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Huang M, Zhang H, Ren M, Ji B, Sun K. The synthesis of ectoine enhance the assimilation of ammonia nitrogen in hypersaline wastewater by the salt-tolerant assimilation bacteria sludge. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169694. [PMID: 38160842 DOI: 10.1016/j.scitotenv.2023.169694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 12/23/2023] [Accepted: 12/24/2023] [Indexed: 01/03/2024]
Abstract
In contrast to nitrification-denitrification microorganisms that convert ammonia nitrogen in hypersaline wastewater into nitrogen for discharge, this research utilizes sludge enriched with salt-tolerant assimilation bacteria (STAB) to assimilate organic matter and ammonia nitrogen in hypersaline wastewater into ectoine - a biomass with high economic value and resistance to external osmotic pressure. The study investigates the relationship between the synthesis of ectoine and nitrogen removal efficiency of STAB sludge in three sequencing batch reactors (SBR) operated at different salinities (50, 75, and 100 g/L) and organic matter concentrations. The research reveals that, under low concentration carbon sources (TOC/N = 4, NH4+-N = 60 mg/L), the ammonia nitrogen removal efficiency of SBR reactors increased by 14.51 % and 17.25 % within 5 d and 2 d, respectively, when salinity increased from 50 g/L to 75 g/L and 100 g/L. Under high concentration carbon sources (TOC/N = 8, NH4+-N = 60 mg/L), the ammonia nitrogen removal efficiency of STAB sludge in the three reactors stabilized at 80.20 %, 76.71 %, and 72.87 %, and the total nitrogen removal efficiency was finally stabilized at 80.47 %, 73.15 %, and 65.53 %, respectively. The nitrogen removal performance by ammonium-assimilating of STAB sludge is more sustainable under low salinity, while it is more short-term explosive under high salinity. Moreover, the intracellular ectoine concentration of STAB sludge was found to be related to this behavior. Empirical formulas confirm that STAB sludge synthesizes ectoine from nutrients in wastewater through assimilation, and intracellular ectoine has a threshold defect (150 mg/gVss). The ectoine metabolism pathways of STAB sludge was constructed using the Kyoto Encyclopedia of Genes and Genomes (KEGG). The ammonia nitrogen in sewage is converted into glutamic acid under the action of assimilation genes. It then undergoes a tricarboxylic acid cycle to synthesize the crucial precursor of ectoine - aspartic acid. Subsequently, ectoine is produced through ectoine synthase. The findings suggest that when the synthesis of intracellular ectoine reaches saturation, it inhibits the continuous nitrogen removal performance of STAB sludge under high salinity. STAB sludge does not actively release ectoine through channels under stable external osmotic pressure.
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Affiliation(s)
- Minglei Huang
- Zhejiang University, 310013, China; NingboTech University, 315100, China
| | | | - Min Ren
- Ningbo Marine Center, Ministry of Natural Resources, 315100, China
| | - Bixiao Ji
- NingboTech University, 315100, China
| | - Keying Sun
- Zhejiang University, 310013, China; NingboTech University, 315100, China
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Abdullah K, Wilkins D, Ferrari BC. Utilization of-Omic technologies in cold climate hydrocarbon bioremediation: a text-mining approach. Front Microbiol 2023; 14:1113102. [PMID: 37396353 PMCID: PMC10313077 DOI: 10.3389/fmicb.2023.1113102] [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] [Received: 12/01/2022] [Accepted: 05/02/2023] [Indexed: 07/04/2023] Open
Abstract
Hydrocarbon spills in cold climates are a prominent and enduring form of anthropogenic contamination. Bioremediation is one of a suite of remediation tools that has emerged as a cost-effective strategy for transforming these contaminants in soil, ideally into less harmful products. However, little is understood about the molecular mechanisms driving these complex, microbially mediated processes. The emergence of -omic technologies has led to a revolution within the sphere of environmental microbiology allowing for the identification and study of so called 'unculturable' organisms. In the last decade, -omic technologies have emerged as a powerful tool in filling this gap in our knowledge on the interactions between these organisms and their environment in vivo. Here, we utilize the text mining software Vosviewer to process meta-data and visualize key trends relating to cold climate bioremediation projects. The results of text mining of the literature revealed a shift over time from optimizing bioremediation experiments on the macro/community level to, in more recent years focusing on individual organisms of interest, interactions within the microbiome and the investigation of novel metabolic degradation pathways. This shift in research focus was made possible in large part by the rise of omics studies allowing research to focus not only what organisms/metabolic pathways are present but those which are functional. However, all is not harmonious, as the development of downstream analytical methods and associated processing tools have outpaced sample preparation methods, especially when dealing with the unique challenges posed when analyzing soil-based samples.
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Affiliation(s)
- Kristopher Abdullah
- Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Daniel Wilkins
- Environmental Stewardship Program, Australian Antarctic Division, Department of Climate Change, Energy, Environment and Water, Kingston, TAS, Australia
| | - Belinda C. Ferrari
- Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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Panwar P, Williams TJ, Allen MA, Cavicchioli R. Population structure of an Antarctic aquatic cyanobacterium. MICROBIOME 2022; 10:207. [PMID: 36457105 PMCID: PMC9716671 DOI: 10.1186/s40168-022-01404-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/29/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Ace Lake is a marine-derived, stratified lake in the Vestfold Hills of East Antarctica with an upper oxic and lower anoxic zone. Cyanobacteria are known to reside throughout the water column. A Synechococcus-like species becomes the most abundant member in the upper sunlit waters during summer while persisting annually even in the absence of sunlight and at depth in the anoxic zone. Here, we analysed ~ 300 Gb of Ace Lake metagenome data including 59 Synechococcus-like metagenome-assembled genomes (MAGs) to determine depth-related variation in cyanobacterial population structure. Metagenome data were also analysed to investigate viruses associated with this cyanobacterium and the host's capacity to defend against or evade viruses. RESULTS A single Synechococcus-like species was found to exist in Ace Lake, Candidatus Regnicoccus frigidus sp. nov., consisting of one phylotype more abundant in the oxic zone and a second phylotype prevalent in the oxic-anoxic interface and surrounding depths. An important aspect of genomic variation pertained to nitrogen utilisation, with the capacity to perform cyanide assimilation and asparagine synthesis reflecting the depth distribution of available sources of nitrogen. Both specialist (host specific) and generalist (broad host range) viruses were identified with a predicted ability to infect Ca. Regnicoccus frigidus. Host-virus interactions were characterised by a depth-dependent distribution of virus type (e.g. highest abundance of specialist viruses in the oxic zone) and host phylotype capacity to defend against (e.g. restriction-modification, retron and BREX systems) and evade viruses (cell surface proteins and cell wall biosynthesis and modification enzymes). CONCLUSION In Ace Lake, specific environmental factors such as the seasonal availability of sunlight affects microbial abundances and the associated processes that the microbial community performs. Here, we find that the population structure for Ca. Regnicoccus frigidus has evolved differently to the other dominant phototroph in the lake, Candidatus Chlorobium antarcticum. The geography (i.e. Antarctica), limnology (e.g. stratification) and abiotic (e.g. sunlight) and biotic (e.g. microbial interactions) factors determine the types of niches that develop in the lake. While the lake community has become increasingly well studied, metagenome-based studies are revealing that niche adaptation can take many paths; these paths need to be determined in order to make reasonable predictions about the consequences of future ecosystem perturbations. Video Abstract.
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Affiliation(s)
- Pratibha Panwar
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Michelle A Allen
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia.
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Molecular dietary analysis of Adélie (Pygoscelis adeliae) and Gentoo (Pygoscelis papua) penguins breeding sympatrically on Antarctic Ardley Island using fecal DNA. Polar Biol 2022. [DOI: 10.1007/s00300-022-03051-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Panwar P, Allen MA, Williams TJ, Haque S, Brazendale S, Hancock AM, Paez-Espino D, Cavicchioli R. Remarkably coherent population structure for a dominant Antarctic Chlorobium species. MICROBIOME 2021; 9:231. [PMID: 34823595 PMCID: PMC8620254 DOI: 10.1186/s40168-021-01173-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 10/09/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND In Antarctica, summer sunlight enables phototrophic microorganisms to drive primary production, thereby "feeding" ecosystems to enable their persistence through the long, dark winter months. In Ace Lake, a stratified marine-derived system in the Vestfold Hills of East Antarctica, a Chlorobium species of green sulphur bacteria (GSB) is the dominant phototroph, although its seasonal abundance changes more than 100-fold. Here, we analysed 413 Gb of Antarctic metagenome data including 59 Chlorobium metagenome-assembled genomes (MAGs) from Ace Lake and nearby stratified marine basins to determine how genome variation and population structure across a 7-year period impacted ecosystem function. RESULTS A single species, Candidatus Chlorobium antarcticum (most similar to Chlorobium phaeovibrioides DSM265) prevails in all three aquatic systems and harbours very little genomic variation (≥ 99% average nucleotide identity). A notable feature of variation that did exist related to the genomic capacity to biosynthesize cobalamin. The abundance of phylotypes with this capacity changed seasonally ~ 2-fold, consistent with the population balancing the value of a bolstered photosynthetic capacity in summer against an energetic cost in winter. The very high GSB concentration (> 108 cells ml-1 in Ace Lake) and seasonal cycle of cell lysis likely make Ca. Chlorobium antarcticum a major provider of cobalamin to the food web. Analysis of Ca. Chlorobium antarcticum viruses revealed the species to be infected by generalist (rather than specialist) viruses with a broad host range (e.g., infecting Gammaproteobacteria) that were present in diverse Antarctic lakes. The marked seasonal decrease in Ca. Chlorobium antarcticum abundance may restrict specialist viruses from establishing effective lifecycles, whereas generalist viruses may augment their proliferation using other hosts. CONCLUSION The factors shaping Antarctic microbial communities are gradually being defined. In addition to the cold, the annual variation in sunlight hours dictates which phototrophic species can grow and the extent to which they contribute to ecosystem processes. The Chlorobium population studied was inferred to provide cobalamin, in addition to carbon, nitrogen, hydrogen, and sulphur cycling, as critical ecosystem services. The specific Antarctic environmental factors and major ecosystem benefits afforded by this GSB likely explain why such a coherent population structure has developed in this Chlorobium species. Video abstract.
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Affiliation(s)
- Pratibha Panwar
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Michelle A Allen
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Sabrina Haque
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- Present address: Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, 2109, Australia
| | - Sarah Brazendale
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- , Present address: Pegarah, Australia
| | - Alyce M Hancock
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- Present address: Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Battery Point, Tasmania, Australia
| | - David Paez-Espino
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Present address: Mammoth Biosciences, Inc., 1000 Marina Blvd. Suite 600, Brisbane, CA, USA
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia.
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Saccò M, White NE, Harrod C, Salazar G, Aguilar P, Cubillos CF, Meredith K, Baxter BK, Oren A, Anufriieva E, Shadrin N, Marambio-Alfaro Y, Bravo-Naranjo V, Allentoft ME. Salt to conserve: a review on the ecology and preservation of hypersaline ecosystems. Biol Rev Camb Philos Soc 2021; 96:2828-2850. [PMID: 34747117 DOI: 10.1111/brv.12780] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 02/01/2023]
Abstract
When it comes to the investigation of key ecosystems in the world, we often omit salt from the ecological recipe. In fact, despite occupying almost half of the volume of inland waters and providing crucial services to humanity and nature, inland saline ecosystems are often overlooked in discussions regarding the preservation of global aquatic resources of our planet. As a result, our knowledge of the biological and geochemical dynamics shaping these environments remains incomplete and we are hesitant in framing effective protective strategies against the increasing natural and anthropogenic threats faced by such habitats. Hypersaline lakes, water bodies where the concentration of salt exceeds 35 g/l, occur mainly in arid and semiarid areas resulting from hydrological imbalances triggering the accumulation of salts over time. Often considered the 'exotic siblings' within the family of inland waters, these ecosystems host some of the most extremophile communities worldwide and provide essential habitats for waterbirds and many other organisms in already water-stressed regions. These systems are often highlighted as natural laboratories, ideal for addressing central ecological questions due to their relatively low complexity and simple food web structures. However, recent studies on the biogeochemical mechanisms framing hypersaline communities have challenged this archetype, arguing that newly discovered highly diverse communities are characterised by specific trophic interactions shaped by high levels of specialisation. The main goal of this review is to explore our current understanding of the ecological dynamics of hypersaline ecosystems by addressing four main research questions: (i) why are hypersaline lakes unique from a biological and geochemical perspective; (ii) which biota inhabit these ecosystems and how have they adapted to the high salt conditions; (iii) how do we protect biodiversity from increasing natural and anthropogenic threats; and (iv) which scientific tools will help us preserve hypersaline ecosystems in the future? First, we focus on the ecological characterisation of hypersaline ecosystems, illustrate hydrogeochemical dynamics regulating such environments, and outline key ecoregions supporting hypersaline systems across the globe. Second, we depict the diversity and functional aspects of key taxa found in hypersaline lakes, from microorganisms to plants, invertebrates, waterbirds and upper trophic levels. Next, we describe ecosystem services and discuss possible conservation guidelines. Finally, we outline how cutting-edge technologies can provide new insights into the study of hypersaline ecology. Overall, this review sheds further light onto these understudied ecosystems, largely unrecognised as important sources of unique biological and functional diversity. We provide perspectives for key future research avenues, and advocate that the conservation of hypersaline lakes should not be taken with 'a grain of salt'.
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Affiliation(s)
- Mattia Saccò
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA, 6102, Australia
| | - Nicole E White
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA, 6102, Australia
| | - Chris Harrod
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile.,Núcleo Milenio INVASAL, Concepción, 3349001, Chile
| | - Gonzalo Salazar
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile.,Núcleo Milenio INVASAL, Concepción, 3349001, Chile
| | - Pablo Aguilar
- Núcleo Milenio INVASAL, Concepción, 3349001, Chile.,Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile
| | - Carolina F Cubillos
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile
| | - Karina Meredith
- Australian Nuclear Science and Technology Organisation (ANSTO), Locked Bag 2001, Kirrawee DC, NSW, 2232, Australia
| | - Bonnie K Baxter
- Great Salt Lake Institute, Westminster College, Salt Lake City, UT, 84105, U.S.A
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, the Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Elena Anufriieva
- A.O. Kovalevsky Institute of Biology of the Southern Seas, Russian Academy of Sciences, 2 Nakhimov Avenue 2, Sevastopol, 299011, Russia
| | - Nickolai Shadrin
- A.O. Kovalevsky Institute of Biology of the Southern Seas, Russian Academy of Sciences, 2 Nakhimov Avenue 2, Sevastopol, 299011, Russia
| | - Yeri Marambio-Alfaro
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile
| | - Víctor Bravo-Naranjo
- Facultad de Ciencias, Universidad de La Serena, Benavente 980, La Serena, Coquimbo, Chile
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA, 6102, Australia.,Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
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Li J, Gao Y, Dong H, Sheng GP. Haloarchaea, excellent candidates for removing pollutants from hypersaline wastewater. Trends Biotechnol 2021; 40:226-239. [PMID: 34284891 DOI: 10.1016/j.tibtech.2021.06.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/23/2021] [Accepted: 06/23/2021] [Indexed: 11/25/2022]
Abstract
Hypersaline wastewater is difficult to treat due to the inhibition of salt stress on microbes' viability and metabolic capabilities. Haloarchaea, native microorganisms that thrive in hypersaline habitats, overcome this key obstacle naturally. This review provides a comprehensive overview of the metabolic versatility of Haloarchaea in hypersaline wastewater treatment, including carbon, nitrogen, phosphorus, sulfur, and heavy metal metabolism. It also analyzes factors affecting pollutant removal and addresses metabolic mechanisms. Additionally, haloarchaea microbial characteristics and strategies to cope with salt stress are highlighted. Finally, the biotechnological potential of biomolecules produced from haloarchaea is investigated. To get better insight into the potential of haloarchaea, a deeper investigation of basic metabolism and more in-depth studies of their genomics and applications in actual wastewater are also necessary.
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Affiliation(s)
- Jin Li
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China.
| | - Yuanyuan Gao
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China
| | - Huiyu Dong
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Guo-Ping Sheng
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China.
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Cui HL, Dyall-Smith ML. Cultivation of halophilic archaea (class Halobacteria) from thalassohaline and athalassohaline environments. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:243-251. [PMID: 37073340 PMCID: PMC10077297 DOI: 10.1007/s42995-020-00087-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/25/2020] [Indexed: 05/03/2023]
Abstract
As a group, the halophilic archaea (class Halobacteria) are the most salt-requiring and salt-resistant microorganisms within the domain Archaea. Halophilic archaea flourish in thalassohaline and athalassohaline environments and require over 100-150 g/L NaCl for growth and structural stability. Natural hypersaline environments vary in salt concentration, chemical composition and pH, and occur in climates ranging from tropical to polar and even under-sea. Accordingly, their resident haloarchaeal species vary enormously, as do their individual population compositions and community structures. These diverse halophilic archaeal strains are precious resources for theoretical and applied research but assessing their taxonomic and metabolic novelty and diversity in natural environments has been technically difficult up until recently. Environmental DNA-based high-throughput sequencing technology has now matured sufficiently to allow inexpensive recovery of massive amounts of sequence data, revealing the distribution and community composition of halophilic archaea in different hypersaline environments. While cultivation of haloarchaea is slow and tedious, and only recovers a fraction of the natural diversity, it is the conventional means of describing new species, and provides strains for detailed study. As of the end of May 2020, the class Halobacteria contains 71 genera and 275 species, 49.8% of which were first isolated from the marine salt environment and 50.2% from the inland salt environment, indicating that both thalassohaline and athalassohaline environments contain diverse halophilic archaea. However, there remain taxa that have not yet been isolated in pure culture, such as the nanohaloarchaea, which are widespread in the salt environment and may be one of the hot spots in the field of halophilic archaea research in the future. In this review, we focus on the cultivation strategies that have been used to isolate extremely halophilic archaea and point out some of the pitfalls and challenges. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-020-00087-3.
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Affiliation(s)
- Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013 China
| | - Mike L. Dyall-Smith
- Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, 3010 Australia
- Computational Biology Group, Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany
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Abstract
Despite the typical human notion that the Earth is a habitable planet, over three quarters of our planet is uninhabitable by us without assistance. The organisms that live and thrive in these “inhospitable” environments are known by the name extremophiles and are found in all Domains of Life. Despite our general lack of knowledge about them, they have already assisted humans in many ways and still have much more to give. In this review, I describe how they have adapted to live/thrive/survive in their niches, helped scientists unlock major scientific discoveries, advance the field of biotechnology, and inform us about the boundaries of Life and where we might find it in the Universe.
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Affiliation(s)
- James A Coker
- Department of Sciences, University of Maryland Global Campus, Adelphi, MD, USA
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Abstract
We demonstrate that Candidatus Nanohaloarchaeum antarcticus requires Halorubrum lacusprofundi for growth, illustrating that Nanohaloarchaeota require a host rather than being free living as previously proposed. Developing the means of cultivating Nanohaloarchaeota in the laboratory provides the capacity to advance understanding of how archaea interact and the factors that control their symbiotic relationship (e.g. mutualism, commensalism, antagonism). Our findings amplify the view that Antarctic lakes are a treasure trove for the discovery of microbes with previously unknown properties. In hypersaline environments, Nanohaloarchaeota (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaeota [DPANN] superphylum) are thought to be free-living microorganisms. We report cultivation of 2 strains of Antarctic Nanohaloarchaeota and show that they require the haloarchaeon Halorubrum lacusprofundi for growth. By performing growth using enrichments and fluorescence-activated cell sorting, we demonstrated successful cultivation of Candidatus Nanohaloarchaeum antarcticus, purification of Ca. Nha. antarcticus away from other species, and growth and verification of Ca. Nha. antarcticus with Hrr. lacusprofundi; these findings are analogous to those required for fulfilling Koch’s postulates. We use fluorescent in situ hybridization and transmission electron microscopy to assess cell structures and interactions; metagenomics to characterize enrichment taxa, generate metagenome assembled genomes, and interrogate Antarctic communities; and proteomics to assess metabolic pathways and speculate about the roles of certain proteins. Metagenome analysis indicates the presence of a single species, which is endemic to Antarctic hypersaline systems that support the growth of haloarchaea. The presence of unusually large proteins predicted to function in attachment and invasion of hosts plus the absence of key biosynthetic pathways (e.g., lipids) in metagenome assembled genomes of globally distributed Nanohaloarchaeota indicate that all members of the lineage have evolved as symbionts. Our work expands the range of archaeal symbiotic lifestyles and provides a genetically tractable model system for advancing understanding of the factors controlling microbial symbiotic relationships.
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Martínez FL, Orce IG, Rajal VB, Irazusta VP. Salar del Hombre Muerto, source of lithium-tolerant bacteria. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2019; 41:529-543. [PMID: 29995192 DOI: 10.1007/s10653-018-0148-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 06/29/2018] [Indexed: 06/08/2023]
Abstract
The Salar del Hombre Muerto is a flat salt with great microbial activity despite the existing extreme conditions like high altitude, lack of water, low level of oxygen, high radiation and high concentration of sodium and lithium chloride. Despite these unfavorable conditions, we found microbial diversity with the presence of fungi, algae, and bacteria. From aqueous solutions and soil samples, a total of 238 bacteria were isolated and 186 of them were able to grow in the presence of salt. About 30% of the strains showed the ability to grow in solid medium proximally to a LiCl solution close to saturation (636 g/L). These isolates were characterized taking into account the morphology, Gram stain, ability to form biofilms and to produce pigments, and mainly according to the tolerance against lithium chloride. Bacillus was predominant among the most tolerant 26 microorganisms found, followed by Micrococcus and Brevibacterium. Members of the genera Kocuria, Curtobacterium and Halomonas were also represented among the bacteria with tolerance to 30 and 60 g/L of LiCl in defined liquid medium. All the capacities found in these microorganisms make them extremely interesting for biotechnological applications.
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Affiliation(s)
- Fabiana Lilian Martínez
- Instituto de Investigaciones para la Industria Química (INIQUI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Salta (UNSa), Av. Bolivia 5150, 4400, Salta, Argentina
| | - Ingrid Georgina Orce
- Instituto de Investigaciones para la Industria Química (INIQUI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Salta (UNSa), Av. Bolivia 5150, 4400, Salta, Argentina
| | - Verónica Beatriz Rajal
- Instituto de Investigaciones para la Industria Química (INIQUI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Salta (UNSa), Av. Bolivia 5150, 4400, Salta, Argentina
- Facultad de Ingeniería, UNSa, Salta, Argentina
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Verónica Patricia Irazusta
- Instituto de Investigaciones para la Industria Química (INIQUI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Salta (UNSa), Av. Bolivia 5150, 4400, Salta, Argentina.
- Facultad de Ciencias Naturales, UNSa, Salta, Argentina.
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Sucrose Metabolism in Haloarchaea: Reassessment Using Genomics, Proteomics, and Metagenomics. Appl Environ Microbiol 2019; 85:AEM.02935-18. [PMID: 30658981 DOI: 10.1128/aem.02935-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 01/10/2019] [Indexed: 12/21/2022] Open
Abstract
The canonical pathway for sucrose metabolism in haloarchaea utilizes a modified Embden-Meyerhof-Parnas pathway (EMP), in which ketohexokinase and 1-phosphofructokinase phosphorylate fructose released from sucrose hydrolysis. However, our survey of haloarchaeal genomes determined that ketohexokinase and 1-phosphofructokinase genes were not present in all species known to utilize fructose and sucrose, thereby indicating that alternative mechanisms exist for fructose metabolism. A fructokinase gene was identified in the majority of fructose- and sucrose-utilizing species, whereas only a small number possessed a ketohexokinase gene. Analysis of a range of hypersaline metagenomes revealed that haloarchaeal fructokinase genes were far more abundant (37 times) than haloarchaeal ketohexokinase genes. We used proteomic analysis of Halohasta litchfieldiae (which encodes fructokinase) and identified changes in protein abundance that relate to growth on sucrose. Proteins inferred to be involved in sucrose metabolism included fructokinase, a carbohydrate primary transporter, a putative sucrose hydrolase, and two uncharacterized carbohydrate-related proteins encoded in the same gene cluster as fructokinase and the transporter. Homologs of these proteins were present in the genomes of all haloarchaea that use sugars for growth. Enzymes involved in the semiphosphorylative Entner-Doudoroff pathway also had higher abundances in sucrose-grown H. litchfieldiae cells, consistent with this pathway functioning in the catabolism of the glucose moiety of sucrose. The study revises the current understanding of fundamental pathways for sugar utilization in haloarchaea and proposes alternatives to the modified EMP pathway used by haloarchaea for sucrose and fructose utilization.IMPORTANCE Our ability to infer the function that microorganisms perform in the environment is predicated on assumptions about metabolic capacity. When genomic or metagenomic data are used, metabolic capacity is inferred from genetic potential. Here, we investigate the pathways by which haloarchaea utilize sucrose. The canonical haloarchaeal pathway for fructose metabolism involving ketohexokinase occurs only in a small proportion of haloarchaeal genomes and is underrepresented in metagenomes. Instead, fructokinase genes are present in the majority of genomes/metagenomes. In addition to genomic and metagenomic analyses, we used proteomic analysis of Halohasta litchfieldiae (which encodes fructokinase but lacks ketohexokinase) and identified changes in protein abundance that related to growth on sucrose. In this way, we identified novel proteins implicated in sucrose metabolism in haloarchaea, comprising a transporter and various catabolic enzymes (including proteins that are annotated as hypothetical).
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13
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Yau S, Seth-Pasricha M. Viruses of Polar Aquatic Environments. Viruses 2019; 11:v11020189. [PMID: 30813316 PMCID: PMC6410135 DOI: 10.3390/v11020189] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/13/2019] [Accepted: 02/18/2019] [Indexed: 02/07/2023] Open
Abstract
The poles constitute 14% of the Earth’s biosphere: The aquatic Arctic surrounded by land in the north, and the frozen Antarctic continent surrounded by the Southern Ocean. In spite of an extremely cold climate in addition to varied topographies, the polar aquatic regions are teeming with microbial life. Even in sub-glacial regions, cellular life has adapted to these extreme environments where perhaps there are traces of early microbes on Earth. As grazing by macrofauna is limited in most of these polar regions, viruses are being recognized for their role as important agents of mortality, thereby influencing the biogeochemical cycling of nutrients that, in turn, impact community dynamics at seasonal and spatial scales. Here, we review the viral diversity in aquatic polar regions that has been discovered in the last decade, most of which has been revealed by advances in genomics-enabled technologies, and we reflect on the vast extent of the still-to-be explored polar microbial diversity and its “enigmatic virosphere”.
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Affiliation(s)
- Sheree Yau
- Integrative Marine Biology Laboratory (BIOM), CNRS, UMR7232, Sorbonne Université, 66650 Banyuls-sur-Mer, France.
| | - Mansha Seth-Pasricha
- Institute of Earth, Ocean, and Atmospheric Sciences, Rutgers University, New Brunswick, NJ 08901, USA.
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA.
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14
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La Cono V, Bortoluzzi G, Messina E, La Spada G, Smedile F, Giuliano L, Borghini M, Stumpp C, Schmitt-Kopplin P, Harir M, O'Neill WK, Hallsworth JE, Yakimov M. The discovery of Lake Hephaestus, the youngest athalassohaline deep-sea formation on Earth. Sci Rep 2019; 9:1679. [PMID: 30737448 PMCID: PMC6368551 DOI: 10.1038/s41598-018-38444-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 12/27/2018] [Indexed: 12/30/2022] Open
Abstract
Hydrated, magnesium-rich minerals and subglacial brines exist on the martian surface, so the habitability of high-Mg2+ environments on Earth has extraterrestrial (as well as terrestrial) implications. Here, we report the discovery of a MgCl2-dominated (4.72 M) brine lake on the floor of the Mediterranean Ridge that underlies a 3500-m water column, and name it Lake Hephaestus. Stable isotope analyses indicated that the Hephaestus brine is derived from interactions between ancient bishofite-enriched evaporites and subsurface fluids. Analyses of sediment pore waters indicated that the Hephaestus depression had contained the MgCl2 brine for a remarkably short period; only 700 years. Lake Hephaestus is, therefore, the youngest among currently known submarine athalassohaline brine lakes on Earth. Due to its biologically hostile properties (low water-activity and extreme chaotropicity), the Hephaestus brine is devoid of life. By contrast, the seawater-Hephaestus brine interface has been shown to act as refuge for extremely halophilic and magnesium-adapted stratified communities of microbes, even at MgCl2 concentrations that approach the water-activity limit for life (0.653).
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Affiliation(s)
- Violetta La Cono
- CNR, Institute for Coastal Marine Environment, Messina, 98122, Italy
| | | | - Enzo Messina
- CNR, Institute for Coastal Marine Environment, Messina, 98122, Italy
| | - Gina La Spada
- CNR, Institute for Coastal Marine Environment, Messina, 98122, Italy
| | - Francesco Smedile
- CNR, Institute for Coastal Marine Environment, Messina, 98122, Italy
| | - Laura Giuliano
- Mediterranean Science Commission (CIESM), MC, 98000, Monaco
| | | | - Christine Stumpp
- Institute of Groundwater Ecology, Helmholtz Centre Munich, Neuherberg, 85764, Germany.,Institute of Hydraulics and Rural Water Management, University of Natural Resources and Life Sciences Vienna, Wien, 1190, Austria
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Centre Munich, Neuherberg, 85764, Germany.,Technische Universität München, Lehrstuhl für Analytische Lebensmittelchemie, Freising, 85354, Germany
| | - Mourad Harir
- Research Unit Analytical BioGeoChemistry, Helmholtz Centre Munich, Neuherberg, 85764, Germany
| | - William K O'Neill
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland, UK
| | - John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland, UK
| | - Michail Yakimov
- CNR, Institute for Coastal Marine Environment, Messina, 98122, Italy. .,Institute of Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad, 236016, Russia.
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15
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Lvov DK, Sizikova TE, Lebedev VN, Borisevich SV. [Plasmids of archaea as possible ancestors of DNA-containing viruses]. Vopr Virusol 2018; 63:197-201. [PMID: 30550095 DOI: 10.18821/0507-4088-2018-63-5-197-201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 06/19/2018] [Indexed: 11/17/2022]
Abstract
Тhе kingdom Archaea, as well as Bacteria, belongs to the overkingdom Prokaryota. Halophilic archaea (Halorubrum lacusprofundi) isolated from Antarctic saline lakes contain plasmids (pR1SE) that code proteins taking part in the formation of membranes of archaea vesicles. The molecular and biological properties of pR1SE and the peculiarity of its interaction with sensitive cells are considered in this article. The role of structural proteins coded by pR1S in the process of formation of vesicle membrane complex is paid special attention. Plasmid-containing archaea vesicles model some properties of viruses. Archaea plasmids can be viewed as possible ancestors of DNA-containing viruses.
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Affiliation(s)
- D K Lvov
- National Research Center for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya, Moscow, 123098, Russian Federation
| | - T E Sizikova
- 48 Central Scientific Research Institute, Sergiev Posad, 141306, Russian Federation
| | - V N Lebedev
- 48 Central Scientific Research Institute, Sergiev Posad, 141306, Russian Federation
| | - S V Borisevich
- 48 Central Scientific Research Institute, Sergiev Posad, 141306, Russian Federation
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16
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Tschitschko B, Erdmann S, DeMaere MZ, Roux S, Panwar P, Allen MA, Williams TJ, Brazendale S, Hancock AM, Eloe-Fadrosh EA, Cavicchioli R. Genomic variation and biogeography of Antarctic haloarchaea. MICROBIOME 2018; 6:113. [PMID: 29925429 PMCID: PMC6011602 DOI: 10.1186/s40168-018-0495-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/06/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND The genomes of halophilic archaea (haloarchaea) often comprise multiple replicons. Genomic variation in haloarchaea has been linked to viral infection pressure and, in the case of Antarctic communities, can be caused by intergenera gene exchange. To expand understanding of genome variation and biogeography of Antarctic haloarchaea, here we assessed genomic variation between two strains of Halorubrum lacusprofundi that were isolated from Antarctic hypersaline lakes from different regions (Vestfold Hills and Rauer Islands). To assess variation in haloarchaeal populations, including the presence of genomic islands, metagenomes from six hypersaline Antarctic lakes were characterised. RESULTS The sequence of the largest replicon of each Hrr. lacusprofundi strain (primary replicon) was highly conserved, while each of the strains' two smaller replicons (secondary replicons) were highly variable. Intergenera gene exchange was identified, including the sharing of a type I-B CRISPR system. Evaluation of infectivity of an Antarctic halovirus provided experimental evidence for the differential susceptibility of the strains, bolstering inferences that strain variation is important for modulating interactions with viruses. A relationship was found between genomic structuring and the location of variation within replicons and genomic islands, demonstrating that the way in which haloarchaea accommodate genomic variability relates to replicon structuring. Metagenome read and contig mapping and clustering and scaling analyses demonstrated biogeographical patterning of variation consistent with environment and distance effects. The metagenome data also demonstrated that specific haloarchaeal species dominated the hypersaline systems indicating they are endemic to Antarctica. CONCLUSION The study describes how genomic variation manifests in Antarctic-lake haloarchaeal communities and provides the basis for future assessments of Antarctic regional and global biogeography of haloarchaea.
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Affiliation(s)
- Bernhard Tschitschko
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- Present Address: Climate Change Cluster, Department of Environmental Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Susanne Erdmann
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Matthew Z DeMaere
- i3 Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Simon Roux
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Pratibha Panwar
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Michelle A Allen
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Sarah Brazendale
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- , Present Address: 476 Lancaster Rd, Pegarah, Australia
| | - Alyce M Hancock
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- Present Address: University of Tasmania Institute of Marine and Antarctic Studies, Antarctic Gateway Partnership and Antarctic Climate and Ecosystem Research Centre, Battery Point, Tasmania, Australia
| | | | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia.
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17
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Williams TJ, Liao Y, Ye J, Kuchel RP, Poljak A, Raftery MJ, Cavicchioli R. Cold adaptation of the Antarctic haloarchaea
Halohasta litchfieldiae
and
Halorubrum lacusprofundi. Environ Microbiol 2017; 19:2210-2227. [DOI: 10.1111/1462-2920.13705] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 01/17/2017] [Accepted: 02/08/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Timothy J. Williams
- School of Biotechnology and Biomolecular SciencesThe University of New South WalesSydney New South Wales2052 Australia
| | - Yan Liao
- School of Biotechnology and Biomolecular SciencesThe University of New South WalesSydney New South Wales2052 Australia
| | - Jun Ye
- School of Biotechnology and Biomolecular SciencesThe University of New South WalesSydney New South Wales2052 Australia
- Centre for Marine Bio‐InnovationThe University of New South WalesSydney New South Wales2052 Australia
| | - Rhiannon P. Kuchel
- Electron Microscopy UnitThe University of New South WalesSydney New South Wales2052 Australia
| | - Anne Poljak
- Bioanalytical Mass Spectrometry FacilityThe University of New South WalesSydney New South Wales2052 Australia
| | - Mark J. Raftery
- Bioanalytical Mass Spectrometry FacilityThe University of New South WalesSydney New South Wales2052 Australia
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular SciencesThe University of New South WalesSydney New South Wales2052 Australia
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18
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Liao Y, Williams TJ, Ye J, Charlesworth J, Burns BP, Poljak A, Raftery MJ, Cavicchioli R. Morphological and proteomic analysis of biofilms from the Antarctic archaeon, Halorubrum lacusprofundi. Sci Rep 2016; 6:37454. [PMID: 27874045 PMCID: PMC5118699 DOI: 10.1038/srep37454] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/26/2016] [Indexed: 12/21/2022] Open
Abstract
Biofilms enhance rates of gene exchange, access to specific nutrients, and cell survivability. Haloarchaea in Deep Lake, Antarctica, are characterized by high rates of intergenera gene exchange, metabolic specialization that promotes niche adaptation, and are exposed to high levels of UV-irradiation in summer. Halorubrum lacusprofundi from Deep Lake has previously been reported to form biofilms. Here we defined growth conditions that promoted the formation of biofilms and used microscopy and enzymatic digestion of extracellular material to characterize biofilm structures. Extracellular DNA was found to be critical to biofilms, with cell surface proteins and quorum sensing also implicated in biofilm formation. Quantitative proteomics was used to define pathways and cellular processes involved in forming biofilms; these included enhanced purine synthesis and specific cell surface proteins involved in DNA metabolism; post-translational modification of cell surface proteins; specific pathways of carbon metabolism involving acetyl-CoA; and specific responses to oxidative stress. The study provides a new level of understanding about the molecular mechanisms involved in biofilm formation of this important member of the Deep Lake community.
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Affiliation(s)
- Y Liao
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - T J Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - J Ye
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia.,Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - J Charlesworth
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - B P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - A Poljak
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales, Australia
| | - M J Raftery
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales, Australia
| | - R Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
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19
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Williams TJ, Allen M, Tschitschko B, Cavicchioli R. Glycerol metabolism of haloarchaea. Environ Microbiol 2016; 19:864-877. [PMID: 27768817 DOI: 10.1111/1462-2920.13580] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Haloarchaea are heterotrophic members of the Archaea that thrive in hypersaline environments, often feeding off the glycerol that is produced as an osmolyte by eucaryotic Dunaliella during primary production. In this study we analyzed glycerol metabolism genes in closed genomes of haloarchaea and examined published data describing the growth properties of haloarchaea and experimental data for the enzymes involved. By integrating the genomic data with knowledge from the literature, we derived an understanding of the ecophysiology and evolutionary properties of glycerol catabolic pathways in haloarchaea.
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Affiliation(s)
- Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, New South Wales, Australia
| | - Michelle Allen
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, New South Wales, Australia
| | - Bernhard Tschitschko
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, New South Wales, Australia
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, New South Wales, Australia
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20
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Liao Y, Williams TJ, Walsh JC, Ji M, Poljak A, Curmi PMG, Duggin IG, Cavicchioli R. Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: investigating acetamidase gene function. Sci Rep 2016; 6:34639. [PMID: 27708407 PMCID: PMC5052560 DOI: 10.1038/srep34639] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/16/2016] [Indexed: 01/04/2023] Open
Abstract
No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms.
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Affiliation(s)
- Y Liao
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - T J Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - J C Walsh
- School of Physics, The University of New South Wales, Sydney, New South Wales, 2052, Australia.,The ithree institute, University of Technology Sydney, Broadway, New South Wales, 2007, Australia
| | - M Ji
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - A Poljak
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales, Australia
| | - P M G Curmi
- School of Physics, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - I G Duggin
- The ithree institute, University of Technology Sydney, Broadway, New South Wales, 2007, Australia
| | - R Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
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21
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Anderson IJ, DasSarma P, Lucas S, Copeland A, Lapidus A, Del Rio TG, Tice H, Dalin E, Bruce DC, Goodwin L, Pitluck S, Sims D, Brettin TS, Detter JC, Han CS, Larimer F, Hauser L, Land M, Ivanova N, Richardson P, Cavicchioli R, DasSarma S, Woese CR, Kyrpides NC. Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34. Stand Genomic Sci 2016; 11:70. [PMID: 27617060 PMCID: PMC5018182 DOI: 10.1186/s40793-016-0194-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/03/2016] [Indexed: 01/26/2023] Open
Abstract
Halorubrum lacusprofundi is an extreme halophile within the archaeal phylum Euryarchaeota. The type strain ACAM 34 was isolated from Deep Lake, Antarctica. H. lacusprofundi is of phylogenetic interest because it is distantly related to the haloarchaea that have previously been sequenced. It is also of interest because of its psychrotolerance. We report here the complete genome sequence of H. lacusprofundi type strain ACAM 34 and its annotation. This genome is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea.
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Affiliation(s)
| | - Priya DasSarma
- Institute of Marine and Environmental Technology, Columbus Center, University of Maryland School of Medicine, University System of Maryland, Baltimore, MD 21202 USA
| | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Alex Copeland
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | | | - Hope Tice
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Eileen Dalin
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - David C Bruce
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Lynne Goodwin
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - David Sims
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Thomas S Brettin
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - John C Detter
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Cliff S Han
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Frank Larimer
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA ; Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Loren Hauser
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA ; Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA ; Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | | | | | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052 Australia
| | - Shiladitya DasSarma
- Institute of Marine and Environmental Technology, Columbus Center, University of Maryland School of Medicine, University System of Maryland, Baltimore, MD 21202 USA
| | - Carl R Woese
- B103 Chemical and Life Sciences Laboratory, University of Illinois at Urbana-Champaign, MC-110, 601 South Goodwin Avenue, Urbana, IL 61801 USA
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