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Miralles-Robledillo JM, Martínez-Espinosa RM, Pire C. Transcriptomic profiling of haloarchaeal denitrification through RNA-Seq analysis. Appl Environ Microbiol 2024; 90:e0057124. [PMID: 38814058 PMCID: PMC11218638 DOI: 10.1128/aem.00571-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 04/26/2024] [Indexed: 05/31/2024] Open
Abstract
Denitrification, a crucial biochemical pathway prevalent among haloarchaea in hypersaline ecosystems, has garnered considerable attention in recent years due to its ecological implications. Nevertheless, the underlying molecular mechanisms and genetic regulation governing this respiration/detoxification process in haloarchaea remain largely unexplored. In this study, RNA-sequencing was used to compare the transcriptomes of the haloarchaeon Haloferax mediterranei under oxic and denitrifying conditions, shedding light on the intricate metabolic alterations occurring within the cell, such as the accurate control of the metal homeostasis. Furthermore, the investigation identifies several genes encoding transcriptional regulators and potential accessory proteins with putative roles in denitrification. Among these are bacterioopsin-like transcriptional activators, proteins harboring a domain of unknown function (DUF2249), and cyanoglobin. In addition, the study delves into the genetic regulation of denitrification, finding a regulatory motif within promoter regions that activates numerous denitrification-related genes. This research serves as a starting point for future molecular biology studies in haloarchaea, offering a promising avenue to unravel the intricate mechanisms governing haloarchaeal denitrification, a pathway of paramount ecological importance.IMPORTANCEDenitrification, a fundamental process within the nitrogen cycle, has been subject to extensive investigation due to its close association with anthropogenic activities, and its contribution to the global warming issue, mainly through the release of N2O emissions. Although our comprehension of denitrification and its implications is generally well established, most studies have been conducted in non-extreme environments with mesophilic microorganisms. Consequently, there is a significant knowledge gap concerning extremophilic denitrifiers, particularly those inhabiting hypersaline environments. The significance of this research was to delve into the process of haloarchaeal denitrification, utilizing the complete denitrifier haloarchaeon Haloferax mediterranei as a model organism. This research led to the analysis of the metabolic state of this microorganism under denitrifying conditions and the identification of regulatory signals and genes encoding proteins potentially involved in this pathway, serving as a valuable resource for future molecular studies.
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Affiliation(s)
- Jose María Miralles-Robledillo
- Biochemistry, Molecular Biology, Edaphology and Agricultural Chemistry Department, Faculty of Sciences, Universitat d'Alacant, Alicante, Spain
| | - Rosa María Martínez-Espinosa
- Biochemistry, Molecular Biology, Edaphology and Agricultural Chemistry Department, Faculty of Sciences, Universitat d'Alacant, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Alicante, Spain
| | - Carmen Pire
- Biochemistry, Molecular Biology, Edaphology and Agricultural Chemistry Department, Faculty of Sciences, Universitat d'Alacant, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Alicante, Spain
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Font-Verdera F, Liébana R, Aldeguer-Riquelme B, Gangloff V, Santos F, Viver T, Rosselló-Móra R. Inverted microbial community stratification and spatial-temporal stability in hypersaline anaerobic sediments from the S'Avall solar salterns. Syst Appl Microbiol 2021; 44:126231. [PMID: 34332366 DOI: 10.1016/j.syapm.2021.126231] [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: 03/31/2021] [Revised: 06/01/2021] [Accepted: 07/06/2021] [Indexed: 11/25/2022]
Abstract
The anaerobic hypersaline sediments of an ephemeral pond from the S'Avall solar salterns constituted an excellent study system because of their easy accessibility, as well as the analogy of their microbial assemblages with some known deep-sea hypersaline anaerobic brines. By means of shotgun metagenomics and 16S rRNA gene amplicon sequencing, the microbial composition of the sediment was shown to be stable in time and space. The communities were formed by prokaryote representatives with a clear inferred anaerobic metabolism, mainly related to the methane, sulfur and nitrate cycles. The most conspicuous finding was the inverted nature of the vertical stratification. Contrarily to what could be expected, a methanogenic archaeal metabolism was found to dominate in the upper layers, whereas Bacteria with fermentative and anaerobic respiration metabolisms increased with depth. We could demonstrate the methanogenic nature of the members of candidate lineages DHVE2 and MSBL1, which were present in high abundance in this system, and described, for the first time, viruses infecting these lineages. Members of the putatively active aerobic genera Salinibacter and Halorubrum were detected especially in the deepest layers for which we hypothesize that either oxygen could be sporadically available, or they could perform anaerobic metabolisms. We also report a novel repertoire of virus species thriving in these sediments, which had special relevance because of their lysogenic lifestyles.
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Affiliation(s)
- Francisca Font-Verdera
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), Esporles, Spain.
| | - Raquel Liébana
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), Esporles, Spain
| | - Borja Aldeguer-Riquelme
- Department of Physiology, Genetics and Microbiology, Universidad de Alicante, Alicante, Spain
| | - Valentin Gangloff
- Department of Physiology, Genetics and Microbiology, Universidad de Alicante, Alicante, Spain
| | - Fernando Santos
- Department of Physiology, Genetics and Microbiology, Universidad de Alicante, Alicante, Spain
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), Esporles, Spain
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), Esporles, Spain
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Thompson TP, Kelly SA, Skvortsov T, Plunkett G, Ruffell A, Hallsworth JE, Hopps J, Gilmore BF. Microbiology of a
NaCl
stalactite ‘salticle’ in Triassic halite. Environ Microbiol 2021; 23:3881-3895. [DOI: 10.1111/1462-2920.15524] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 12/19/2022]
Affiliation(s)
- Thomas P. Thompson
- Biofilm Research Group, School of Pharmacy Queen's University Belfast, Medical Biology Centre Belfast BT9 7BL UK
| | - Stephen A. Kelly
- Biofilm Research Group, School of Pharmacy Queen's University Belfast, Medical Biology Centre Belfast BT9 7BL UK
| | - Timofey Skvortsov
- Biofilm Research Group, School of Pharmacy Queen's University Belfast, Medical Biology Centre Belfast BT9 7BL UK
| | - Gill Plunkett
- School of Natural and Built Environment, Department of Archaeology, Geography and Palaeoecology Queen's University Belfast Belfast BT7 1NN UK
| | - Alastair Ruffell
- School of Natural and Built Environment, Department of Archaeology, Geography and Palaeoecology Queen's University Belfast Belfast BT7 1NN UK
| | - John E. Hallsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast Belfast BT9 5DL UK
| | - Jason Hopps
- Irish Salt Mining & Exploration Company Ltd. Carrickfergus BT38 9BT UK
| | - Brendan F. Gilmore
- Biofilm Research Group, School of Pharmacy Queen's University Belfast, Medical Biology Centre Belfast BT9 7BL UK
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast Belfast BT9 5DL UK
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Zhu D, Shen G, Wang Z, Han R, Long Q, Gao X, Xing J, Li Y, Wang R. Distinctive distributions of halophilic Archaea across hypersaline environments within the Qaidam Basin of China. Arch Microbiol 2021; 203:2029-2042. [PMID: 33554274 DOI: 10.1007/s00203-020-02181-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/12/2020] [Accepted: 12/31/2020] [Indexed: 10/22/2022]
Abstract
Halophilic Archaea are widely distributed globally in hypersaline environments. However, little is known of how dominant halophilic archaeal genera are distributed across environments and how they may co-associate across ecosystems. Here, the archaeal community composition and diversity from hypersaline environments (> 300 g/L salinity; total of 33 samples) in the Qaidam Basin of China were investigated using high-throughput Illumina sequencing of 16S rRNA genes. The archaeal communities (total of 3,419 OTUs) were dominated by the class Halobacteria (31.7-99.6% relative abundances) within the phylum Euryarchaeota (90.8-99.9%). Five predominant taxa, including Halorubrum, Halobacterium, Halopenitus, Methanothrix, and Halomicrobium, were observed across most samples. However, several distinct genera were associated with individual samples and were inconsistently distributed across samples, which contrast with previous studies of hypersaline archaeal communities. Additionally, co-occurrence network analysis indicated that five network clusters were present and potentially reflective of interspecies interactions among the environments, including three clusters (clusters II, III, and IV) comprising halophilic archaeal taxa within the Halobacteriaceae and Haloferacaceae families. In addition, two other clusters (clusters I and V) were identified that comprised methanogens. Finally, salinity comprising ionic concentrations (in the order of Na+ > Ca2+ > Mg2+) and pH were most correlated with taxonomic distributions across sample sites.
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Affiliation(s)
- Derui Zhu
- Research Center of Basic Medical Science, Medical College, Qinghai University, Xining, 810016, Qinghai, China
| | - Guoping Shen
- Research Center of Basic Medical Science, Medical College, Qinghai University, Xining, 810016, Qinghai, China
| | - Zhibo Wang
- Research Center of Basic Medical Science, Medical College, Qinghai University, Xining, 810016, Qinghai, China
| | - Rui Han
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China
| | - Qifu Long
- Research Center of Basic Medical Science, Medical College, Qinghai University, Xining, 810016, Qinghai, China
| | - Xiang Gao
- Research Center of Basic Medical Science, Medical College, Qinghai University, Xining, 810016, Qinghai, China
| | - Jiangwa Xing
- Research Center of Basic Medical Science, Medical College, Qinghai University, Xining, 810016, Qinghai, China
| | - Yongzhen Li
- Research Center of Basic Medical Science, Medical College, Qinghai University, Xining, 810016, Qinghai, China
| | - Rong Wang
- Research Center of Basic Medical Science, Medical College, Qinghai University, Xining, 810016, Qinghai, China.
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Payler SJ, Biddle JF, Sherwood Lollar B, Fox-Powell MG, Edwards T, Ngwenya BT, Paling SM, Cockell CS. An Ionic Limit to Life in the Deep Subsurface. Front Microbiol 2019; 10:426. [PMID: 30915051 PMCID: PMC6422919 DOI: 10.3389/fmicb.2019.00426] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/19/2019] [Indexed: 11/18/2022] Open
Abstract
The physical and chemical factors that can limit or prevent microbial growth in the deep subsurface are not well defined. Brines from an evaporite sequence were sampled in the Boulby Mine, United Kingdom between 800 and 1300 m depth. Ionic, hydrogen and oxygen isotopic composition were used to identify two brine sources, an aquifer situated in strata overlying the mine, and another ambiguous source distinct from the regional groundwater. The ability of the brines to support microbial replication was tested with culturing experiments using a diversity of inocula. The examined brines were found to be permissive for growth, except one. Testing this brine's physicochemical properties showed it to have low water activity and to be chaotropic, which we attribute to the high concentration of magnesium and chloride ions. Metagenomic sequencing of the brines that supported growth showed their microbial communities to be similar to each other and comparable to those found in other hypersaline environments. These data show that solutions high in dissolved ions can shape the microbial diversity of the continental deep subsurface biosphere. Furthermore, under certain circumstances, complex brines can establish a hard limit to microbial replication in the deep biosphere, highlighting the potential for subsurface uninhabitable aqueous environments at depths far shallower than a geothermally-defined limit to life.
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Affiliation(s)
- Samuel J. Payler
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Jennifer F. Biddle
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, DE, United States
| | | | - Mark G. Fox-Powell
- School of Earth and Environmental Sciences, University of St. Andrews, St. Andrews, United Kingdom
| | | | - Bryne T. Ngwenya
- School of Geosciences, Kings Buildings, University of Edinburgh, Edinburgh, United Kingdom
| | - Sean M. Paling
- Boulby Underground Science Facility, Science and Technology Facilities Council, Swindon, United Kingdom
| | - Charles S. Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
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Han R, Zhang X, Liu J, Long Q, Chen L, Liu D, Zhu D. Microbial community structure and diversity within hypersaline Keke Salt Lake environments. Can J Microbiol 2017; 63:895-908. [PMID: 28850799 DOI: 10.1139/cjm-2016-0773] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Keke Salt Lake is located in the Qaidamu Basin of China. It is a unique magnesium sulfate-subtype hypersaline lake that exhibits a halite domain ecosystem, yet its microbial diversity has remained unstudied. Here, the microbial community structure and diversity was investigated via high-throughput sequencing of the V3-V5 regions of 16S rRNA genes. A high diversity of operational taxonomic units was detected for Bacteria and Archaea (734 and 747, respectively), comprising 21 phyla, 43 classes, and 201 genera of Bacteria and 4 phyla, 4 classes, and 39 genera of Archaea. Salt-saturated samples were dominated by the bacterial genera Bacillus (51.52%-58.35% relative abundance), Lactococcus (9.52%-10.51%), and Oceanobacillus (8.82%-9.88%) within the Firmicutes phylum (74.81%-80.99%), contrasting with other hypersaline lakes. The dominant Archaea belonged to the Halobacteriaceae family, and in particular, the genera (with an abundance of >10% of communities) Halonotius, Halorubellus, Halapricum, Halorubrum, and Natronomonas. Additionally, we report the presence of Nanohaloarchaeota and Woesearchaeota in Qinghai-Tibet Plateau lakes, which has not been previously documented. Total salinity (especially Mg2+, Cl-, Na+, and K+) mostly correlated with taxonomic distribution across samples. These results expand our understanding of microbial resource utilization within hypersaline lakes and the potential adaptations of dominant microorganisms that allow them to inhabit such environments.
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Affiliation(s)
- Rui Han
- a Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China.,b Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, Qinghai 810016, People's Republic of China
| | - Xin Zhang
- c Research Center of Basic Medical Sciences, Qinghai University Medical College, Xining, Qinghai 810016, People's Republic of China
| | - Jing Liu
- c Research Center of Basic Medical Sciences, Qinghai University Medical College, Xining, Qinghai 810016, People's Republic of China
| | - Qifu Long
- c Research Center of Basic Medical Sciences, Qinghai University Medical College, Xining, Qinghai 810016, People's Republic of China
| | - Laisheng Chen
- b Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, Qinghai 810016, People's Republic of China
| | - Deli Liu
- a Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Derui Zhu
- c Research Center of Basic Medical Sciences, Qinghai University Medical College, Xining, Qinghai 810016, People's Republic of China
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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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Perchlorate and halophilic prokaryotes: implications for possible halophilic life on Mars. Extremophiles 2013; 18:75-80. [PMID: 24150694 DOI: 10.1007/s00792-013-0594-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Accepted: 10/10/2013] [Indexed: 10/26/2022]
Abstract
In view of the finding of perchlorate among the salts detected by the Phoenix Lander on Mars, we investigated the relationships of halophilic heterotrophic microorganisms (archaea of the family Halobacteriaceae and the bacterium Halomonas elongata) toward perchlorate. All strains tested grew well in NaCl-based media containing 0.4 M perchlorate, but at the highest perchlorate concentrations, tested cells were swollen or distorted. Some species (Haloferax mediterranei, Haloferax denitrificans, Haloferax gibbonsii, Haloarcula marismortui, Haloarcula vallismortis) could use perchlorate as an electron acceptor for anaerobic growth. Although perchlorate is highly oxidizing, its presence at a concentration of 0.2 M for up to 2 weeks did not negatively affect the ability of a yeast extract-based medium to support growth of the archaeon Halobacterium salinarum. These findings show that presence of perchlorate among the salts on Mars does not preclude the possibility of halophilic life. If indeed the liquid brines that may exist on Mars are inhabited by salt-requiring or salt-tolerant microorganisms similar to the halophiles on Earth, presence of perchlorate may even be stimulatory when it can serve as an electron acceptor for respiratory activity in the anaerobic Martian environment.
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