1
|
Sorokin DY, Messina E, Smedile F, La Cono V, Hallsworth JE, Yakimov MM. Carbohydrate‐dependent sulfur respiration in halo(alkali)philic archaea. Environ Microbiol 2021; 23:3789-3808. [DOI: 10.1111/1462-2920.15421] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/03/2021] [Accepted: 02/01/2021] [Indexed: 12/16/2022]
Affiliation(s)
- Dimitry Y. Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology Russian Academy of Sciences Moscow Russia
- Department of Biotechnology Delft University of Technology Delft The Netherlands
| | - Enzo Messina
- Institute of Biological Resources and Marine Biotechnology, IRBIM‐CNR Messina Italy
| | - Francesco Smedile
- Institute of Biological Resources and Marine Biotechnology, IRBIM‐CNR Messina Italy
| | - Violetta La Cono
- Institute of Biological Resources and Marine Biotechnology, IRBIM‐CNR Messina Italy
| | - John E. Hallsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast Belfast, Northern Ireland BT9 5DL UK
| | - Michail M. Yakimov
- Institute of Biological Resources and Marine Biotechnology, IRBIM‐CNR Messina Italy
| |
Collapse
|
2
|
Zhao D, Zhang S, Xue Q, Chen J, Zhou J, Cheng F, Li M, Zhu Y, Yu H, Hu S, Zheng Y, Liu S, Xiang H. Abundant Taxa and Favorable Pathways in the Microbiome of Soda-Saline Lakes in Inner Mongolia. Front Microbiol 2020; 11:1740. [PMID: 32793172 PMCID: PMC7393216 DOI: 10.3389/fmicb.2020.01740] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 07/03/2020] [Indexed: 12/14/2022] Open
Abstract
Soda-saline lakes are a special type of alkaline lake in which the chloride concentration is greater than the carbonate/bicarbonate concentration. Due to the high pH and a usually higher osmotic pressure than that of a normal soda lake, the microbes may need more energy to thrive in such a double-extreme environment. In this study, we systematically investigated the microbiome of the brine and sediment samples of nine artificially separated ponds (salinities from 5.5% to saturation) within two soda-saline lakes in Inner Mongolia of China, assisted by deep metagenomic sequencing. The main inorganic ions shaped the microbial community in both the brines and sediments, and the chloride concentration exhibited the most significant effect. A total of 385 metagenome-assembled genomes (MAGs) were generated, in which 38 MAGs were revealed as the abundant species in at least one of the eighteen different samples. Interestingly, these abundant species also represented the most branches of the microbiome of the soda-saline lakes at the phylum level. These abundant taxa were close relatives of microorganisms from classic soda lakes and neutral saline environments, but forming a combination of both habitats. Notably, approximately half of the abundant MAGs had the potential to drive dissimilatory sulfur cycling. These MAGs included four autotrophic Ectothiorhodospiraceae MAGs, one Cyanobacteria MAG and nine heterotrophic MAGs with the potential to oxidize sulfur, as well as four abundant MAGs containing genes for elemental sulfur respiration. The possible reason is that reductive sulfur compounds could provide additional energy for the related species, and reductions of oxidative sulfur compounds are more prone to occur under alkaline conditions which support the sulfur cycling. In addition, a unique 1,4-alpha-glucan phosphorylation pathway, but not a normal hydrolysis one, was found in the abundant Candidatus Nanohaloarchaeota MAG NHA-1, which would produce more energy in polysaccharide degradation. In summary, this work has revealed the abundant taxa and favorable pathways in the soda-saline lakes, indicating that efficient energy regeneration pathway may increase the capacity for environmental adaptation in such saline-alkaline environments. These findings may help to elucidate the relationship between microbial metabolism and adaptation to extreme environments.
Collapse
Affiliation(s)
- Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shengjie Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qiong Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Junyu Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jian Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Feiyue Cheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yaxin Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Haiying Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yanning Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuangjiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
3
|
Zavarzina DG, Zhilina TN, Kostrikina NA, Toshchakov SV, Kublanov IV. Isachenkonia alkalipeptolytica gen. nov. sp. nov., a new anaerobic, alkaliphilic proteolytic bacterium capable of reducing Fe(III) and sulfur. Int J Syst Evol Microbiol 2020; 70:4730-4738. [PMID: 32697189 DOI: 10.1099/ijsem.0.004341] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An obligately alkaliphilic, anaerobic, proteolytic bacterium was isolated from a sample of Tanatar III soda lake sediment (Altai region, Russia) and designated as strain Z-1701T. Cells of strain Z-1701T were short, straight, motile Gram-stain-positive rods. Growth of Z-1701T obligately depended on the presence of sodium carbonate. Strain Z-1701T could utilize various peptides mixtures, such as beef and yeast extracts, peptone, soytone, trypticase and tryptone, as well as such proteins as albumin, gelatin and sodium caseinate. It was able to grow oligotrophically with 0.02 g l-1 yeast extract as the sole energy and carbon source. Carbohydrates did not support the growth of strain Z-1701T. The main products released during the growth of strain Z-1701T on tryptone were formate, acetate and ammonium. Strain Z-1701T was able to reduce ferrihydrite, Fe(III)-EDTA, anthraquinone-2,6-disulfonate and elemental sulfur, using proteinaceous substrates as electron donors. In all cases the presence of the electron acceptor in the medium stimulated growth. The main cellular fatty acids were iso-C15 : 0, iso-C15 : 0 aldehyde, iso-C15 : 1 ω6, C16 : 0, iso-C17 : 0 aldehyde, C16 : 0 aldehyde and C14 : 0. The DNA G+C content of the isolate was 43.9 mol%. Phylogenetic analysis based on the concatenated alignment of 120 protein-marker sequences revealed that strain Z-1701T falls into a cluster with the genus Tindallia, family Clostridiaceae. 16S rRNA gene sequence identity between strain Z-1701T and Tindallia species were 88.3-89.75 %. On the basis of its phenotypic characteristics and phylogenetic position, the novel isolate is considered to be a representative of a novel genus and species for which the name Isachenkonia alkalipeptolytica gen. nov., sp. nov. is proposed, with Z-1701T (=JCM 32929Т=DSM 109060Т=VKM B-3261Т) as its type strain.
Collapse
Affiliation(s)
- Daria G Zavarzina
- Winogradsky Institute of Microbiology of Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60-let Oktyabrya prospect 7/2, 117312, Moscow, Russia
| | - Tatyana N Zhilina
- Winogradsky Institute of Microbiology of Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60-let Oktyabrya prospect 7/2, 117312, Moscow, Russia
| | - Nadegda A Kostrikina
- Winogradsky Institute of Microbiology of Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60-let Oktyabrya prospect 7/2, 117312, Moscow, Russia
| | - Stepan V Toshchakov
- Winogradsky Institute of Microbiology of Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60-let Oktyabrya prospect 7/2, 117312, Moscow, Russia
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology of Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60-let Oktyabrya prospect 7/2, 117312, Moscow, Russia
| |
Collapse
|
4
|
Sorokin DY, Yakimov M, Messina E, Merkel AY, Bale NJ, Sinninghe Damsté JS. Natronolimnobius sulfurireducens sp. nov. and Halalkaliarchaeum desulfuricum gen. nov., sp. nov., the first sulfur-respiring alkaliphilic haloarchaea from hypersaline alkaline lakes. Int J Syst Evol Microbiol 2019; 69:2662-2673. [DOI: 10.1099/ijsem.0.003506] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Dimitry Y. Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
- Department of Biotechnology, TU Delft, CD Delft, The Netherlands
| | | | - Enzo Messina
- IAMC-CNR, Spianata S.Raineri 86, 98122 Messina, Italy
| | - Alexander Y. Merkel
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
| | - Nicole J. Bale
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, PO Box 59, 1790 AB Den Burg, Texel, The Netherlands
| | - Jaap S. Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, PO Box 59, 1790 AB Den Burg, Texel, The Netherlands
| |
Collapse
|
5
|
Vavourakis CD, Mehrshad M, Balkema C, van Hall R, Andrei AŞ, Ghai R, Sorokin DY, Muyzer G. Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake. BMC Biol 2019; 17:69. [PMID: 31438955 PMCID: PMC6704655 DOI: 10.1186/s12915-019-0688-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 08/09/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The planetary sulfur cycle is a complex web of chemical reactions that can be microbial-mediated or can occur spontaneously in the environment, depending on the temperature and pH. Inorganic sulfur compounds can serve as energy sources for specialized prokaryotes and are important substrates for microbial growth in general. Here, we investigate dissimilatory sulfur cycling in the brine and sediments of a southwestern Siberian soda lake characterized by an extremely high pH and salinity, combining meta-omics analyses of its uniquely adapted highly diverse prokaryote communities with biogeochemical profiling to identify key microbial players and expand our understanding of sulfur cycling under haloalkaline conditions. RESULTS Peak microbial activity was found in the top 4 cm of the sediments, a layer with a steep drop in oxygen concentration and redox potential. The majority of sulfur was present as sulfate or iron sulfide. Thiosulfate was readily oxidized by microbes in the presence of oxygen, but oxidation was partially inhibited by light. We obtained 1032 metagenome-assembled genomes, including novel population genomes of characterized colorless sulfur-oxidizing bacteria (SOB), anoxygenic purple sulfur bacteria, heterotrophic SOB, and highly active lithoautotrophic sulfate reducers. Surprisingly, we discovered the potential for nitrogen fixation in a new genus of colorless SOB, carbon fixation in a new species of phototrophic Gemmatimonadetes, and elemental sulfur/sulfite reduction in the "Candidatus Woesearchaeota." Polysulfide/thiosulfate and tetrathionate reductases were actively transcribed by various (facultative) anaerobes. CONCLUSIONS The recovery of over 200 genomes that encoded enzymes capable of catalyzing key reactions in the inorganic sulfur cycle indicates complete cycling between sulfate and sulfide at moderately hypersaline and extreme alkaline conditions. Our results suggest that more taxonomic groups are involved in sulfur dissimilation than previously assumed.
Collapse
Affiliation(s)
- Charlotte D Vavourakis
- Microbial Systems Ecology, Department of Freshwater and Marine Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, the Netherlands
| | - Maliheh Mehrshad
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Cherel Balkema
- Microbial Systems Ecology, Department of Freshwater and Marine Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, the Netherlands
| | - Rutger van Hall
- Department of Ecosystem & Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
| | - Adrian-Ştefan Andrei
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russian Federation
- Department of Biotechnology, Environmental Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, the Netherlands.
| |
Collapse
|
6
|
Berben T, Overmars L, Sorokin DY, Muyzer G. Diversity and Distribution of Sulfur Oxidation-Related Genes in Thioalkalivibrio, a Genus of Chemolithoautotrophic and Haloalkaliphilic Sulfur-Oxidizing Bacteria. Front Microbiol 2019; 10:160. [PMID: 30837958 PMCID: PMC6382920 DOI: 10.3389/fmicb.2019.00160] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/22/2019] [Indexed: 12/20/2022] Open
Abstract
Soda lakes are saline alkaline lakes characterized by high concentrations of sodium carbonate/bicarbonate which lead to a stable elevated pH (>9), and moderate to extremely high salinity. Despite this combination of extreme conditions, biodiversity in soda lakes is high, and the presence of diverse microbial communities provides a driving force for highly active biogeochemical cycles. The sulfur cycle is one of the most important of these and bacterial sulfur oxidation is dominated by members of the obligately chemolithoautotrophic genus Thioalkalivibrio. Currently, 10 species have been described in this genus, but over one hundred isolates have been obtained from soda lake samples. The genomes of 75 strains were sequenced and annotated previously, and used in this study to provide a comprehensive picture of the diversity and distribution of genes related to dissimilatory sulfur metabolism in Thioalkalivibrio. Initially, all annotated genes in 75 Thioalkalivibrio genomes were placed in ortholog groups and filtered by bi-directional best BLAST analysis. Investigation of the ortholog groups containing genes related to sulfur oxidation showed that flavocytochrome c (fcc), the truncated sox system, and sulfite:quinone oxidoreductase (soe) are present in all strains, whereas dissimilatory sulfite reductase (dsr; which catalyzes the oxidation of elemental sulfur) was found in only six strains. The heterodisulfide reductase system (hdr), which is proposed to oxidize sulfur to sulfite in strains lacking both dsr and soxCD, was detected in 73 genomes. Hierarchical clustering of strains based on sulfur gene repertoire correlated closely with previous phylogenomic analysis. The phylogenetic analysis of several sulfur oxidation genes showed a complex evolutionary history. All in all, this study presents a comprehensive investigation of sulfur metabolism-related genes in cultivated Thioalkalivibrio strains and provides several avenues for future research.
Collapse
Affiliation(s)
- Tom Berben
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Lex Overmars
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Dimitry Y Sorokin
- Winogradsky Institute for Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| |
Collapse
|
7
|
Timmers PHA, Vavourakis CD, Kleerebezem R, Damsté JSS, Muyzer G, Stams AJM, Sorokin DY, Plugge CM. Metabolism and Occurrence of Methanogenic and Sulfate-Reducing Syntrophic Acetate Oxidizing Communities in Haloalkaline Environments. Front Microbiol 2018; 9:3039. [PMID: 30619130 PMCID: PMC6295475 DOI: 10.3389/fmicb.2018.03039] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/26/2018] [Indexed: 01/31/2023] Open
Abstract
Anaerobic syntrophic acetate oxidation (SAO) is a thermodynamically unfavorable process involving a syntrophic acetate oxidizing bacterium (SAOB) that forms interspecies electron carriers (IECs). These IECs are consumed by syntrophic partners, typically hydrogenotrophic methanogenic archaea or sulfate reducing bacteria. In this work, the metabolism and occurrence of SAOB at extremely haloalkaline conditions were investigated, using highly enriched methanogenic (M-SAO) and sulfate-reducing (S-SAO) cultures from south-western Siberian hypersaline soda lakes. Activity tests with the M-SAO and S-SAO cultures and thermodynamic calculations indicated that H2 and formate are important IECs in both SAO cultures. Metagenomic analysis of the M-SAO cultures showed that the dominant SAOB was ‘Candidatus Syntrophonatronum acetioxidans,’ and a near-complete draft genome of this SAOB was reconstructed. ‘Ca. S. acetioxidans’ has all genes necessary for operating the Wood–Ljungdahl pathway, which is likely employed for acetate oxidation. It also encodes several genes essential to thrive at haloalkaline conditions; including a Na+-dependent ATP synthase and marker genes for ‘salt-out‘ strategies for osmotic homeostasis at high soda conditions. Membrane lipid analysis of the M-SAO culture showed the presence of unusual bacterial diether membrane lipids which are presumably beneficial at extreme haloalkaline conditions. To determine the importance of SAO in haloalkaline environments, previously obtained 16S rRNA gene sequencing data and metagenomic data of five different hypersaline soda lake sediment samples were investigated, including the soda lakes where the enrichment cultures originated from. The draft genome of ‘Ca. S. acetioxidans’ showed highest identity with two metagenome-assembled genomes (MAGs) of putative SAOBs that belonged to the highly abundant and diverse Syntrophomonadaceae family present in the soda lake sediments. The 16S rRNA gene amplicon datasets of the soda lake sediments showed a high similarity of reads to ‘Ca. S. acetioxidans’ with abundance as high as 1.3% of all reads, whereas aceticlastic methanogens and acetate oxidizing sulfate-reducers were not abundant (≤0.1%) or could not be detected. These combined results indicate that SAO is the primary anaerobic acetate oxidizing pathway at extreme haloalkaline conditions performed by haloalkaliphilic syntrophic consortia.
Collapse
Affiliation(s)
- Peer H A Timmers
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands.,European Centre of Excellence for Sustainable Water Technology, Wetsus, Leeuwarden, Netherlands
| | - Charlotte D Vavourakis
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Robbert Kleerebezem
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Netherlands Institute for Sea Research, Utrecht University, Utrecht, Netherlands.,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands.,Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Dimity Y Sorokin
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands.,Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands.,European Centre of Excellence for Sustainable Water Technology, Wetsus, Leeuwarden, Netherlands
| |
Collapse
|
8
|
Sorokin DY, Messina E, La Cono V, Ferrer M, Ciordia S, Mena MC, Toshchakov SV, Golyshin PN, Yakimov MM. Sulfur Respiration in a Group of Facultatively Anaerobic Natronoarchaea Ubiquitous in Hypersaline Soda Lakes. Front Microbiol 2018; 9:2359. [PMID: 30333814 PMCID: PMC6176080 DOI: 10.3389/fmicb.2018.02359] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 09/14/2018] [Indexed: 11/21/2022] Open
Abstract
The ubiquity of strictly anaerobic sulfur-respiring haloarchaea in hypersaline systems with circumneutral pH has shaken a traditional concept of this group as predominantly aerobic heterotrophs. Here, we demonstrated that this functional group of haloarchaea also has its representatives in hypersaline alkaline lakes. Sediments from various hypersaline soda lakes showed high activity of sulfur reduction only partially inhibited by antibiotics. Eight pure cultures of sulfur-reducing natronoarchaea were isolated from such sediments using formate and butyrate as electron donors and sulfur as an electron acceptor. Unlike strict anaerobic haloarchaea, these novel sulfur-reducing natronoarchaea are facultative anaerobes, whose metabolic capabilities were inferred from cultivation experiments and genomic/proteomic reconstruction. While sharing many physiological traits with strict anaerobic haloarchaea, following metabolic distinctions make these new organisms be successful in both anoxic and aerobic habitats: the recruiting of heme-copper quinol oxidases as terminal electron sink in aerobic respiratory chain and the utilization of formate, hydrogen or short-chain fatty acids as electron donors during anaerobic growth with elemental sulfur. Obtained results significantly advance the emerging concept of halo(natrono)archaea as important players in the anaerobic sulfur and carbon cycling in various salt-saturated habitats.
Collapse
Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Enzo Messina
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Violetta La Cono
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Manuel Ferrer
- Institute of Catalysis, Spanish National Research Council, Madrid, Spain
| | - Sergio Ciordia
- Proteomics Unit, National Center for Biotechnology, Spanish National Research Council, Madrid, Spain
| | - Maria C Mena
- Proteomics Unit, National Center for Biotechnology, Spanish National Research Council, Madrid, Spain
| | - Stepan V Toshchakov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Peter N Golyshin
- School of Biological Sciences and The Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
| | - Michail M Yakimov
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy.,Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| |
Collapse
|
9
|
Ryzhmanova Y, Oshurkova V, Troshina O, Abashina T, Ariskina E, Avtukh A, Shcherbakova V. Anoxynatronum buryatiense sp. nov., an anaerobic alkaliphilic bacterium from a low mineralization soda lake in Buryatia, Russia. Int J Syst Evol Microbiol 2017; 67:4704-4709. [DOI: 10.1099/ijsem.0.002365] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yana Ryzhmanova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, prospect Nauki 5, Pushchino, Moscow region, 142290, Russia
| | - Victoria Oshurkova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, prospect Nauki 5, Pushchino, Moscow region, 142290, Russia
| | - Olga Troshina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, prospect Nauki 5, Pushchino, Moscow region, 142290, Russia
| | - Tatyana Abashina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, prospect Nauki 5, Pushchino, Moscow region, 142290, Russia
| | - Elena Ariskina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, prospect Nauki 5, Pushchino, Moscow region, 142290, Russia
| | - Alexander Avtukh
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, prospect Nauki 5, Pushchino, Moscow region, 142290, Russia
| | - Viktoria Shcherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, prospect Nauki 5, Pushchino, Moscow region, 142290, Russia
| |
Collapse
|
10
|
Melton ED, Sorokin DY, Overmars L, Lapidus AL, Pillay M, Ivanova N, Del Rio TG, Kyrpides NC, Woyke T, Muyzer G. Draft genome sequence of Dethiobacter alkaliphilus strain AHT1 T, a gram-positive sulfidogenic polyextremophile. Stand Genomic Sci 2017; 12:57. [PMID: 28943998 PMCID: PMC5609068 DOI: 10.1186/s40793-017-0268-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 09/08/2017] [Indexed: 12/01/2022] Open
Abstract
Dethiobacter alkaliphilus strain AHT1T is an anaerobic, sulfidogenic, moderately salt-tolerant alkaliphilic chemolithotroph isolated from hypersaline soda lake sediments in northeastern Mongolia. It is a Gram-positive bacterium with low GC content, within the phylum Firmicutes. Here we report its draft genome sequence, which consists of 34 contigs with a total sequence length of 3.12 Mbp. D. alkaliphilus strain AHT1T was sequenced by the Joint Genome Institute (JGI) as part of the Community Science Program due to its relevance to bioremediation and biotechnological applications.
Collapse
Affiliation(s)
- Emily Denise Melton
- Department of Freshwater and Marine Ecology, Microbial Systems Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, RAS, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Lex Overmars
- Department of Freshwater and Marine Ecology, Microbial Systems Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Alla L Lapidus
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State, University, St. Petersburg, Russia
| | - Manoj Pillay
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | | | | | - Nikos C Kyrpides
- Joint Genome Institute, Walnut Creek, CA USA.,Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA.,Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Tanja Woyke
- Joint Genome Institute, Walnut Creek, CA USA
| | - Gerard Muyzer
- Department of Freshwater and Marine Ecology, Microbial Systems Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
11
|
Sousa JAB, Bijmans MFM, Stams AJM, Plugge CM. Thiosulfate Conversion to Sulfide by a Haloalkaliphilic Microbial Community in a Bioreactor Fed with H 2 Gas. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:914-923. [PMID: 27997142 DOI: 10.1021/acs.est.6b04497] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In industrial gas biodesulfurization systems, where haloalkaline conditions prevail, a thiosulfate containing bleed stream is produced. This bleed stream can be treated in a separate bioreactor by reducing thiosulfate to sulfide and recycling it. By performing treatment and recycling of the bleed stream, its disposal decreases and less caustics are required to maintain the high pH. In this study, anaerobic microbial thiosulfate conversion to sulfide in a H2/CO2 fed bioreactor operated at haloalkaline conditions was investigated. Thiosulfate was converted by reduction to sulfide as well as disproportionation to sulfide and sulfate. Formate production from H2/CO2 was observed as an important reaction in the bioreactor. Formate, rather than H2, might have been used as the main electron donor by thiosulfate/sulfate-reducing bacteria. The microbial community was dominated by bacteria belonging to the family Clostridiaceae most closely related to Tindallia texcoconensis. Bacteria phylogenetically related to known haloalkaline sulfate and thiosulfate reducers, thiosulfate-disproportionating bacteria, and remarkably sulfur-oxidizing bacteria were also detected. On the basis of the results, two approaches to treat the biodesulfurization waste stream are proposed: (i) addition of electron donor to reduce thiosulfate to sulfide and (ii) thiosulfate disproportionation without the need for an electron donor. The concept of application of solely thiosulfate disproportionation is discussed.
Collapse
Affiliation(s)
- João A B Sousa
- Laboratory of Microbiology, Wageningen University , Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Wetsus , European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands
| | - Martijn F M Bijmans
- Wetsus , European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University , Stippeneng 4, 6708 WE Wageningen, The Netherlands
- CEB-Centre of Biological Engineering, University of Minho , Campus de Gualtar, 4710-057, Braga, Portugal
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University , Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Wetsus , European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands
| |
Collapse
|
12
|
Draft Genome Sequence of the Type Strain Desulfuribacillus alkaliarsenatis AHT28, an Obligately Anaerobic, Sulfidogenic Bacterium Isolated from Russian Soda Lake Sediments. GENOME ANNOUNCEMENTS 2016; 4:4/6/e01244-16. [PMID: 27834702 PMCID: PMC5105095 DOI: 10.1128/genomea.01244-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Desulfuribacillus alkaliarsenatis AHT28T is an obligately anaerobic, sulfur- and arsenate-reducing haloalkaliphile that was isolated from Russian soda lake sediments. Here, we present the 3.1-Mb draft genome sequence for this strain, consisting of 36 contigs with a G+C content of 37.5% and 2,978 protein-coding sequences.
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Poser A, Lohmayer R, Vogt C, Knoeller K, Planer-Friedrich B, Sorokin D, Richnow HH, Finster K. Disproportionation of elemental sulfur by haloalkaliphilic bacteria from soda lakes. Extremophiles 2013; 17:1003-12. [PMID: 24030483 DOI: 10.1007/s00792-013-0582-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 08/26/2013] [Indexed: 11/25/2022]
Abstract
Microbial disproportionation of elemental sulfur to sulfide and sulfate is a poorly characterized part of the anoxic sulfur cycle. So far, only a few bacterial strains have been described that can couple this reaction to cell growth. Continuous removal of the produced sulfide, for instance by oxidation and/or precipitation with metal ions such as iron, is essential to keep the reaction exergonic. Hitherto, the process has exclusively been reported for neutrophilic anaerobic bacteria. Here, we report for the first time disproportionation of elemental sulfur by three pure cultures of haloalkaliphilic bacteria isolated from soda lakes: the Deltaproteobacteria Desulfurivibrio alkaliphilus and Desulfurivibrio sp. AMeS2, and a member of the Clostridia, Dethiobacter alkaliphilus. All cultures grew in saline media at pH 10 by sulfur disproportionation in the absence of metals as sulfide scavengers. Our data indicate that polysulfides are the dominant sulfur species under highly alkaline conditions and that they might be disproportionated. Furthermore, we report the first organism (Dt. alkaliphilus) from the class Clostridia that is able to grow by sulfur disproportionation.
Collapse
Affiliation(s)
- Alexander Poser
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | | | | | | | | | | | | | | |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Desulfuribacillus alkaliarsenatis gen. nov. sp. nov., a deep-lineage, obligately anaerobic, dissimilatory sulfur and arsenate-reducing, haloalkaliphilic representative of the order Bacillales from soda lakes. Extremophiles 2012; 16:597-605. [PMID: 22622646 PMCID: PMC3386488 DOI: 10.1007/s00792-012-0459-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 05/03/2012] [Indexed: 11/03/2022]
Abstract
An anaerobic enrichment culture inoculated with a sample of sediments from soda lakes of the Kulunda Steppe with elemental sulfur as electron acceptor and formate as electron donor at pH 10 and moderate salinity inoculated with sediments from soda lakes in Kulunda Steppe (Altai, Russia) resulted in the domination of a Gram-positive, spore-forming bacterium strain AHT28. The isolate is an obligate anaerobe capable of respiratory growth using elemental sulfur, thiosulfate (incomplete reduction) and arsenate as electron acceptor with H₂, formate, pyruvate and lactate as electron donor. Growth was possible within a pH range from 9 to 10.5 (optimum at pH 10) and a salt concentration at pH 10 from 0.2 to 2 M total Na+ (optimum at 0.6 M). According to the phylogenetic analysis, strain AHT28 represents a deep independent lineage within the order Bacillales with a maximum of 90 % 16S rRNA gene similarity to its closest cultured representatives. On the basis of its distinct phenotype and phylogeny, the novel haloalkaliphilic anaerobe is suggested as a new genus and species, Desulfuribacillus alkaliarsenatis (type strain AHT28(T) = DSM24608(T) = UNIQEM U855(T)).
Collapse
|
17
|
Abundance, distribution, and activity of Fe(II)-oxidizing and Fe(III)-reducing microorganisms in hypersaline sediments of Lake Kasin, southern Russia. Appl Environ Microbiol 2012; 78:4386-99. [PMID: 22504804 DOI: 10.1128/aem.07637-11] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The extreme osmotic conditions prevailing in hypersaline environments result in decreasing metabolic diversity with increasing salinity. Various microbial metabolisms have been shown to occur even at high salinity, including photosynthesis as well as sulfate and nitrate reduction. However, information about anaerobic microbial iron metabolism in hypersaline environments is scarce. We studied the phylogenetic diversity, distribution, and metabolic activity of iron(II)-oxidizing and iron(III)-reducing Bacteria and Archaea in pH-neutral, iron-rich salt lake sediments (Lake Kasin, southern Russia; salinity, 348.6 g liter(-1)) using a combination of culture-dependent and -independent techniques. 16S rRNA gene clone libraries for Bacteria and Archaea revealed a microbial community composition typical for hypersaline sediments. Most-probable-number counts confirmed the presence of 4.26 × 10(2) to 8.32 × 10(3) iron(II)-oxidizing Bacteria and 4.16 × 10(2) to 2.13 × 10(3) iron(III)-reducing microorganisms per gram dry sediment. Microbial iron(III) reduction was detected in the presence of 5 M NaCl, extending the natural habitat boundaries for this important microbial process. Quantitative real-time PCR showed that 16S rRNA gene copy numbers of total Bacteria, total Archaea, and species dominating the iron(III)-reducing enrichment cultures (relatives of Halobaculum gomorrense, Desulfosporosinus lacus, and members of the Bacilli) were highest in an iron oxide-rich sediment layer. Combined with the presented geochemical and mineralogical data, our findings suggest the presence of an active microbial iron cycle at salt concentrations close to the solubility limit of NaCl.
Collapse
|
18
|
Sorokin DY, Tourova TP, Kolganova TV, Detkova EN, Galinski EA, Muyzer G. Culturable diversity of lithotrophic haloalkaliphilic sulfate-reducing bacteria in soda lakes and the description of Desulfonatronum thioautotrophicum sp. nov., Desulfonatronum thiosulfatophilum sp. nov., Desulfonatronovibrio thiodismutans sp. nov., and Desulfonatronovibrio magnus sp. nov. Extremophiles 2011; 15:391-401. [PMID: 21479878 PMCID: PMC3084936 DOI: 10.1007/s00792-011-0370-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 03/23/2011] [Indexed: 11/30/2022]
Abstract
Soda lake sediments usually contain high concentrations of sulfide indicating active sulfate reduction. Monitoring of sulfate-reducing bacteria (SRB) in soda lakes demonstrated a dominance of two groups of culturable SRB belonging to the order Desulfovibrionales specialized in utilization of inorganic electron donors, such as formate, H2 and thiosulfate. The most interesting physiological trait of the novel haloalkaliphilic SRB isolates was their ability to grow lithotrophically by dismutation of thiosulfate and sulfite. All isolates were obligately alkaliphilic with a pH optimum at 9.5–10 and moderately salt tolerant. Among the fifteen newly isolated strains, four belonged to the genus Desulfonatronum and the others to the genus Desulfonatronovibrio. None of the isolates were closely related to previously described species of these genera. On the basis of phylogenetic, genotypic and phenotypic characterization of the novel soda lake SRB isolates, two novel species each in the genera Desulfonatronum and Desulfonatronovibrio are proposed.
Collapse
Affiliation(s)
- D Y Sorokin
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-let Octyabrya 7/2, 117811, Moscow, Russia.
| | | | | | | | | | | |
Collapse
|
19
|
Sorokin DY, Kuenen JG, Muyzer G. The microbial sulfur cycle at extremely haloalkaline conditions of soda lakes. Front Microbiol 2011; 2:44. [PMID: 21747784 PMCID: PMC3128939 DOI: 10.3389/fmicb.2011.00044] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Accepted: 02/25/2011] [Indexed: 11/13/2022] Open
Abstract
Soda lakes represent a unique ecosystem with extremely high pH (up to 11) and salinity (up to saturation) due to the presence of high concentrations of sodium carbonate in brines. Despite these double extreme conditions, most of the lakes are highly productive and contain a fully functional microbial system. The microbial sulfur cycle is among the most active in soda lakes. One of the explanations for that is high-energy efficiency of dissimilatory conversions of inorganic sulfur compounds, both oxidative and reductive, sufficient to cope with costly life at double extreme conditions. The oxidative part of the sulfur cycle is driven by chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacteria (SOB), which are unique for soda lakes. The haloalkaliphilic SOB are present in the surface sediment layer of various soda lakes at high numbers of up to 10(6) viable cells/cm(3). The culturable forms are so far represented by four novel genera within the Gammaproteobacteria, including the genera Thioalkalivibrio, Thioalkalimicrobium, Thioalkalispira, and Thioalkalibacter. The latter two were only found occasionally and each includes a single species, while the former two are widely distributed in various soda lakes over the world. The genus Thioalkalivibrio is the most physiologically diverse and covers the whole spectrum of salt/pH conditions present in soda lakes. Most importantly, the dominant subgroup of this genus is able to grow in saturated soda brines containing 4 M total Na(+) - a so far unique property for any known aerobic chemolithoautotroph. Furthermore, some species can use thiocyanate as a sole energy source and three out of nine species can grow anaerobically with nitrogen oxides as electron acceptor. The reductive part of the sulfur cycle is active in the anoxic layers of the sediments of soda lakes. The in situ measurements of sulfate reduction rates and laboratory experiments with sediment slurries using sulfate, thiosulfate, or elemental sulfur as electron acceptors demonstrated relatively high sulfate reduction rates only hampered by salt-saturated conditions. However, the highest rates of sulfidogenesis were observed not with sulfate, but with elemental sulfur followed by thiosulfate. Formate, but not hydrogen, was the most efficient electron donor with all three sulfur electron acceptors, while acetate was only utilized as an electron donor under sulfur-reducing conditions. The native sulfidogenic populations of soda lakes showed a typical obligately alkaliphilic pH response, which corresponded well to the in situ pH conditions. Microbiological analysis indicated a domination of three groups of haloalkaliphilic autotrophic sulfate-reducing bacteria belonging to the order Desulfovibrionales (genera Desulfonatronovibrio, Desulfonatronum, and Desulfonatronospira) with a clear tendency to grow by thiosulfate disproportionation in the absence of external electron donor even at salt-saturating conditions. Few novel representatives of the order Desulfobacterales capable of heterotrophic growth with volatile fatty acids and alcohols at high pH and moderate salinity have also been found, while acetate oxidation was a function of a specialized group of haloalkaliphilic sulfur-reducing bacteria, which belong to the phylum Chrysiogenetes.
Collapse
Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Russian Academy of Sciences Moscow, Russia
| | | | | |
Collapse
|
20
|
|