioherms form continuous belts for hundreds of metres to kilometres, subparallel to shorelines. Sublacustrine spring mounds are spaced at hundreds of metres to kilometres and aligned along faults. Hydrothermal travertine mounds and aprons with planar clinoforms or terraced slopes are controlled by faults, thermal water discharge and substrate topography. Fluvial tufa barrages, cascades and terraced slopes are controlled by climate, vegetation and substrate gradient. The wide spectrum of carbonate microfabrics ranges from clotted peloidal micrite and laminated boundstone to crystalline dendrite cementstone. Non-marine carbonate microfabrics cannot be linked to specific depositional environments, and are not deterministic proxies for the interpretation of build-up architecture. Microfabric associations can be indicative, but not exclusive, of specific depositional environments and geometry. Stable isotope geochemistry is a useful tool to distinguish between hydrothermal, karstic freshwater and evaporative lake carbonates. Carbonate precipitation results from a continuum of abiotic and biologically influenced/induced processes in settings where carbonate supersaturation is largely driven by physico-chemical mechanisms and microbial biofilms, even if acting as passive low-energy surface sites for nucleation, are widely present.
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72
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Culturable diversity of aerobic halophilic archaea (Fam. Halobacteriaceae) from hypersaline, meromictic Transylvanian lakes. Extremophiles 2015; 19:525-37. [DOI: 10.1007/s00792-015-0738-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 01/27/2015] [Indexed: 10/24/2022]
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73
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Sorokin DY, Abbas B, Geleijnse M, Pimenov NV, Sukhacheva MV, van Loosdrecht MCM. Methanogenesis at extremely haloalkaline conditions in the soda lakes of Kulunda Steppe (Altai, Russia). FEMS Microbiol Ecol 2015; 91:fiv016. [PMID: 25764464 DOI: 10.1093/femsec/fiv016] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2015] [Indexed: 11/13/2022] Open
Abstract
Microbial methanogenesis at extreme conditions of saline alkaline soda lakes has, so far, been poorly investigated. Despite the obvious domination of sulfidogenesis as the therminal anaerobic process in the hypersaline soda lakes of Kulunda Steppe (Altai, southwestern Siberia), high concentrations of methane were detected in the anaerobic sediments. Potential activity measurements with different substrates gave results significantly deviating from what is commonly found in hypersaline habitats with neutral pH. In particular, not only a non-competitive methylotrophic pathway was active, but also lithotrophic and, in some cases, even acetate-dependent methanogenesis was found to be present in hypersaline soda lake sediments. All three pathways were functioning exclusively within the alkaline pH range between 8 and 10.5, while the salt concentration was the key factor influencing the activity. Methylotrophic and, to a lesser extent, lithotrophic methanogenesis were active up to soda-saturating conditions (4 M total Na(+)). Acetate-dependent methanogenesis was observed at salinities below 3 M total Na(+). Detection of methanogens in sediments using the mcrA gene as a functional marker demonstrated domination of methylotrophic genera Methanolobus and Methanosalsum and lithotrophic Methanocalculus. In a few cases, acetoclastic Methanosaeta was detected, as well as two deep lineage methanogens. Cultivation results corresponded well to the mcrA-based observations. Enrichments for natronophilic methylotrophic methanogens resulted in isolation of Methanolobus strains at moderate salinity, while at salt concentrations above 2 M Na(+) a novel member of the genus Methanosalsum was dominating. Enrichments with H2 or formate invariably resulted in domination of close relatives of Methanocalculus natronophilus. Enrichments with acetate at low salt concentration yielded two acetoclastic alkaliphilic Methanosaeta cultures, while at salinity above 1 M Na(+) syntrophic associations were apparently responsible for the observed acetate conversion to methane. Overall, the results indicated the presence of functionally structured and active methanogenic populations in Siberian hypersaline soda lakes.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-let Octyabrya 7/2, 117811 Moscow, Russia Department of Biotechnology, Delft University of Technology, 2628 BC Delft, the Netherlands
| | - Ben Abbas
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, the Netherlands
| | - Mitchell Geleijnse
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, the Netherlands
| | - Nikolai V Pimenov
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-let Octyabrya 7/2, 117811 Moscow, Russia
| | - Marina V Sukhacheva
- Centre Bioengineering, Russian Academy of Sciences, Prospect 60-let Octyabrya 7/1, 117312 Moscow, Russia
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74
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Tourova TP, Grechnikova MA, Kuznetsov BB, Sorokin DY. Phylogenetic diversity of bacteria in soda lake stratified sediments. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714060186] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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75
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Edwardson CF, Planer-Friedrich B, Hollibaugh JT. Transformation of monothioarsenate by haloalkaliphilic, anoxygenic photosynthetic purple sulfur bacteria. FEMS Microbiol Ecol 2014; 90:858-68. [PMID: 25318694 DOI: 10.1111/1574-6941.12440] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 10/08/2014] [Accepted: 10/11/2014] [Indexed: 10/24/2022] Open
Abstract
Thioarsenates are the dominant arsenic species in arsenic-rich, alkaline, and sulfidic waters, but bacterial interactions with these compounds have only recently been examined. Previous studies have shown that microorganisms play a role in the transformation of monothioarsenate to arsenate, including use of monothioarsenate as a chemolithotrophic electron donor coupled with oxygen as an electron acceptor. We obtained enrichment cultures from two saline, alkaline lakes (Mono Lake, CA and Big Soda Lake, NV) that are able to use monothioarsenate as the sole electron donor for anoxygenic photosynthesis. These anoxic cultures were able to convert a 1 mM mixture of thioarsenates completely to arsenate in c. 13 days and 4 mM monothioarsenate to arsenate in c. 17 days. This conversion was light dependent; thus, monothioarsenate can be used as the sole electron donor for anoxygenic photosynthesis. Both of the Mono Lake and Big Soda Lake enrichment cultures were dominated by an organism closely related to Ectothiorhodospira species. We tested additional strains of purple sulfur bacteria and found widespread ability to use monothioarsenate as an electron donor. The ability of bacteria to transform thioarsenates directly via anoxygenic photosynthesis adds a new perspective to the well-studied arsenic and sulfur cycles.
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Affiliation(s)
- Christian F Edwardson
- Department of Marine Sciences, University of Georgia, Athens, GA, USA; Department of Microbiology, University of Georgia, Athens, GA, USA
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76
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Tourova TP, Slobodova NV, Bumazhkin BK, Sukhacheva MV, Sorokin DY. Diversity of diazotrophs in the sediments of saline and soda lakes analyzed with the use of the nifH gene as a molecular marker. Microbiology (Reading) 2014. [DOI: 10.1134/s002626171404016x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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77
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Sorokin DY, Berben T, Melton ED, Overmars L, Vavourakis CD, Muyzer G. Microbial diversity and biogeochemical cycling in soda lakes. Extremophiles 2014; 18:791-809. [PMID: 25156418 PMCID: PMC4158274 DOI: 10.1007/s00792-014-0670-9] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 06/26/2014] [Indexed: 01/26/2023]
Abstract
Soda lakes contain high concentrations of sodium carbonates resulting in a stable elevated pH, which provide a unique habitat to a rich diversity of haloalkaliphilic bacteria and archaea. Both cultivation-dependent and -independent methods have aided the identification of key processes and genes in the microbially mediated carbon, nitrogen, and sulfur biogeochemical cycles in soda lakes. In order to survive in this extreme environment, haloalkaliphiles have developed various bioenergetic and structural adaptations to maintain pH homeostasis and intracellular osmotic pressure. The cultivation of a handful of strains has led to the isolation of a number of extremozymes, which allow the cell to perform enzymatic reactions at these extreme conditions. These enzymes potentially contribute to biotechnological applications. In addition, microbial species active in the sulfur cycle can be used for sulfur remediation purposes. Future research should combine both innovative culture methods and state-of-the-art 'meta-omic' techniques to gain a comprehensive understanding of the microbes that flourish in these extreme environments and the processes they mediate. Coupling the biogeochemical C, N, and S cycles and identifying where each process takes place on a spatial and temporal scale could unravel the interspecies relationships and thereby reveal more about the ecosystem dynamics of these enigmatic extreme environments.
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Affiliation(s)
- Dimitry Y. Sorokin
- Winogradsky Institute of Microbiology, RAS, Moscow, Russia
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Tom Berben
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Emily Denise Melton
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Lex Overmars
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Charlotte D. Vavourakis
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Gerard Muyzer
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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78
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Diversity and enzymatic profiling of halotolerant micromycetes from Sebkha El Melah, a Saharan salt flat in southern Tunisia. BIOMED RESEARCH INTERNATIONAL 2014; 2014:439197. [PMID: 25136587 PMCID: PMC4124809 DOI: 10.1155/2014/439197] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 06/28/2014] [Indexed: 11/21/2022]
Abstract
Twenty-one moderately halotolerant fungi have been isolated from sample ashes collected from Sebkha El Melah, a Saharan salt flat located in southern Tunisia. Based on morphology and sequence inference from the internal transcribed spacer regions, 28S rRNA gene and other specific genes such as β-tubulin, actin, calmodulin, and glyceraldehyde-3-phosphate dehydrogenase, the isolates were found to be distributed over 15 taxa belonging to 6 genera of Ascomycetes: Cladosporium (n = 3), Alternaria (n = 4), Aspergillus (n = 3), Penicillium (n = 5), Ulocladium (n = 2), and Engyodontium (n = 2). Their tolerance to different concentrations of salt in solid and liquid media was examined. Excepting Cladosporium cladosporioides JA18, all isolates were considered as alkali-halotolerant since they were able to grow in media containing 10% of salt with an initial pH 10. All isolates were resistant to oxidative stresses and low temperature whereas 5 strains belonging to Alternaria, Ulocladium, and Aspergillus genera were able to grow at 45°C. The screening of fungal strains for sets of enzyme production, namely, cellulase (CMCase), amylase, protease, lipase, and laccase, in presence of 10% NaCl, showed a variety of extracellular hydrolytic and oxidative profiles. Protease was the most abundant enzyme produced whereas laccase producers were members of the genus Cladosporium.
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79
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Hu X. Ciliates in extreme environments. J Eukaryot Microbiol 2014; 61:410-8. [PMID: 24801529 DOI: 10.1111/jeu.12120] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 03/26/2014] [Accepted: 03/27/2014] [Indexed: 11/29/2022]
Abstract
As eukaryotic microbial life, ciliated protozoan may be found actively growing in some extreme condition where there is a sufficient energy source to sustain it because they are exceedingly adaptable and not notably less adaptable than the prokaryotes. However, a crucial problem in the study of ciliates in extreme environments is the lack of reliable cultivation techniques. To our knowledge, only a tiny fraction of ciliates can be cultured in the laboratory, even for a very limited period, which can partly explain the paucity of our understanding about ciliates diversity in various extremes although the interest in the biodiversity of extremophiles increased significantly during the past three decades. This mini-review aims to compile the knowledge of several groups of free-living ciliates that can be microscopically observed in extreme environmental samples, although most habitats have not been sufficiently well explored for sound generalizations.
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Affiliation(s)
- Xiaozhong Hu
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity & College of Fisheries, Ocean University of China, Qingdao, 266003, China
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80
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Bacterial diversity in saline-alkali ponds rearing common carp (Cyprinus carpio) as revealed by 16S rRNA gene sequences. Biologia (Bratisl) 2014. [DOI: 10.2478/s11756-014-0378-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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81
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Ishii S, Suzuki S, Norden-Krichmar TM, Phan T, Wanger G, Nealson KH, Sekiguchi Y, Gorby YA, Bretschger O. Microbial population and functional dynamics associated with surface potential and carbon metabolism. THE ISME JOURNAL 2014; 8:963-78. [PMID: 24351938 PMCID: PMC3996694 DOI: 10.1038/ismej.2013.217] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 09/04/2013] [Accepted: 11/02/2013] [Indexed: 11/08/2022]
Abstract
Microbial extracellular electron transfer (EET) to solid surfaces is an important reaction for metal reduction occurring in various anoxic environments. However, it is challenging to accurately characterize EET-active microbial communities and each member's contribution to EET reactions because of changes in composition and concentrations of electron donors and solid-phase acceptors. Here, we used bioelectrochemical systems to systematically evaluate the synergistic effects of carbon source and surface redox potential on EET-active microbial community development, metabolic networks and overall electron transfer rates. The results indicate that faster biocatalytic rates were observed under electropositive electrode surface potential conditions, and under fatty acid-fed conditions. Temporal 16S rRNA-based microbial community analyses showed that Geobacter phylotypes were highly diverse and apparently dependent on surface potentials. The well-known electrogenic microbes affiliated with the Geobacter metallireducens clade were associated with lower surface potentials and less current generation, whereas Geobacter subsurface clades 1 and 2 were associated with higher surface potentials and greater current generation. An association was also observed between specific fermentative phylotypes and Geobacter phylotypes at specific surface potentials. When sugars were present, Tolumonas and Aeromonas phylotypes were preferentially associated with lower surface potentials, whereas Lactococcus phylotypes were found to be closely associated with Geobacter subsurface clades 1 and 2 phylotypes under higher surface potential conditions. Collectively, these results suggest that surface potentials provide a strong selective pressure, at the species and strain level, for both solid surface respirators and fermentative microbes throughout the EET-active community development.
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Affiliation(s)
- Shun'ichi Ishii
- J. Craig Venter Institute, La Jolla, CA, USA
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
- Japan Society for the Promotion of Science (JSPS), Chiyoda-ku, Tokyo, Japan
| | | | | | - Tony Phan
- J. Craig Venter Institute, La Jolla, CA, USA
| | - Greg Wanger
- J. Craig Venter Institute, La Jolla, CA, USA
| | - Kenneth H Nealson
- J. Craig Venter Institute, La Jolla, CA, USA
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Yuri A Gorby
- J. Craig Venter Institute, La Jolla, CA, USA
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
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82
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Farías ME, Contreras M, Rasuk MC, Kurth D, Flores MR, Poiré DG, Novoa F, Visscher PT. Characterization of bacterial diversity associated with microbial mats, gypsum evaporites and carbonate microbialites in thalassic wetlands: Tebenquiche and La Brava, Salar de Atacama, Chile. Extremophiles 2014; 18:311-29. [DOI: 10.1007/s00792-013-0617-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 12/05/2013] [Indexed: 02/01/2023]
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83
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Baricz A, Coman C, Andrei AS, Muntean V, Keresztes ZG, Păuşan M, Alexe M, Banciu HL. Spatial and temporal distribution of archaeal diversity in meromictic, hypersaline Ocnei Lake (Transylvanian Basin, Romania). Extremophiles 2014; 18:399-413. [PMID: 24414798 DOI: 10.1007/s00792-013-0625-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/29/2013] [Indexed: 12/31/2022]
Abstract
Saline, meromictic lakes with significant depth are usually formed as a result of salt mining activity. Ocnei Lake is one of the largest Transylvanian (Central Romania) neutral, hypersaline lake of man-made origin. We aimed to survey the seasonal dynamics of archaeal diversity in the water column of Ocnei Lake by employing microbiological methods as well as molecular techniques based on the sequence analysis of the 16S rRNA gene. We found that archaeal diversity in the water column increased with depth and salinity, with 8 OTUs being detected in the epilimnion compared to 21 found in the chemocline, and 32 OTUs in the monimolimnion. Down to 3.5 m depth, the archaeal community was markedly dominated by the presence of an unclassified archaeon sharing 93% sequence identity to Halogeometricum spp. At the chemocline, the shift in archaeal community composition was associated with an increase in salinity, the main factor affecting the vertical distribution of archaeal assemblages. It appears that the microoxic and hypersaline monimolimnion is populated by several major haloarchaeal taxa, with minor fluctuations in their relative abundances throughout all seasons. The culturable diversity was reasonably correlated to the dominant OTUs obtained by molecular methods. Our results indicate that Ocnei Lake represents a relatively stable extreme habitat, accommodating a diverse and putatively novel archaeal community, as 30% of OTUs could not be classified at the genus level.
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Affiliation(s)
- Andreea Baricz
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, 5-7 Clinicilor Street, 400006, Cluj-Napoca, Romania
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84
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Bacterial diversity and hydrography of Etoliko, an anoxic semi-enclosed coastal basin in Western Greece. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0700-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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85
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Lanzén A, Simachew A, Gessesse A, Chmolowska D, Jonassen I, Øvreås L. Surprising prokaryotic and eukaryotic diversity, community structure and biogeography of Ethiopian soda lakes. PLoS One 2013; 8:e72577. [PMID: 24023625 PMCID: PMC3758324 DOI: 10.1371/journal.pone.0072577] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 07/11/2013] [Indexed: 11/18/2022] Open
Abstract
Soda lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. This makes them valuable model systems for studying the connection between community structure and abiotic parameters such as pH and salinity. For the first time, we apply high-throughput sequencing to accurately estimate phylogenetic richness and composition in five soda lakes, located in the Ethiopian Rift Valley. The lakes were selected for their contrasting pH, salinities and stratification and several depths or spatial positions were covered in each lake. DNA was extracted and analyzed from all lakes at various depths and RNA extracted from two of the lakes, analyzed using both amplicon- and shotgun sequencing. We reveal a surprisingly high biodiversity in all of the studied lakes, similar to that of freshwater lakes. Interestingly, diversity appeared uncorrelated or positively correlated to pH and salinity, with the most “extreme” lakes showing the highest richness. Together, pH, dissolved oxygen, sodium- and potassium concentration explained approximately 30% of the compositional variation between samples. A diversity of prokaryotic and eukaryotic taxa could be identified, including several putatively involved in carbon-, sulfur- or nitrogen cycling. Key processes like methane oxidation, ammonia oxidation and ‘nitrifier denitrification’ were also confirmed by mRNA transcript analyses.
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Affiliation(s)
- Anders Lanzén
- Department of Biology and Centre for Geobiology, University of Bergen, Bergen, Norway
- Computational Biology Unit, Uni Computing, Uni Research AS, Bergen, Norway
- * E-mail:
| | - Addis Simachew
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Amare Gessesse
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Dominika Chmolowska
- Institute of Environmental Sciences, Jagiellonian University, Krakow, Poland
| | - Inge Jonassen
- Computational Biology Unit, Uni Computing, Uni Research AS, Bergen, Norway
- Department of Informatics, University of Bergen, Bergen, Norway
| | - Lise Øvreås
- Department of Biology and Centre for Geobiology, University of Bergen, Bergen, Norway
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86
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Oueriaghli N, Béjar V, Quesada E, Martínez-Checa F. Molecular ecology techniques reveal both spatial and temporal variations in the diversity of archaeal communities within the athalassohaline environment of Rambla Salada, Spain. MICROBIAL ECOLOGY 2013; 66:297-311. [PMID: 23354292 DOI: 10.1007/s00248-013-0176-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 01/01/2013] [Indexed: 05/04/2023]
Abstract
We have studied the distribution of the archaeal communities in Rambla Salada (Murcia, Spain) over three different seasons and observed the influence upon them of the environmental variables, salinity, pH, oxygen and temperature. Samples were collected from three representative sites in order to gain an insight into the archaeal population of the rambla as a whole. Denaturing gradient gel electrophoresis patterns and diversity indexes indicate that the diversity of the archaeal community in Rambla Salada changed mainly according to the season. We found no significant differences between the types of sample studied: watery sediments and soils. The upwelling zone showed most diversity in its archaeal community. The overall archaeal community was composed mainly of Halobacteriales and Thermoplasmatales, accounting for 72.6 and 12.1 % of the total, respectively. Haloarcula was the most abundant genus, being present at all three sites during all three seasons. Some few Crenarchaeota were always found, mainly at low-salinity levels. Ordination canonical correspondence analysis demonstrated that salinity affected the structure of the community significantly, whilst pH, oxygen and temperature did so to a lesser extent. Most Halobacteriales correlated positively with salinity and pH, whilst Thermoplasmatales correlated negatively with both salinity and pH and positively with temperature and oxygen. The archaeal community with the highest diversity was sampled during June 2006, the season with the highest salt concentration. Catalyzed reporter deposition-fluorescence in situ hybridization showed that the percentage of archaea in Rambla Salada compared to the total number of microorganisms (as measured by DAPI) ranged from 11.1 to 16.7 %. Our research group had isolated the most abundant taxon, Haloarcula, previously in Rambla Salada using classical culture techniques, but on this occasion, using culture-independent methods, we were also able to identify some phylotypes, Halorubrum, Methanolobus, Natronomonas, Halomicrobium, Halobacterium, Halosimplex, uncultured Thermoplasmatales and uncultured Crenarchaeota, that had remained undetected during our earlier studies in this habitat.
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Affiliation(s)
- Nahid Oueriaghli
- Microbial Exopolysaccharide Research Group, Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071, Granada, Spain
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87
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Zhang L, Gao G, Tang X, Shao K, Bayartu S, Dai J. Bacterial community changes along a salinity gradient in a Chinese wetland. Can J Microbiol 2013; 59:611-9. [PMID: 24011344 DOI: 10.1139/cjm-2013-0212] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We analyzed the composition and diversity of a bacterial community to determine its response to increasing salinity in the Xiangsi Lake wetland in the arid region of northwest China. We studied 12 sites, ranging from freshwater to saltwater habitats, using polymerase chain reaction (PCR)-based terminal restriction fragment length polymorphism (T-RFLP) and sequencing of the 16S rRNA genes of 5 selected samples. Cluster analysis and phylogenetic analysis revealed that the bacterial community changed significantly in response to increased salinity within the small-scale wetland (50.8 km(2)). Detailed analysis showed that (i) Betaproteobacteria can maintain balanced growth over a salinity range (from 0.34 to 6.86 g/L) through intergenus changes in community structure, followed by a sharp decrease in relative abundance (from 62.2% to 16.0%) when salinity reaches 26.18 g/L; (ii) salt-sensitive and halophobic taxa were progressively replaced by halotolerant and halophilic taxa with increasing salinity; (iii) bacterial diversity was lowest at intermediate salinity levels (6.86 g/L); and (iv) an increasing percentage of unclassified bacterial taxa were found with increasing salinity. This study has implications to improve understanding of bacterial community response to water salinization.
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Affiliation(s)
- Lei Zhang
- a State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing 210008, People's Republic of China
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88
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Zeng J, Deng LJ, Lou K, Zhang T, Yang HM, Shi YW, Lin Q. Molecular characterization of the planktonic microorganisms in water of two mountain brackish lakes. J Basic Microbiol 2013; 54:509-20. [DOI: 10.1002/jobm.201300187] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 05/25/2013] [Indexed: 12/13/2022]
Affiliation(s)
- Jun Zeng
- Institute of Microbiology; Xinjiang Academy of Agriculture Science; Urumqi China
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Li-Juan Deng
- Institute of Microbiology; Xinjiang Academy of Agriculture Science; Urumqi China
| | - Kai Lou
- Institute of Microbiology; Xinjiang Academy of Agriculture Science; Urumqi China
| | - Tao Zhang
- Institute of Microbiology; Xinjiang Academy of Agriculture Science; Urumqi China
| | - Hong-Mei Yang
- Institute of Microbiology; Xinjiang Academy of Agriculture Science; Urumqi China
| | - Ying-Wu Shi
- Institute of Microbiology; Xinjiang Academy of Agriculture Science; Urumqi China
| | - Qing Lin
- Institute of Microbiology; Xinjiang Academy of Agriculture Science; Urumqi China
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89
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Cai HY, Yan ZS, Wang AJ, Krumholz LR, Jiang HL. Analysis of the attached microbial community on mucilaginous cyanobacterial aggregates in the eutrophic Lake Taihu reveals the importance of Planctomycetes. MICROBIAL ECOLOGY 2013; 66:73-83. [PMID: 23571665 DOI: 10.1007/s00248-013-0224-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 03/22/2013] [Indexed: 05/12/2023]
Abstract
The phylogenetic diversity of the microbial community assemblage of the carpet-like mucilaginous cyanobacterial blooms in the eutrophic Lake Taihu was investigated. 16S ribosomal DNA clone libraries produced from the DNA of cyanobacterial assemblages that had been washed to remove unattached bacteria contained only cyanobacteria. However, a further treatment which included grinding the freeze-dried material to physically detach cells followed by the removal of larger cells by filtration allowed us to detect a large variety of bacteria within the cyanobacterial bloom community. Interestingly, the dominant members of the microbial community were Planctomycetes followed by Cytophaga-Flavobacterium-Bacteroides (CFB), Betaproteobacteria, and Gammaproteobacteria. The analysis of the 16S ribosomal DNA clone libraries made from enrichment culture revealed much higher phylogenetic diversity of bacteria. Dominant bacterial groups in the enrichment system were identified as members of the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria subdivisions, CFB group, and Planctomycetes. In addition, the clone libraries constructed from Planctomycetes-specific 16S ribosomal RNA primers also verified that the enrichment allowed a diversity of Planctomycetes to proliferate, although the community composition was altered after enrichment.
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Affiliation(s)
- Hai-Yuan Cai
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, People's Republic of China
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90
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Casamayor EO, Triadó-Margarit X, Castañeda C. Microbial biodiversity in saline shallow lakes of the Monegros Desert, Spain. FEMS Microbiol Ecol 2013; 85:503-18. [DOI: 10.1111/1574-6941.12139] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/18/2013] [Accepted: 04/19/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
- Emilio O. Casamayor
- Biodiversity and Biogeodynamics Group; Centre d'Estudis Avançats de Blanes; CSIC; Blanes Spain
| | - Xavier Triadó-Margarit
- Biodiversity and Biogeodynamics Group; Centre d'Estudis Avançats de Blanes; CSIC; Blanes Spain
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91
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Yau S, Lauro FM, Williams TJ, Demaere MZ, Brown MV, Rich J, Gibson JA, Cavicchioli R. Metagenomic insights into strategies of carbon conservation and unusual sulfur biogeochemistry in a hypersaline Antarctic lake. ISME JOURNAL 2013; 7:1944-61. [PMID: 23619305 DOI: 10.1038/ismej.2013.69] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 03/20/2013] [Accepted: 03/24/2013] [Indexed: 01/14/2023]
Abstract
Organic Lake is a shallow, marine-derived hypersaline lake in the Vestfold Hills, Antarctica that has the highest reported concentration of dimethylsulfide (DMS) in a natural body of water. To determine the composition and functional potential of the microbial community and learn about the unusual sulfur chemistry in Organic Lake, shotgun metagenomics was performed on size-fractionated samples collected along a depth profile. Eucaryal phytoflagellates were the main photosynthetic organisms. Bacteria were dominated by the globally distributed heterotrophic taxa Marinobacter, Roseovarius and Psychroflexus. The dominance of heterotrophic degradation, coupled with low fixation potential, indicates possible net carbon loss. However, abundant marker genes for aerobic anoxygenic phototrophy, sulfur oxidation, rhodopsins and CO oxidation were also linked to the dominant heterotrophic bacteria, and indicate the use of photo- and lithoheterotrophy as mechanisms for conserving organic carbon. Similarly, a high genetic potential for the recycling of nitrogen compounds likely functions to retain fixed nitrogen in the lake. Dimethylsulfoniopropionate (DMSP) lyase genes were abundant, indicating that DMSP is a significant carbon and energy source. Unlike marine environments, DMSP demethylases were less abundant, indicating that DMSP cleavage is the likely source of high DMS concentration. DMSP cleavage, carbon mixotrophy (photoheterotrophy and lithoheterotrophy) and nitrogen remineralization by dominant Organic Lake bacteria are potentially important adaptations to nutrient constraints. In particular, carbon mixotrophy relieves the extent of carbon oxidation for energy production, allowing more carbon to be used for biosynthetic processes. The study sheds light on how the microbial community has adapted to this unique Antarctic lake environment.
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Affiliation(s)
- Sheree Yau
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia
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92
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Planktonic bacterial community composition of an extremely shallow soda pond during a phytoplankton bloom revealed by cultivation and molecular cloning. Extremophiles 2013; 17:575-84. [DOI: 10.1007/s00792-013-0540-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 04/11/2013] [Indexed: 10/26/2022]
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93
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Paul Antony C, Kumaresan D, Hunger S, Drake HL, Murrell JC, Shouche YS. Microbiology of Lonar Lake and other soda lakes. THE ISME JOURNAL 2013; 7:468-76. [PMID: 23178675 PMCID: PMC3578565 DOI: 10.1038/ismej.2012.137] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 09/17/2012] [Accepted: 09/28/2012] [Indexed: 11/08/2022]
Abstract
Soda lakes are saline and alkaline ecosystems that are believed to have existed throughout the geological record of Earth. They are widely distributed across the globe, but are highly abundant in terrestrial biomes such as deserts and steppes and in geologically interesting regions such as the East African Rift valley. The unusual geochemistry of these lakes supports the growth of an impressive array of microorganisms that are of ecological and economic importance. Haloalkaliphilic Bacteria and Archaea belonging to all major trophic groups have been described from many soda lakes, including lakes with exceptionally high levels of heavy metals. Lonar Lake is a soda lake that is centered at an unusual meteorite impact structure in the Deccan basalts in India and its key physicochemical and microbiological characteristics are highlighted in this article. The occurrence of diverse functional groups of microbes, such as methanogens, methanotrophs, phototrophs, denitrifiers, sulfur oxidizers, sulfate reducers and syntrophs in soda lakes, suggests that these habitats harbor complex microbial food webs that (a) interconnect various biological cycles via redox coupling and (b) impact on the production and consumption of greenhouse gases. Soda lake microorganisms harbor several biotechnologically relevant enzymes and biomolecules (for example, cellulases, amylases, ectoine) and there is the need to augment bioprospecting efforts in soda lake environments with new integrated approaches. Importantly, some saline and alkaline lake ecosystems around the world need to be protected from anthropogenic pressures that threaten their long-term existence.
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Affiliation(s)
| | | | - Sindy Hunger
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Harold L Drake
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Yogesh S Shouche
- Microbial Culture Collection, National Centre for Cell Science, Pune, India
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94
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Abstract
Extremely acidic (pH < 3) and extremely alkaline (pH > 9) environments support a diversity of single-cell and to a lesser extent, multicellular eukaryotic life. This study compared alpha and beta diversity in eukaryotic communities from seven diverse aquatic environments with pH values ranging from 2 to 11 using massively-parallel pyrotag sequencing targeting the V9 hypervariable region of the 18S ribosomal RNA (rRNA) gene. A total of 946 operational taxonomic units (OTUs) were recovered at a 6% cut-off level (94% similarity) across the sampled environments. Hierarchical clustering of the samples segregated the communities into acidic and alkaline groups. Similarity percentage (SIMPER) analysis followed by indicator OTU analysis (IOA) and non-metric multidimensional scaling (NMDS) were used to determine which characteristic groups of eukaryotic taxa typify acidic or alkaline extremes and the extent to which pH explains eukaryotic community structure in these environments. Spain's Rio Tinto yielded the fewest observed OTUs while Nebraska Sandhills alkaline lakes yielded the most. Distinct OTUs, including metazoan OTUs, numerically dominated pH extreme sites. Indicator OTUs included the diatom Pinnularia and unidentified opisthokonts (Fungi and Filasterea) in the extremely acidic environments, and the ciliate Frontonia across the extremely alkaline sites. Inferred from NMDS, pH explained only a modest fraction of the variation across the datasets, indicating that other factors influence the underlying community structure in these environments. The findings from this study suggest that the ability for eukaryotes to adapt to pH extremes over a broad range of values may be rare, but further study of taxa that can broadly adapt across diverse acidic and alkaline environments, respectively present good models for understanding adaptation and should be targeted for future investigations.
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Affiliation(s)
- Linda A Amaral-Zettler
- Marine Biological Laboratory, Josephine Bay Paul Center for Comparative Molecular Biology and Evolution Woods Hole, MA, USA ; Department of Geological Sciences, Brown University Providence, RI, USA
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95
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Paganin P, Chiarini L, Bevivino A, Dalmastri C, Farcomeni A, Izzo G, Signorini A, Varrone C, Tabacchioni S. Vertical distribution of bacterioplankton in Lake Averno in relation to water chemistry. FEMS Microbiol Ecol 2012; 84:176-88. [DOI: 10.1111/1574-6941.12048] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 10/24/2012] [Accepted: 11/22/2012] [Indexed: 11/26/2022] Open
Affiliation(s)
- Patrizia Paganin
- ENEA C. R. Casaccia; Technical Unit for Sustainable Development and Innovation of Agroindustrial System; Rome; Italy
| | - Luigi Chiarini
- ENEA C. R. Casaccia; Technical Unit for Sustainable Development and Innovation of Agroindustrial System; Rome; Italy
| | - Annamaria Bevivino
- ENEA C. R. Casaccia; Technical Unit for Sustainable Development and Innovation of Agroindustrial System; Rome; Italy
| | - Claudia Dalmastri
- ENEA C. R. Casaccia; Technical Unit for Sustainable Development and Innovation of Agroindustrial System; Rome; Italy
| | - Alessio Farcomeni
- Department of Public Health and Infectious Diseases; Statistics Section; Sapienza - University of Rome; Rome; Italy
| | - Giulio Izzo
- ENEA C. R. Casaccia; Technical Unit for Renewable Energy Resources; Rome; Italy
| | - Antonella Signorini
- ENEA C. R. Casaccia; Technical Unit for Renewable Energy Resources; Rome; Italy
| | - Cristiano Varrone
- ENEA C. R. Casaccia; Technical Unit for Renewable Energy Resources; Rome; Italy
| | - Silvia Tabacchioni
- ENEA C. R. Casaccia; Technical Unit for Sustainable Development and Innovation of Agroindustrial System; Rome; Italy
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96
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Tourova TP, Slobodova NV, Bumazhkin BK, Kolganova TV, Muyzer G, Sorokin DY. Analysis of community composition of sulfur-oxidizing bacteria in hypersaline and soda lakes usingsoxB as a functional molecular marker. FEMS Microbiol Ecol 2012; 84:280-9. [DOI: 10.1111/1574-6941.12056] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 12/06/2012] [Accepted: 12/10/2012] [Indexed: 11/29/2022] Open
Affiliation(s)
- Tatjana P. Tourova
- Winogradsky Institute of Microbiology; Russian Academy of Sciences; Moscow; Russia
| | | | | | | | - Gerard Muyzer
- Department of Aquatic Microbiology; Institute for Biodiversity and Ecosystem Dynamics; University of Amsterdam; Amsterdam; The Netherlands
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97
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Vertical distribution of microbial communities in a perennially stratified Arctic lake with saline, anoxic bottom waters. Sci Rep 2012; 2:604. [PMID: 22930670 PMCID: PMC3428602 DOI: 10.1038/srep00604] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 08/09/2012] [Indexed: 11/25/2022] Open
Abstract
Meromictic lakes are useful biogeochemical models because of their stratified chemical gradients and separation of redox reactions down the water column. Perennially ice-covered meromictic lakes are particularly stable, with long term constancy in their density profiles. Here we sampled Lake A, a deep meromictic lake at latitude 83°N in High Arctic Canada. Sampling was before (May) and after (August) an unusual ice-out event during the warm 2008 summer. We determined the bacterial and archaeal community composition by high-throughput 16S rRNA gene tag-pyrosequencing. Both prokaryote communities were stratified by depth and the Bacteria differed between dates, indicating locally driven selection processes. We matched taxa to known taxon-specific biogeochemical functions and found a close correspondence between the depth of functional specialists and chemical gradients. These results indicate a rich microbial diversity despite the extreme location, with pronounced vertical structure in taxonomic and potential functional composition, and with community shifts during ice-out.
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98
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Armitage DW, Gallagher KL, Youngblut ND, Buckley DH, Zinder SH. Millimeter-scale patterns of phylogenetic and trait diversity in a salt marsh microbial mat. Front Microbiol 2012; 3:293. [PMID: 22908010 PMCID: PMC3415947 DOI: 10.3389/fmicb.2012.00293] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 07/24/2012] [Indexed: 01/01/2023] Open
Abstract
Intertidal microbial mats are comprised of distinctly colored millimeter-thick layers whose communities organize in response to environmental gradients such as light availability, oxygen/sulfur concentrations, and redox potential. Here, slight changes in depth correspond to sharp niche boundaries. We explore the patterns of biodiversity along this depth gradient as it relates to functional groups of bacteria, as well as trait-encoding genes. We used molecular techniques to determine how the mat’s layers differed from one another with respect to taxonomic, phylogenetic, and trait diversity, and used these metrics to assess potential drivers of community assembly. We used a range of null models to compute the degree of phylogenetic and functional dispersion for each layer. The SSU-rRNA reads were dominated by Cyanobacteria and Chromatiales, but contained a high taxonomic diversity. The composition of each mat core was significantly different for developmental stage, year, and layer. Phylogenetic richness and evenness positively covaried with depth, and trait richness tended to decrease with depth. We found evidence for significant phylogenetic clustering for all bacteria below the surface layer, supporting the role of habitat filtering in the assembly of mat layers. However, this signal disappeared when the phylogenetic dispersion of particular functional groups, such as oxygenic phototrophs, was measured. Overall, trait diversity measured by orthologous genes was also lower than would be expected by chance, except for genes related to photosynthesis in the topmost layer. Additionally, we show how the choice of taxa pools, null models, spatial scale, and phylogenies can impact our ability to test hypotheses pertaining to community assembly. Our results demonstrate that given the appropriate physiochemical conditions, strong phylogenetic, and trait variation, as well as habitat filtering, can occur at the millimeter-scale.
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Affiliation(s)
- David W Armitage
- Department of Integrative Biology, University of California Berkeley Berkeley, CA, USA
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99
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Exploration and characterization of agriculturally and industrially important haloalkaliphilic bacteria from environmental samples of hypersaline Sambhar lake, India. World J Microbiol Biotechnol 2012; 28:3207-17. [PMID: 22828794 DOI: 10.1007/s11274-012-1131-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 07/12/2012] [Indexed: 10/28/2022]
Abstract
Screening of bacteria from Sambhar lake, an extreme hypersaline environment of India, led to the isolation of 93 haloalkaliphilic bacteria growing optimally in media with 2-25 % salt and 6-12 pH. Based on 16S rRNA gene sequences, 93 isolates were further categorized into 32 groups, with each group representing a different taxa belonging to 3 phyla (Firmicutes, Proteobacteria and Actinobacteria). Majority of the isolates (53.12 %) showed similarity with phylum Firmicutes which was followed by Proteobacteria (40.63 %) and Actinobacteria (6.25 %). The isolates belonging to 32 representative groups were further evaluated for the production of extracellular enzymes viz. amylase, cellulase, protease and xylanase, plant growth promoting attributes and BIOLOG™ substrate usage. Among all the isolates, xylanase producing isolates were in maximum (68 %) as compared to protease (56 %), cellulase (40 %), and amylase (37 %) producing strains. Similarly, among plant growth promoting activities, ammonia producing isolates were highest (56 %) when compared to those producing ACC deaminase (53 %), IAA (50 %), hydrogen cyanide (28 %), siderophore (21 %) and solubilizing P (34 %). Isolates showing enzymatic and PGP activities could be further utilized for promoting plant growth in saline affected area.
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100
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Klepac-Ceraj V, Hayes CA, Gilhooly WP, Lyons TW, Kolter R, Pearson A. Microbial diversity under extreme euxinia: Mahoney Lake, Canada. GEOBIOLOGY 2012; 10:223-235. [PMID: 22329601 DOI: 10.1111/j.1472-4669.2012.00317.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Mahoney Lake, British Columbia, Canada, is a stratified, 15-m deep saline lake with a euxinic (anoxic, sulfidic) hypolimnion. A dense plate of phototrophic purple sulfur bacteria is found at the chemocline, but to date the rest of the Mahoney Lake microbial ecosystem has been underexamined. In particular, the microbial community that resides in the aphotic hypolimnion and/or in the lake sediments is unknown, and it is unclear whether the sulfate reducers that supply sulfide for phototrophy live only within, or also below, the plate. Here we profiled distributions of 16S rRNA genes using gene clone libraries and PhyloChip microarrays. Both approaches suggest that microbial diversity is greatest in the hypolimnion (8 m) and sediments. Diversity is lowest in the photosynthetic plate (7 m). Shallower depths (5 m, 7 m) are rich in Actinobacteria, Alphaproteobacteria, and Gammaproteobacteria, while deeper depths (8 m, sediments) are rich in Crenarchaeota, Natronoanaerobium, and Verrucomicrobia. The heterogeneous distribution of Deltaproteobacteria and Epsilonproteobacteria between 7 and 8 m is consistent with metabolisms involving sulfur intermediates in the chemocline, but complete sulfate reduction in the hypolimnion. Overall, the results are consistent with the presence of distinct microbial niches and suggest zonation of sulfur cycle processes in this stratified system.
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MESH Headings
- Archaea/classification
- Archaea/isolation & purification
- Bacteria/classification
- Bacteria/isolation & purification
- Biota
- British Columbia
- Cluster Analysis
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fresh Water/microbiology
- Genes, rRNA
- Geologic Sediments/microbiology
- Phylogeny
- RNA, Archaeal/genetics
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- V Klepac-Ceraj
- Department of Molecular Genetics, Forsyth Institute, Cambridge, MA, USA.
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