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Ramasamy KP, Mahawar L, Rajasabapathy R, Rajeshwari K, Miceli C, Pucciarelli S. Comprehensive insights on environmental adaptation strategies in Antarctic bacteria and biotechnological applications of cold adapted molecules. Front Microbiol 2023; 14:1197797. [PMID: 37396361 PMCID: PMC10312091 DOI: 10.3389/fmicb.2023.1197797] [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: 03/31/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023] Open
Abstract
Climate change and the induced environmental disturbances is one of the major threats that have a strong impact on bacterial communities in the Antarctic environment. To cope with the persistent extreme environment and inhospitable conditions, psychrophilic bacteria are thriving and displaying striking adaptive characteristics towards severe external factors including freezing temperature, sea ice, high radiation and salinity which indicates their potential in regulating climate change's environmental impacts. The review illustrates the different adaptation strategies of Antarctic microbes to changing climate factors at the structural, physiological and molecular level. Moreover, we discuss the recent developments in "omics" approaches to reveal polar "blackbox" of psychrophiles in order to gain a comprehensive picture of bacterial communities. The psychrophilic bacteria synthesize distinctive cold-adapted enzymes and molecules that have many more industrial applications than mesophilic ones in biotechnological industries. Hence, the review also emphasizes on the biotechnological potential of psychrophilic enzymes in different sectors and suggests the machine learning approach to study cold-adapted bacteria and engineering the industrially important enzymes for sustainable bioeconomy.
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Affiliation(s)
| | - Lovely Mahawar
- Department of Plant Physiology, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, Nitra, Slovakia
| | - Raju Rajasabapathy
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, Tamilnadu, India
| | | | - Cristina Miceli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
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2
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Thompson TP, Busetti A, Gilmore BF. Quorum Sensing in Halorubrum saccharovorum Facilitates Cross-Domain Signaling between Archaea and Bacteria. Microorganisms 2023; 11:1271. [PMID: 37317245 DOI: 10.3390/microorganisms11051271] [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: 02/10/2023] [Revised: 05/10/2023] [Accepted: 05/10/2023] [Indexed: 06/16/2023] Open
Abstract
Quorum Sensing (QS) is a well-studied intercellular communication mechanism in bacteria, regulating collective behaviors such as biofilm formation, virulence, and antibiotic resistance. However, cell-cell signaling in haloarchaea remains largely unexplored. The coexistence of bacteria and archaea in various environments, coupled with the known cell-cell signaling mechanisms in both prokaryotic and eukaryotic microorganisms and the presence of cell-cell signaling mechanisms in both prokaryotic and eukaryotic microorganisms, suggests a possibility for haloarchaea to possess analogous cell-cell signaling or QS systems. Recently, N-acylhomoserine lactone (AHL)-like compounds were identified in haloarchaea; yet, their precise role-for example, persister cell formation-remains ambiguous. This study investigated the capacity of crude supernatant extract from the haloarchaeon Halorubrum saccharovorum CSM52 to stimulate bacterial AHL-dependent QS phenotypes using bioreporter strains. Our findings reveal that these crude extracts induced several AHL-dependent bioreporters and modulated pyocyanin and pyoverdine production in Pseudomonas aeruginosa. Importantly, our study suggests cross-domain communication between archaea and bacterial pathogens, providing evidence for archaea potentially influencing bacterial virulence. Using Thin Layer Chromatography overlay assays, lactonolysis, and colorimetric quantification, the bioactive compound was inferred to be a chemically modified AHL-like compound or a diketopiperazine-like molecule, potentially involved in biofilm formation in H. saccharovorum CSM52. This study offers new insights into putative QS mechanisms in haloarchaea and their potential role in interspecies communication and coordination, thereby enriching our understanding of microbial interactions in diverse environments.
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Affiliation(s)
- Thomas P Thompson
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Alessandro Busetti
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Brendan F Gilmore
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
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3
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Su X, Cui H, Zhang W. Copiotrophy in a Marine-Biofilm-Derived Roseobacteraceae Bacterium Can Be Supported by Amino Acid Metabolism and Thiosulfate Oxidation. Int J Mol Sci 2023; 24:ijms24108617. [PMID: 37239957 DOI: 10.3390/ijms24108617] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/28/2023] Open
Abstract
Copiotrophic bacteria that respond rapidly to nutrient availability, particularly high concentrations of carbon sources, play indispensable roles in marine carbon cycling. However, the molecular and metabolic mechanisms governing their response to carbon concentration gradients are not well understood. Here, we focused on a new member of the family Roseobacteraceae isolated from coastal marine biofilms and explored the growth strategy at different carbon concentrations. When cultured in a carbon-rich medium, the bacterium grew to significantly higher cell densities than Ruegeria pomeroyi DSS-3, although there was no difference when cultured in media with reduced carbon. Genomic analysis showed that the bacterium utilized various pathways involved in biofilm formation, amino acid metabolism, and energy production via the oxidation of inorganic sulfur compounds. Transcriptomic analysis indicated that 28.4% of genes were regulated by carbon concentration, with increased carbon concentration inducing the expression of key enzymes in the EMP, ED, PP, and TCA cycles, genes responsible for the transformation of amino acids into TCA intermediates, as well as the sox genes for thiosulfate oxidation. Metabolomics showed that amino acid metabolism was enhanced and preferred in the presence of a high carbon concentration. Mutation of the sox genes decreased cell proton motive force when grown with amino acids and thiosulfate. In conclusion, we propose that copiotrophy in this Roseobacteraceae bacterium can be supported by amino acid metabolism and thiosulfate oxidation.
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Affiliation(s)
- Xiaoyan Su
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Han Cui
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Weipeng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
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4
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Robinson A, Ulrich SM. Haloferax volcanii Remains Viable and Shows Morphological Changes under Anoxic (CO 2-Enriched) and Hypobaric (2.4 kPa) Atmospheric Conditions. ASTROBIOLOGY 2022; 22:829-837. [PMID: 35325555 DOI: 10.1089/ast.2021.0076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Potentially habitable zones have been discovered on Mars today in underground areas containing perchlorate brines. Understanding the low-pressure adaptations of microorganisms is essential in learning more about what life could potentially be found on Mars today or could have existed in the distant past. Many studies have looked at low-pressure adaptations in bacteria; however, studies aimed at understanding these adaptations in archaea are scarcer. Haloferax volcanii is a species of halophilic archaea documented to tolerate high concentrations of oxidizing agents present on Mars (i.e., perchlorates and nitrates). In this study, we expose H. volcanii to a hypobaric (2.4 kPa) and an anoxic CO2-enriched atmosphere in the presence of perchlorate, chlorate, and nitrate. While no growth was observed during incubation in these conditions, survivability was increased in cultures incubated in low-pressure atmospheric conditions compared to ambient Earth atmospheric pressures. Scanning electron microscopy observations showed morphological changes in low-pressure conditions not observed at ambient Earth atmospheric pressures. Results suggest that previously undocumented low-pressure adaptations in H. volcanii increase survivability in simulated subsurface martian conditions. Future experiments to understand the changes in gene expression under these conditions may be valuable to understand more about low-pressure adaptations in archaea.
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Affiliation(s)
- Adam Robinson
- Department of Natural Science, St. Petersburg College, Clearwater, Florida, USA
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5
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Casillo A, D’Angelo C, Parrilli E, Tutino ML, Corsaro MM. Membrane and Extracellular Matrix Glycopolymers of Colwellia psychrerythraea 34H: Structural Changes at Different Growth Temperatures. Front Microbiol 2022; 13:820714. [PMID: 35283851 PMCID: PMC8914368 DOI: 10.3389/fmicb.2022.820714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/11/2022] [Indexed: 11/13/2022] Open
Abstract
Colwellia psychrerythraea 34H is a marine Gram-negative psychrophile; it was isolated from Arctic marine sediments, but it is considered cosmopolitan in cold environments. This microorganism is considered a model to study adaptive strategies to sub-zero temperatures, and its lifestyle has been the object of numerous studies. In the last few years, we focused our studies on the glycoconjugates produced by C. psychrerythraea 34H at 4°C, resulting in the isolation and characterization of very interesting molecules. It produces an unusual lipooligosaccharide molecule and both capsular and medium released polysaccharides. In this study, we described the response of these glycoconjugates in terms of production and chemical structure produced by C. psychrerythraea 34H grown in planktonic conditions at −2, 4, and 8°C. The glycopolymers have been detected by chemical methods and spectroscopic analyses. Moreover, the glycopolymer content of the biofilm matrix of C. psychrerythraea 34H has been evaluated, through confocal microscopy and glycosyl analysis. The results highlighted that C. psychrerythraea 34H adjusts both the production and the typology of its glyconjugates in response to temperature fluctuations.
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Schulze S, Pohlschroder M. Proteomic Sample Preparation and Data Analysis in Line with the Archaeal Proteome Project. Methods Mol Biol 2022; 2522:287-300. [PMID: 36125757 DOI: 10.1007/978-1-0716-2445-6_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Despite the ecological, evolutionary and economical significance of archaea, key aspects of their cell biology, metabolic pathways, and adaptations to a wide spectrum of environmental conditions, remain to be elucidated. Proteomics allows for the system-wide analysis of proteins, their changes in abundance between different conditions, as well as their post-translational modifications, providing detailed insights into the function of proteins and archaeal cell biology. In this chapter, we describe a sample preparation and mass spectrometric analysis workflow that has been designed for Haloferax volcanii but can be applied to a broad range of archaeal species. Furthermore, proteomics experiments provide a wealth of data that is invaluable to various disciplines. Therefore, we previously initiated the Archaeal Proteome Project (ArcPP), a community project that combines the analysis of multiple datasets with expert knowledge in various fields of archaeal research. The corresponding bioinformatic analysis, allowing for the integration of new proteomics data into the ArcPP, as well as the interactive exploration of ArcPP results is also presented here. In combination, these protocols facilitate an optimized, detailed and collaborative approach to archaeal proteomics.
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Affiliation(s)
- Stefan Schulze
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
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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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8
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Makkay AM, Louyakis AS, Ram-Mohan N, Gophna U, Gogarten JP, Papke RT. Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model archaeon. Sci Rep 2020; 10:22297. [PMID: 33339886 PMCID: PMC7749143 DOI: 10.1038/s41598-020-79296-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/19/2020] [Indexed: 12/16/2022] Open
Abstract
Horizontal gene transfer is a means by which bacteria, archaea, and eukaryotes are able to trade DNA within and between species. While there are a variety of mechanisms through which this genetic exchange can take place, one means prevalent in the archaeon Haloferax volcanii involves the transient formation of cytoplasmic bridges between cells and is referred to as mating. This process can result in the exchange of very large fragments of DNA between the participating cells. Genes governing the process of mating, including triggers to initiate mating, mechanisms of cell fusion, and DNA exchange, have yet to be characterized. We used a transcriptomic approach to gain a more detailed knowledge of how mating might transpire. By examining the differential expression of genes expressed in cells harvested from mating conditions on a filter over time and comparing them to those expressed in a shaking culture, we were able to identify genes and pathways potentially associated with mating. These analyses provide new insights into both the mechanisms and barriers of mating in Hfx. volcanii.
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Affiliation(s)
- Andrea M Makkay
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Artemis S Louyakis
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Nikhil Ram-Mohan
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Uri Gophna
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, P.O. Box 39040, 6997801, Tel Aviv, Israel
| | - J Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
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9
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Charlesworth J, Kimyon O, Manefield M, Beloe CJ, Burns BP. Archaea join the conversation: detection of AHL-like activity across a range of archaeal isolates. FEMS Microbiol Lett 2020; 367:5874252. [PMID: 32691824 DOI: 10.1093/femsle/fnaa123] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/17/2020] [Indexed: 12/24/2022] Open
Abstract
Quorum sensing is a mechanism of genetic control allowing single cell organisms to coordinate phenotypic response(s) across a local population and is often critical for ecosystem function. Although quorum sensing has been extensively studied in bacteria comparatively less is known about this mechanism in Archaea. Given the growing significance of Archaea in both natural and anthropogenic settings, it is important to delineate how widespread this phenomenon of signaling is in this domain. Employing a plasmid-based AHL biosensor in conjunction with thin-layer chromatography (TLC), the present study screened a broad range of euryarchaeota isolates for potential signaling activity. Data indicated the presence of 11 new Archaeal isolates with AHL-like activity against the LuxR-based AHL biosensor, including for the first time putative AHL activity in a thermophile. The presence of multiple signals and distinct changes between growth phases were also shown via TLC. Multiple signal molecules were detected using TLC in Haloferax mucosum, Halorubrum kocurii, Natronococcus occultus and Halobacterium salinarium. The finding of multiple novel signal producers suggests the potential for quorum sensing to play an important role not only in the regulation of complex phenotypes within Archaea but the potential for cross-talk with bacterial systems.
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Affiliation(s)
- James Charlesworth
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia.,Australian Centre for Astrobiology, University of New South Wales Sydney, 2052, Australia
| | - Onder Kimyon
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia.,School of Civil and Environmental Engineering, The University of New South Wales, Sydney, 2052 Australia
| | - Michael Manefield
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia.,School of Civil and Environmental Engineering, The University of New South Wales, Sydney, 2052 Australia.,School of Chemical Engineering, The University of New South Wales, Sydney, 2052, Australia
| | - Charlotte J Beloe
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia.,Australian Centre for Astrobiology, University of New South Wales Sydney, 2052, Australia
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia.,Australian Centre for Astrobiology, University of New South Wales Sydney, 2052, Australia
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10
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The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics. Nat Commun 2020; 11:3145. [PMID: 32561711 PMCID: PMC7305310 DOI: 10.1038/s41467-020-16784-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 05/18/2020] [Indexed: 11/08/2022] Open
Abstract
While many aspects of archaeal cell biology remain relatively unexplored, systems biology approaches like mass spectrometry (MS) based proteomics offer an opportunity for rapid advances. Unfortunately, the enormous amount of MS data generated often remains incompletely analyzed due to a lack of sophisticated bioinformatic tools and field-specific biological expertise for data interpretation. Here we present the initiation of the Archaeal Proteome Project (ArcPP), a community-based effort to comprehensively analyze archaeal proteomes. Starting with the model archaeon Haloferax volcanii, we reanalyze MS datasets from various strains and culture conditions. Optimized peptide spectrum matching, with strict control of false discovery rates, facilitates identifying > 72% of the reference proteome, with a median protein sequence coverage of 51%. These analyses, together with expert knowledge in diverse aspects of cell biology, provide meaningful insights into processes such as N-terminal protein maturation, N-glycosylation, and metabolism. Altogether, ArcPP serves as an invaluable blueprint for comprehensive prokaryotic proteomics.
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Abstract
Biofilms are structured and organized communities of microorganisms that represent one of the most successful forms of life on Earth. Bacterial biofilms have been studied in great detail, and many molecular details are known about the processes that govern bacterial biofilm formation, however, archaea are ubiquitous in almost all habitats on Earth and can also form biofilms. In recent years, insights have been gained into the development of archaeal biofilms, how archaea communicate to form biofilms and how the switch from a free-living lifestyle to a sessile lifestyle is regulated. In this Review, we explore the different stages of archaeal biofilm development and highlight similarities and differences between archaea and bacteria on a molecular level. We also consider the role of archaeal biofilms in industry and their use in different industrial processes.
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Affiliation(s)
- Marleen van Wolferen
- Molecular Biology of Archaea, Institute of Biology II, Microbiology, University of Freiburg, Freiburg, Germany
| | - Alvaro Orell
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, Microbiology, University of Freiburg, Freiburg, Germany.
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12
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Booker AE, Hoyt DW, Meulia T, Eder E, Nicora CD, Purvine SO, Daly RA, Moore JD, Wunch K, Pfiffner SM, Lipton MS, Mouser PJ, Wrighton KC, Wilkins MJ. Deep-Subsurface Pressure Stimulates Metabolic Plasticity in Shale-Colonizing Halanaerobium spp. Appl Environ Microbiol 2019; 85:e00018-19. [PMID: 30979840 PMCID: PMC6544827 DOI: 10.1128/aem.00018-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/10/2019] [Indexed: 01/12/2023] Open
Abstract
Bacterial Halanaerobium strains become the dominant persisting microbial community member in produced fluids across geographically distinct hydraulically fractured shales. Halanaerobium is believed to be inadvertently introduced into this environment during the drilling and fracturing process and must therefore tolerate large changes in pressure, temperature, and salinity. Here, we used a Halanaerobium strain isolated from a natural gas well in the Utica Point Pleasant formation to investigate metabolic and physiological responses to growth under high-pressure subsurface conditions. Laboratory incubations confirmed the ability of Halanaerobium congolense strain WG8 to grow under pressures representative of deep shale formations (21 to 48 MPa). Under these conditions, broad metabolic and physiological shifts were identified, including higher abundances of proteins associated with the production of extracellular polymeric substances. Confocal laser scanning microscopy indicated that extracellular polymeric substance (EPS) production was associated with greater cell aggregation when biomass was cultured at high pressure. Changes in Halanaerobium central carbon metabolism under the same conditions were inferred from nuclear magnetic resonance (NMR) and gas chromatography measurements, revealing large per-cell increases in production of ethanol, acetate, and propanol and cessation of hydrogen production. These metabolic shifts were associated with carbon flux through 1,2-propanediol in response to slower fluxes of carbon through stage 3 of glycolysis. Together, these results reveal the potential for bioclogging and corrosion (via organic acid fermentation products) associated with persistent Halanaerobium growth in deep, hydraulically fractured shale ecosystems, and offer new insights into cellular mechanisms that enable these strains to dominate deep-shale microbiomes.IMPORTANCE The hydraulic fracturing of deep-shale formations for hydrocarbon recovery accounts for approximately 60% of U.S. natural gas production. Microbial activity associated with this process is generally considered deleterious due to issues associated with sulfide production, microbially induced corrosion, and bioclogging in the subsurface. Here we demonstrate that a representative Halanaerobium species, frequently the dominant microbial taxon in hydraulically fractured shales, responds to pressures characteristic of the deep subsurface by shifting its metabolism to generate more corrosive organic acids and produce more polymeric substances that cause "clumping" of biomass. While the potential for increased corrosion of steel infrastructure and clogging of pores and fractures in the subsurface may significantly impact hydrocarbon recovery, these data also offer new insights for microbial control in these ecosystems.
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Affiliation(s)
- Anne E Booker
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA
| | - David W Hoyt
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tea Meulia
- College of Food, Agricultural, and Environmental Sciences, Ohio State University, Columbus, Ohio, USA
| | - Elizabeth Eder
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Rebecca A Daly
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA
| | - Joseph D Moore
- DowDuPont Industrial Biosciences, Wilmington, Delaware, USA
| | - Kenneth Wunch
- DowDuPont Industrial Biosciences, Wilmington, Delaware, USA
| | - Susan M Pfiffner
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
| | - Mary S Lipton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Paula J Mouser
- Department of Civil and Environmental Engineering, University of New Hampshire, Durham, New Hampshire, USA
| | - Kelly C Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
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13
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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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14
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Kan G, Wang X, Jiang J, Zhang C, Chi M, Ju Y, Shi C. Copper stress response in yeast Rhodotorula mucilaginosa AN5 isolated from sea ice, Antarctic. Microbiologyopen 2019; 8:e00657. [PMID: 29926536 PMCID: PMC6436437 DOI: 10.1002/mbo3.657] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 03/24/2018] [Accepted: 04/26/2018] [Indexed: 12/26/2022] Open
Abstract
Heavy metal pollution in Antarctic is serious by anthropogenic emissions and atmospheric transport. To dissect the heavy metal adaptation mechanisms of sea-ice organisms, a basidiomycetous yeast strain AN5 was isolated and its cellular changes were analyzed. Morphological, physiological, and biochemical characterization indicated that this yeast strain belonged to Rhodotorula mucilaginosa AN5. Heavy metal resistance pattern of Cd > Pb = Mn > Cu > Cr > Hg was observed. Scanning electron microscopic (SEM) results exhibited altered cell surface morphology under the influence of copper metal compared to that with control. The determination of physiological and biochemical changes manifested that progressive copper treatment significantly increased antioxidative reagents content and enzymes activity in the red yeast, which quench the active oxygen species to maintain the intercellular balance of redox state and ensure the cellular fission and growth. Comparative proteomic analysis revealed that, under 2 mM copper stress, 95 protein spots were tested reproducible changes of at least 10-fold in cells. Among 95 protein spots, 43 were elevated and 52 were decreased synthesis. After MALDI TOF MS/MS analysis, 51 differentially expressed proteins were identified successfully and classified into six functional groups, including carbohydrate and energy metabolism, nucleotide and protein metabolism, protein folding, antioxidant system, signaling, and unknown function proteins. Function analysis indicated that carbohydrate and energy metabolism-, nucleotide and protein metabolism-, and protein folding-related proteins played central role to the heavy metal resistance of Antarctic yeast. Generally, the results revealed that the yeast has a great capability to cope with heavy metal stress and activate the physiological and protein mechanisms, which allow more efficient recovery after copper stress. Our studies increase understanding of the molecular resistance mechanism of polar yeast to heavy metal, which will be benefitted for the sea-ice isolates to be a potential candidate for bioremediation of metal-contaminated environments.
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Affiliation(s)
- Guangfeng Kan
- School of Marine Science and TechnologyHarbin Institute of Technology at WeihaiWeihaiChina
| | - Xiaofei Wang
- School of Marine Science and TechnologyHarbin Institute of Technology at WeihaiWeihaiChina
| | - Jie Jiang
- School of Marine Science and TechnologyHarbin Institute of Technology at WeihaiWeihaiChina
| | - Chengsheng Zhang
- Tobacco Integrated Pest Management of China TobaccoTobacco Research Institute of Chinese Academy of Agricultural ScienceQingdaoChina
| | - Minglei Chi
- School of Marine Science and TechnologyHarbin Institute of Technology at WeihaiWeihaiChina
| | - Yun Ju
- School of Marine Science and TechnologyHarbin Institute of Technology at WeihaiWeihaiChina
| | - Cuijuan Shi
- School of Marine Science and TechnologyHarbin Institute of Technology at WeihaiWeihaiChina
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15
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Blanco Y, Rivas LA, González-Toril E, Ruiz-Bermejo M, Moreno-Paz M, Parro V, Palacín A, Aguilera Á, Puente-Sánchez F. Environmental parameters, and not phylogeny, determine the composition of extracellular polymeric substances in microbial mats from extreme environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 650:384-393. [PMID: 30199683 DOI: 10.1016/j.scitotenv.2018.08.440] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/30/2018] [Accepted: 08/31/2018] [Indexed: 06/08/2023]
Abstract
The ability to establish biofilms is a key trait for microorganisms growing in extreme environments. The extracellular polymeric substances (EPS) present in biofilms provide not only surface attachment, but also protection against all kinds of environmental stressors, including desiccation, salinity, temperature or heavy metal pollution. The acquisition of suitable biofilm characteristics might thus be an important process mediating the adaptation of microorganisms to novel environmental conditions. In this work we have characterized the EPS of 20 phylogenetically diverse biofilms collected in situ from five contrasting extreme environments, including two geothermal areas (Copahue, Argentina; Seltun, Iceland), two cold areas (Pastoruri glacier, Peru; Byers Peninsula, Antarctica) and one extremely acidic river (Río Tinto, Spain). Biofilms were subjected to biochemical characterization, glycan profiling and immunoprofiling with an antibody microarray. Our results showed that environmental conditions strongly influence biofilm characteristics, with microorganisms from the same environment achieving similar EPS compositions regardless of the phylogeny of their main species. The concentration of some monosaccharides in the EPS could be related to environmental conditions such as temperature or heavy metal toxicity, suggesting that in some cases stress resistance can be mediated by specific sugars. Overall, our results highlight the existence of conserved EPS compositional patterns for each extreme environment, which could in turn be exploited to engineer ecological adaptations in genetically modified microorganisms.
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Affiliation(s)
- Yolanda Blanco
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Luis Alfonso Rivas
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Elena González-Toril
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Marta Ruiz-Bermejo
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Mercedes Moreno-Paz
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Víctor Parro
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Arantxa Palacín
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Ángeles Aguilera
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Fernando Puente-Sánchez
- Systems Biology Program, Centro Nacional de Biotecnología, C/Darwin n° 3, Campus de Cantoblanco, 28049 Madrid, Spain.
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16
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Environmental conditions shape the biofilm of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125. Microbiol Res 2018; 218:66-75. [PMID: 30454660 DOI: 10.1016/j.micres.2018.09.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/24/2018] [Accepted: 09/28/2018] [Indexed: 11/21/2022]
Abstract
Biofilms are the most widely distributed and successful microbial modes of life. The capacity of bacteria to colonize surfaces provides stability in the growth environment, allows the capturing of nutrients and affords protection from a range of environmental challenges and stress. Bacteria living in cold environments, like Antarctica, can be found as biofilms, even though the mechanisms of how this lifestyle is related to their environmental adaptation have been poorly investigated. In this paper, the biofilm of Pseudoalteromonas haloplanktis TAC125, one of the model organisms of cold-adapted bacteria, has been characterized in terms of biofilm typology and matrix composition. The characterization was performed on biofilms produced by the bacterium in response to different nutrient abundance and temperatures; in particular, this is the first report describing the structure of a biofilm formed at 0 °C. The results reported demonstrate that PhTAC125 produces biofilms in different amount and endowed with different physico-chemical properties, like hydrophobicity and roughness, by modulating the relative amount of the different macromolecules present in the biofilm matrix. The capability of PhTAC125 to adopt different biofilm structures in response to environment changes appears to be an interesting adaptation strategy and gives the first hints about the biofilm formation in cold environments.
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17
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Moissl-Eichinger C, Pausan M, Taffner J, Berg G, Bang C, Schmitz RA. Archaea Are Interactive Components of Complex Microbiomes. Trends Microbiol 2017; 26:70-85. [PMID: 28826642 DOI: 10.1016/j.tim.2017.07.004] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 07/06/2017] [Accepted: 07/21/2017] [Indexed: 02/06/2023]
Abstract
Recent findings have shaken our picture of the biology of the archaea and revealed novel traits beyond archaeal extremophily and supposed 'primitiveness'. The archaea constitute a considerable fraction of the Earth's ecosystems, and their potential to shape their surroundings by a profound interaction with their biotic and abiotic environment has been recognized. Moreover, archaea have been identified as a substantial component, or even as keystone species, in complex microbiomes - in the environment or accompanying a holobiont. Species of the Euryarchaeota (methanogens, halophiles) and Thaumarchaeota, in particular, have the capacity to coexist in plant, animal, and human microbiomes, where syntrophy allows them to thrive under energy-deficiency stress. Due to methodological limitations, the archaeome remains mysterious, and many questions with respect to potential pathogenicity, function, and structural interactions with their host and other microorganisms remain.
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Affiliation(s)
| | - Manuela Pausan
- Medical University Graz, Internal Medicine, Graz, Austria
| | | | | | - Corinna Bang
- Christian-Albrechts-University Kiel, Kiel, Germany
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18
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An Acidic Exopolysaccharide from Haloarcula hispanica ATCC33960 and Two Genes Responsible for Its Synthesis. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2017. [PMID: 28634434 PMCID: PMC5467301 DOI: 10.1155/2017/5842958] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A 1.1 × 106 Da acidic exopolysaccharide (EPS) was purified from an extremely halophilic archaeon Haloarcula hispanica ATCC33960 with a production of 30 mg L-1 when grown in AS-168 medium, which mainly composed of mannose and galactose with a small amount of glucose in a molar ratio of 55.9 : 43.2 : 0.9. Two glycosyltransferase genes (HAH_1662 and HAH_1667) were identified to be responsible for synthesis of the acidic EPS. Deletion of either HAH_1662 or HAH_1667 led to loss of the acidic EPS. The mutants displayed a different cell surface morphology, retarded growth in low salty environment, an increased adhesion, and swimming ability. Our results suggest that biosynthesis of the acidic EPS might act as an adaptable mechanism to protect the cells against harsh environments.
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19
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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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