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Sorokin DY, Elcheninov AG, Merkel AY, Bale NJ, Sininghe-Damste J, Kublanov IV. Halapricum hydrolyticum sp. nov., a beta-1,3-glucan utilizing haloarchaeon from hypersaline lakes. Syst Appl Microbiol 2023; 46:126471. [PMID: 37826928 DOI: 10.1016/j.syapm.2023.126471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/10/2023] [Accepted: 10/06/2023] [Indexed: 10/14/2023]
Abstract
Two strains of neutrophilic haloaloarchaea were selectively enriched from hypersaline lakes in southwestern Siberia using β-1,3-glucans as a substrate. The strains were nearly identical in their phenotypes and according to phylogenomic analysis, and represent a distant novel species group in the genus Halapricum of the family Haloarculaceae. The main phenotypic property of the novel isolates is the ability to hydrolyze and grow with the polysaccharides curdlan and pachyman. Such potential has, to date, not been seen in any other haloarchaea in pure cultures. The strains are obligately aerobic saccharolytics. Apart from the insoluble β-1,3-glucans, they utilized soluble α-glucans (starch, pullulan and glycogen) and a limited number of sugars. The major ether-bound polar phospholipids include PGP-Me and PG. The glyco- and sulfolipids were absent. The major respiratory menaquinone is MK-8:8. On the basis of their unique physiological properties and the results of phylogenomic analysis, the isolates are suggested to be classified into a novel species Halapricum hydrolyticum sp. nov. (type strain HArc-curdl5-1T = DSM 114193T = UQM 41587T).
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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.
| | - Alexander G Elcheninov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Y Merkel
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nicole J Bale
- NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Texel, The Netherlands
| | - Jaap Sininghe-Damste
- NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Texel, The Netherlands
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
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2
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La Cono V, Messina E, Reva O, Smedile F, La Spada G, Crisafi F, Marturano L, Miguez N, Ferrer M, Selivanova EA, Golyshina OV, Golyshin PN, Rohde M, Krupovic M, Merkel AY, Sorokin DY, Hallsworth JE, Yakimov MM. Nanohaloarchaea as beneficiaries of xylan degradation by haloarchaea. Microb Biotechnol 2023; 16:1803-1822. [PMID: 37317055 PMCID: PMC10443357 DOI: 10.1111/1751-7915.14272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/18/2023] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
Climate change, desertification, salinisation of soils and the changing hydrology of the Earth are creating or modifying microbial habitats at all scales including the oceans, saline groundwaters and brine lakes. In environments that are saline or hypersaline, the biodegradation of recalcitrant plant and animal polysaccharides can be inhibited by salt-induced microbial stress and/or by limitation of the metabolic capabilities of halophilic microbes. We recently demonstrated that the chitinolytic haloarchaeon Halomicrobium can serve as the host for an ectosymbiont, nanohaloarchaeon 'Candidatus Nanohalobium constans'. Here, we consider whether nanohaloarchaea can benefit from the haloarchaea-mediated degradation of xylan, a major hemicellulose component of wood. Using samples of natural evaporitic brines and anthropogenic solar salterns, we describe genome-inferred trophic relations in two extremely halophilic xylan-degrading three-member consortia. We succeeded in genome assembly and closure for all members of both xylan-degrading cultures and elucidated the respective food chains within these consortia. We provide evidence that ectosymbiontic nanohaloarchaea is an active ecophysiological component of extremely halophilic xylan-degrading communities (although by proxy) in hypersaline environments. In each consortium, nanohaloarchaea occur as ectosymbionts of Haloferax, which in turn act as scavenger of oligosaccharides produced by xylan-hydrolysing Halorhabdus. We further obtained and characterised the nanohaloarchaea-host associations using microscopy, multi-omics and cultivation approaches. The current study also doubled culturable nanohaloarchaeal symbionts and demonstrated that these enigmatic nano-sized archaea can be readily isolated in binary co-cultures using an appropriate enrichment strategy. We discuss the implications of xylan degradation by halophiles in biotechnology and for the United Nation's Sustainable Development Goals.
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Affiliation(s)
| | | | - Oleg Reva
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Centre for Bioinformatics and Computational BiologyUniversity of PretoriaPretoriaSouth Africa
| | | | | | | | | | - Noa Miguez
- Instituto de Catalisis y Petroleoquimica (ICP), CSICMadridSpain
| | - Manuel Ferrer
- Instituto de Catalisis y Petroleoquimica (ICP), CSICMadridSpain
| | - Elena A. Selivanova
- Institute for Cellular and Intracellular SymbiosisUral Branch, Russian Academy of SciencesOrenburgRussia
| | | | | | - Manfred Rohde
- Central Facility for MicrobiologyHelmholtz Centre for Infection ResearchBraunschweigGermany
| | - Mart Krupovic
- Institut PasteurUniversité Paris Cité, Archaeal Virology UnitParisFrance
| | - Alexander Y. Merkel
- Winogradsky Institute of MicrobiologyResearch Centre of Biotechnology, Russian Academy of SciencesMoscowRussia
| | - Dimitry Y. Sorokin
- Winogradsky Institute of MicrobiologyResearch Centre of Biotechnology, Russian Academy of SciencesMoscowRussia
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - John E. Hallsworth
- Institute for Global Food Security, School of Biological SciencesQueen's University BelfastNorthern IrelandUK
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Elcheninov AG, Ugolkov YA, Elizarov IM, Klyukina AA, Kublanov IV, Sorokin DY. Cellulose metabolism in halo(natrono)archaea: a comparative genomics study. Front Microbiol 2023; 14:1112247. [PMID: 37323904 PMCID: PMC10267330 DOI: 10.3389/fmicb.2023.1112247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
Extremely halophilic archaea are one of the principal microbial community components in hypersaline environments. The majority of cultivated haloarchaea are aerobic heterotrophs using peptides or simple sugars as carbon and energy sources. At the same time, a number of novel metabolic capacities of these extremophiles were discovered recently among which is a capability of growing on insoluble polysaccharides such as cellulose and chitin. Still, polysaccharidolytic strains are in minority among cultivated haloarchaea and their capacities of hydrolyzing recalcitrant polysaccharides are hardly investigated. This includes the mechanisms and enzymes involved in cellulose degradation, which are well studied for bacterial species, while almost unexplored in archaea and haloarchaea in particular. To fill this gap, a comparative genomic analysis of 155 cultivated representatives of halo(natrono)archaea, including seven cellulotrophic strains belonging to the genera Natronobiforma, Natronolimnobius, Natrarchaeobius, Halosimplex, Halomicrobium and Halococcoides was performed. The analysis revealed a number of cellulases, encoded in the genomes of cellulotrophic strains but also in several haloarchaea, for which the capacity to grow on cellulose was not shown. Surprisingly, the cellulases genes, especially of GH5, GH9 and GH12 families, were significantly overrepresented in the cellulotrophic haloarchaea genomes in comparison with other cellulotrophic archaea and even cellulotrophic bacteria. Besides cellulases, the genes for GH10 and GH51 families were also abundant in the genomes of cellulotrophic haloarchaea. These results allowed to propose the genomic patterns, determining the capability of haloarchaea to grow on cellulose. The patterns helped to predict cellulotrophic capacity for several halo(natrono)archaea, and for three of them it was experimentally confirmed. Further genomic search revealed that glucose and cellooligosaccharides import occurred by means of porters and ABC (ATP-binding cassette) transporters. Intracellular glucose oxidation occurred through glycolysis or the semi-phosphorylative Entner-Dudoroff pathway which occurrence was strain-specific. Comparative analysis of CAZymes toolbox and available cultivation-based information allowed proposing two possible strategies used by haloarchaea capable of growing on cellulose: so-called specialists are more effective in degradation of cellulose while generalists are more flexible in nutrient spectra. Besides CAZymes profiles the groups differed in genome sizes, as well as in variability of mechanisms of import and central metabolism of sugars.
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Affiliation(s)
- Alexander G. Elcheninov
- Winogradsky Institute of Microbiology, Federal Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Yaroslav A. Ugolkov
- Winogradsky Institute of Microbiology, Federal Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Ivan M. Elizarov
- Winogradsky Institute of Microbiology, Federal Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexandra A. Klyukina
- Winogradsky Institute of Microbiology, Federal Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, Federal Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Dimitry Y. Sorokin
- Winogradsky Institute of Microbiology, Federal Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
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Reva O, Messina E, La Cono V, Crisafi F, Smedile F, La Spada G, Marturano L, Selivanova EA, Rohde M, Krupovic M, Yakimov MM. Functional diversity of nanohaloarchaea within xylan-degrading consortia. Front Microbiol 2023; 14:1182464. [PMID: 37323909 PMCID: PMC10266531 DOI: 10.3389/fmicb.2023.1182464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
Extremely halophilic representatives of the phylum Candidatus Nanohaloarchaeota (members of the DPANN superphyla) are obligately associated with extremely halophilic archaea of the phylum Halobacteriota (according to the GTDB taxonomy). Using culture-independent molecular techniques, their presence in various hypersaline ecosystems around the world has been confirmed over the past decade. However, the vast majority of nanohaloarchaea remain uncultivated, and thus their metabolic capabilities and ecophysiology are currently poorly understood. Using the (meta)genomic, transcriptomic, and DNA methylome platforms, the metabolism and functional prediction of the ecophysiology of two novel extremely halophilic symbiotic nanohaloarchaea (Ca. Nanohalococcus occultus and Ca. Nanohalovita haloferacivicina) stably cultivated in the laboratory as members of a xylose-degrading binary culture with a haloarchaeal host, Haloferax lucentense, was determined. Like all known DPANN superphylum nanoorganisms, these new sugar-fermenting nanohaloarchaea lack many fundamental biosynthetic repertoires, making them exclusively dependent on their respective host for survival. In addition, given the cultivability of the new nanohaloarchaea, we managed to discover many unique features in these new organisms that have never been observed in nano-sized archaea both within the phylum Ca. Nanohaloarchaeota and the entire superphylum DPANN. This includes the analysis of the expression of organism-specific non-coding regulatory (nc)RNAs (with an elucidation of their 2D-secondary structures) as well as profiling of DNA methylation. While some ncRNA molecules have been predicted with high confidence as RNAs of an archaeal signal recognition particle involved in delaying protein translation, others resemble the structure of ribosome-associated ncRNAs, although none belong to any known family. Moreover, the new nanohaloarchaea have very complex cellular defense mechanisms. In addition to the defense mechanism provided by the type II restriction-modification system, consisting of Dcm-like DNA methyltransferase and Mrr restriction endonuclease, Ca. Nanohalococcus encodes an active type I-D CRISPR/Cas system, containing 77 spacers divided into two loci. Despite their diminutive genomes and as part of their host interaction mechanism, the genomes of new nanohaloarchaea do encode giant surface proteins, and one of them (9,409 amino acids long) is the largest protein of any sequenced nanohaloarchaea and the largest protein ever discovered in cultivated archaea.
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Affiliation(s)
- Oleg Reva
- Department of Biochemistry, Genetics and Microbiology, Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, South Africa
| | | | - Violetta La Cono
- Extreme Microbiology, Biotechnology and Astrobiology Group, Institute of Polar Research, ISP-CNR, Messina, Italy
| | - Francesca Crisafi
- Extreme Microbiology, Biotechnology and Astrobiology Group, Institute of Polar Research, ISP-CNR, Messina, Italy
| | - Francesco Smedile
- Extreme Microbiology, Biotechnology and Astrobiology Group, Institute of Polar Research, ISP-CNR, Messina, Italy
| | - Gina La Spada
- Extreme Microbiology, Biotechnology and Astrobiology Group, Institute of Polar Research, ISP-CNR, Messina, Italy
| | - Laura Marturano
- Extreme Microbiology, Biotechnology and Astrobiology Group, Institute of Polar Research, ISP-CNR, Messina, Italy
| | - Elena A. Selivanova
- Institute for Cellular and Intracellular Symbiosis, Ural Branch, Russian Academy of Sciences, Orenburg, Russia
| | - Manfred Rohde
- Central Facility for Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Michail M. Yakimov
- Extreme Microbiology, Biotechnology and Astrobiology Group, Institute of Polar Research, ISP-CNR, Messina, Italy
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5
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Comparative Genomic Insights into the Evolution of Halobacteria-Associated " Candidatus Nanohaloarchaeota". mSystems 2022; 7:e0066922. [PMID: 36259734 PMCID: PMC9765267 DOI: 10.1128/msystems.00669-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Members of the phylum "Candidatus Nanohaloarchaeota," a representative lineage within the DPANN superphylum, are characterized by their nanosized cells and symbiotic lifestyle with Halobacteria. However, the development of the symbiosis remains unclear. Here, we propose two novel families, "Candidatus Nanoanaerosalinaceae" and "Candidatus Nanohalalkaliarchaeaceae" in "Ca. Nanohaloarchaeota," represented by five dereplicated metagenome-assembled genomes obtained from hypersaline sediments or related enrichment cultures of soda-saline lakes. Phylogenetic analyses reveal that the two novel families are placed at the root of the family "Candidatus Nanosalinaceae," including the cultivated taxa. The two novel families prefer hypersaline sediments, and the acid shift of predicted proteomes indicates a "salt-in" strategy for hypersaline adaptation. They contain a lower proportion of putative horizontal gene transfers from Halobacteria than "Ca. Nanosalinaceae," suggesting a weaker association with Halobacteria. Functional prediction and historical events reconstruction disclose that they exhibit divergent potentials in carbohydrate and organic acid metabolism and environmental responses. Globally, comparative genomic analyses based on the new families enrich the taxonomic and functional diversity of "Ca. Nanohaloarchaeota" and provide insights into the evolutionary process of "Ca. Nanohaloarchaeota" and their symbiotic relationship with Halobacteria. IMPORTANCE The DPANN superphylum is a group of archaea widely distributed in various habitats. They generally have small cells and have a symbiotic lifestyle with other archaea. The archaeal symbiotic interaction is vital to understanding microbial communities. However, the formation and evolution of the symbiosis between the DPANN lineages and other diverse archaea remain unclear. Based on phylogeny, habitat distribution, hypersaline adaptation, host prediction, functional potentials, and historical events of "Ca. Nanohaloarchaeota," a representative phylum within the DPANN superphylum, we report two novel families representing intermediate stages, and we infer the evolutionary process of "Ca. Nanohaloarchaeota" and their Halobacteria-associated symbiosis. Altogether, this research helps in understanding the evolution of symbiosis in "Ca. Nanohaloarchaeota" and provides a model for the evolution of other DPANN lineages.
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Natranaeroarchaeum sulfidigenes gen. nov., sp. nov., carbohydrate-utilizing sulfur-respiring haloarchaeon from hypersaline soda lakes, a member of a new family Natronoarchaeaceae fam. nov. in the order Halobacteriales. Syst Appl Microbiol 2022; 45:126356. [DOI: 10.1016/j.syapm.2022.126356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/22/2022] [Accepted: 08/26/2022] [Indexed: 11/19/2022]
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Sorokin DY, Merkel AY, Messina E, Tugui C, Pabst M, Golyshin PN, Yakimov MM. Anaerobic carboxydotrophy in sulfur-respiring haloarchaea from hypersaline lakes. THE ISME JOURNAL 2022; 16:1534-1546. [PMID: 35132120 PMCID: PMC9123189 DOI: 10.1038/s41396-022-01206-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 01/03/2022] [Accepted: 01/27/2022] [Indexed: 05/24/2023]
Abstract
Anaerobic carboxydotrophy is a widespread catabolic trait in bacteria, with two dominant pathways: hydrogenogenic and acetogenic. The marginal mode by direct oxidation to CO2 using an external e-acceptor has only a few examples. Use of sulfidic sediments from two types of hypersaline lakes in anaerobic enrichments with CO as an e-donor and elemental sulfur as an e-acceptor led to isolation of two pure cultures of anaerobic carboxydotrophs belonging to two genera of sulfur-reducing haloarchaea: Halanaeroarchaeum sp. HSR-CO from salt lakes and Halalkaliarchaeum sp. AArc-CO from soda lakes. Anaerobic growth of extremely halophilic archaea with CO was obligatory depended on the presence of elemental sulfur as the electron acceptor and yeast extract as the carbon source. CO served as a direct electron donor and H2 was not generated from CO when cells were incubated with or without sulfur. The genomes of the isolates encode a catalytic Ni,Fe-CODH subunit CooS (distantly related to bacterial homologs) and its Ni-incorporating chaperone CooC (related to methanogenic homologs) within a single genomic locus. Similar loci were also present in a genome of the type species of Halalkaliarchaeum closely related to AArc-CO, and the ability for anaerobic sulfur-dependent carboxydotrophy was confirmed for three different strains of this genus. Moreover, similar proteins are encoded in three of the four genomes of recently described carbohydrate-utilizing sulfur-reducing haloarchaea belonging to the genus Halapricum and in two yet undescribed haloarchaeal species. Overall, this work demonstrated for the first time the potential for anaerobic sulfur-dependent carboxydotrophy in extremely halophilic archaea.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Federal Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia.
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.
| | - Alexander Y Merkel
- Winogradsky Institute of Microbiology, Federal Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Enzo Messina
- IRBIM-CNR, Spianata S.Raineri 86, 98122, Messina, Italy
| | - Claudia Tugui
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Peter N Golyshin
- School of Natural Sciences, Bangor University, Gwynedd, LL57 2UW, UK
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Sorokin DY, Elcheninov AG, Khizhniak TV, Koenen M, Bale NJ, Damsté JSS, Kublanov IV. Natronocalculus amylovorans gen. nov., sp. nov., and Natranaeroarchaeum aerophilus sp. nov., dominant culturable amylolytic natronoarchaea from hypersaline soda lakes in southwestern siberia. Syst Appl Microbiol 2022; 45:126336. [DOI: 10.1016/j.syapm.2022.126336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 10/18/2022]
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9
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Zhou H, Zhao D, Zhang S, Xue Q, Zhang M, Yu H, Zhou J, Li M, Kumar S, Xiang H. Metagenomic insights into the environmental adaptation and metabolism of Candidatus Haloplasmatales, one archaeal order thriving in saline lakes. Environ Microbiol 2022; 24:2239-2258. [PMID: 35048500 DOI: 10.1111/1462-2920.15899] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/06/2021] [Indexed: 02/01/2023]
Abstract
The KTK 4A-related Thermoplasmata thrives in the sediment of saline lakes; however, systematic research on its taxonomy, environmental adaptation and metabolism is lacking. Here, we detected this abundant lineage in the sediment of five artificially separated ponds (salinity 7.0%-33.0%) within a Chinese soda-saline lake using culture-independent metagenomics and archaeal 16S rRNA gene amplicons. The phylogenies based on the 16S rRNA gene, and 122 archaeal ubiquitous single-copy proteins and genome-level identity analyses among the metagenome-assembled genomes demonstrate this lineage forming a novel order, Candidatus Haloplasmatales, comprising four genera affiliated with the identical family. Isoelectric point profiles of predicted proteomes suggest that most members adopt the energetically favourable 'salt-in' strategy. Functional prediction indicates the lithoheterotrophic nature with the versatile metabolic potentials for carbohydrate and organic acids as well as carbon monoxide and hydrogen utilization. Additionally, hydrogenase genes hdrABC-mvhADG are linked with incomplete reductive citrate cycle genes in the genomes, suggesting their functional connection. Comparison with the coupling of HdrABC-MvhADG and methanogenesis pathway provides new insights into the compatibility of laterally acquired methanogenesis with energy metabolism in the related order Methanomassiliicoccales. Globally, our research sheds light on the taxonomy, environmental adaptative mechanisms, metabolic potentials and evolutional significance of Ca. Haloplasmatales.
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Affiliation(s)
- Heng Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - 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
| | - Manqi 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
| | - Haiying Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jian Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Sumit Kumar
- Enzyme and Microbial Biochemistry Lab, Department of Chemistry, Indian Institute of Technology, Delhi, India
| | - 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
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Sorokin DY, Yakimov MM, Messina E, Merkel AY, Koenen M, Bale NJ, Sinninghe Damsté JS. Halapricum desulfuricans sp. nov., carbohydrate-utilizing, sulfur-respiring haloarchaea from hypersaline lakes. Syst Appl Microbiol 2021; 44:126249. [PMID: 34547593 DOI: 10.1016/j.syapm.2021.126249] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 11/19/2022]
Abstract
Nine pure cultures of neutrophilic haloaloarchaea capable of anaerobic growth by carbohydrate-dependent sulfur respiration were isolated from hypersaline lakes in southwestern Siberia and southern Russia. According to phylogenomic analysis the isolates were closely related to each other and formed a new species within the genus Halapricum (family Haloarculaceae). They have three types of catabolism: fermentative, resulting in H2 formation; anaerobic respiration using sulfur compounds as e-acceptors and aerobic respiration. Apart from elemental sulfur, all isolates can also use three different sulfoxides as acceptors and the type strain also grows with thiosulfate, reducing it partially to sulfide and sulfite. All strains utilized sugars and glycerol as the e-donors and C source for anaerobic growth and some can also grow with alpha-glucans, such as starch and dextrins. The major respiratory menaquinones are MK-8:8 and MK-8:7, but 5-19% consists of "thermoplasmata" quinones (MMK-8:8 and MMK-8:7), whose occurrence in haloarchaea is unprecedented. On the basis of their unique physiological properties and results of phylogenomic analysis, the isolates are suggested to be classified into a novel species Halapricum desulfuricans sp. nov. (type strain HSR12-2T = JCM 34032T = UNIQEM U1001T).
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia; Department of Biotechnology, Section of Environmental Biotechnology, TU 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
| | - Michel Koenen
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, PO Box 59, 1790 AB Den Burg, Texel, The Netherlands
| | - Nicole J Bale
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and 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, and Utrecht University, PO Box 59, 1790 AB Den Burg, Texel, The Netherlands; Faculty of Geosciences, Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
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11
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Hallsworth JE, Mancinelli RL, Conley CA, Dallas TD, Rinaldi T, Davila AF, Benison KC, Rapoport A, Cavalazzi B, Selbmann L, Changela H, Westall F, Yakimov MM, Amils R, Madigan MT. Astrobiology of life on Earth. Environ Microbiol 2021; 23:3335-3344. [PMID: 33817931 DOI: 10.1111/1462-2920.15499] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 11/29/2022]
Abstract
Astrobiology is mistakenly regarded by some as a field confined to studies of life beyond Earth. Here, we consider life on Earth through an astrobiological lens. Whereas classical studies of microbiology historically focused on various anthropocentric sub-fields (such as fermented foods or commensals and pathogens of crop plants, livestock and humans), addressing key biological questions via astrobiological approaches can further our understanding of all life on Earth. We highlight potential implications of this approach through the articles in this Environmental Microbiology special issue 'Ecophysiology of Extremophiles'. They report on the microbiology of places/processes including low-temperature environments and chemically diverse saline- and hypersaline habitats; aspects of sulphur metabolism in hypersaline lakes, dysoxic marine waters, and thermal acidic springs; biology of extremophile viruses; the survival of terrestrial extremophiles on the surface of Mars; biological soils crusts and rock-associated microbes of deserts; subsurface and deep biosphere, including a salticle formed within Triassic halite; and interactions of microbes with igneous and sedimentary rocks. These studies, some of which we highlight here, contribute to our understanding of the spatiotemporal reach of Earth'sfunctional biosphere, and the tenacity of terrestrial life. Their findings will help set the stage for future work focused on the constraints for life, and how organisms adapt and evolve to circumvent these constraints.
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Affiliation(s)
- John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 7BL, UK
| | - Rocco L Mancinelli
- Bay Area Environmental Research Institute, NASA Ames Research Center, Mountain View, CA, 94035, USA
| | | | - Tiffany D Dallas
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 7BL, UK
| | - Teresa Rinaldi
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, 00185, Italy
| | | | - Kathleen C Benison
- Department of Geology and Geography, West Virginia University, Morgantown, WV, 26506-6300, USA
| | - Alexander Rapoport
- Laboratory of Cell Biology, Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Str., 1-537, Riga, LV-1004, Latvia
| | - Barbara Cavalazzi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, 40126, Italy
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy.,Italian Antarctic National Museum (MNA), Mycological Section, Genoa, 16128, Italy
| | - Hitesh Changela
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China.,Department of Earth and Planetary Science, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Frances Westall
- CNRS, Ctr Biophys Mol UPR 4301, Rue Charles Sadron, CS 80054, Orleans, F-45071, France
| | - Michail M Yakimov
- Institute of Marine Biological Resources and Biotechnology, IRBIM-CNR, Messina, 98122, Italy
| | - Ricardo Amils
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid (CBMSO, CSICUAM), Cantoblanco, Madrid, 28049, Spain.,Centro de Astrobiología (CAB, INTA-CSIC), Torrejón de Ardoz, 28055, Spain
| | - Michael T Madigan
- School of Biological Sciences, Department of Microbiology, Southern Illinois University, Carbondale, IL, 62901, USA
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