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Cisneros-Martínez AM, Rodriguez-Cruz UE, Alcaraz LD, Becerra A, Eguiarte LE, Souza V. Comparative evaluation of bioinformatic tools for virus-host prediction and their application to a highly diverse community in the Cuatro Ciénegas Basin, Mexico. PLoS One 2024; 19:e0291402. [PMID: 38300968 PMCID: PMC10833507 DOI: 10.1371/journal.pone.0291402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
Due to the enormous diversity of non-culturable viruses, new viruses must be characterized using culture-independent techniques. The associated host is an important phenotypic feature that can be inferred from metagenomic viral contigs thanks to the development of several bioinformatic tools. Here, we compare the performance of recently developed virus-host prediction tools on a dataset of 1,046 virus-host pairs and then apply the best-performing tools to a metagenomic dataset derived from a highly diverse transiently hypersaline site known as the Archaean Domes (AD) within the Cuatro Ciénegas Basin, Coahuila, Mexico. Among host-dependent methods, alignment-based approaches had a precision of 66.07% and a sensitivity of 24.76%, while alignment-free methods had an average precision of 75.7% and a sensitivity of 57.5%. RaFAH, a virus-dependent alignment-based tool, had the best overall performance (F1_score = 95.7%). However, when predicting the host of AD viruses, methods based on public reference databases (such as RaFAH) showed lower inter-method agreement than host-dependent methods run against custom databases constructed from prokaryotes inhabiting AD. Methods based on custom databases also showed the greatest agreement between the source environment and the predicted host taxonomy, habitat, lifestyle, or metabolism. This highlights the value of including custom data when predicting hosts on a highly diverse metagenomic dataset, and suggests that using a combination of methods and qualitative validations related to the source environment and predicted host biology can increase the number of correct predictions. Finally, these predictions suggest that AD viruses infect halophilic archaea as well as a variety of bacteria that may be halophilic, halotolerant, alkaliphilic, thermophilic, oligotrophic, sulfate-reducing, or marine, which is consistent with the specific environment and the known geological and biological evolution of the Cuatro Ciénegas Basin and its microorganisms.
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Affiliation(s)
- Alejandro Miguel Cisneros-Martínez
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Ulises E. Rodriguez-Cruz
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Luis D. Alcaraz
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Arturo Becerra
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Centro de Estudios del Cuaternario de Fuego-Patagonia y Antártica (CEQUA), Punta Arenas, Chile
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2
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Salwan R, Sharma V. Genomics of Prokaryotic Extremophiles to Unfold the Mystery of Survival in Extreme Environments. Microbiol Res 2022; 264:127156. [DOI: 10.1016/j.micres.2022.127156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 07/30/2022] [Accepted: 07/31/2022] [Indexed: 11/26/2022]
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3
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Kuznetsov S, Milenkin A, Antonov I. Translational Frameshifting in the chlD Gene Gives a Clue to the Coevolution of the Chlorophyll and Cobalamin Biosyntheses. Microorganisms 2022; 10:microorganisms10061200. [PMID: 35744718 PMCID: PMC9227772 DOI: 10.3390/microorganisms10061200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/25/2022] [Accepted: 06/02/2022] [Indexed: 12/10/2022] Open
Abstract
Today, hundreds of prokaryotic species are able to synthesize chlorophyll and cobalamin (vitamin B12). An important step in the biosynthesis of these coenzymes is the insertion of a metal ion into a porphyrin ring. Namely, Mg-chelatase ChlIDH and aerobic Co-chelatase CobNST are utilized in the chlorophyll and vitamin B12 pathways, respectively. The corresponding subunits of these enzymes have common evolutionary origin. Recently, we have identified a highly conserved frameshifting signal in the chlD gene. This unusual regulatory mechanism allowed production of both the small and the medium chelatase subunits from the same gene. Moreover, the chlD gene appeared early in the evolution and could be at the starting point in the development of the chlorophyll and B12 pathways. Here, we studied the possible coevolution of these two pathways through the analysis of the chelatase genes. To do that, we developed a specialized Web database with comprehensive information about more than 1200 prokaryotic genomes. Further analysis allowed us to split the coevolution of the chlorophyll and B12 pathway into eight distinct stages.
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Affiliation(s)
- Stepan Kuznetsov
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (S.K.); (A.M.)
| | - Alexander Milenkin
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (S.K.); (A.M.)
| | - Ivan Antonov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Science, 117312 Moscow, Russia
- Laboratory of Bioinformatics, Faculty of Computer Science, National Research University Higher School of Economics, 101000 Moscow, Russia
- Correspondence:
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Hobmeier K, Cantone M, Nguyen QA, Pflüger-Grau K, Kremling A, Kunte HJ, Pfeiffer F, Marin-Sanguino A. Adaptation to Varying Salinity in Halomonas elongata: Much More Than Ectoine Accumulation. Front Microbiol 2022; 13:846677. [PMID: 35432243 PMCID: PMC9006882 DOI: 10.3389/fmicb.2022.846677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
The halophilic γ-proteobacterium Halomonas elongata DSM 2581 T thrives at salt concentrations well above 10 % NaCl (1.7 M NaCl). A well-known osmoregulatory mechanism is the accumulation of the compatible solute ectoine within the cell in response to osmotic stress. While ectoine accumulation is central to osmoregulation and promotes resistance to high salinity in halophilic bacteria, ectoine has this effect only to a much lesser extent in non-halophiles. We carried out transcriptome analysis of H. elongata grown on two different carbon sources (acetate or glucose), and low (0.17 M NaCl), medium (1 M), and high salinity (2 M) to identify additional mechanisms for adaptation to high saline environments. To avoid a methodological bias, the transcripts were evaluated by applying two methods, DESeq2 and Transcripts Per Million (TPM). The differentially transcribed genes in response to the available carbon sources and salt stress were then compared to the transcriptome profile of Chromohalobacter salexigens, a closely related moderate halophilic bacterium. Transcriptome profiling supports the notion that glucose is degraded via the cytoplasmic Entner-Doudoroff pathway, whereas the Embden-Meyerhoff-Parnas pathway is employed for gluconeogenesis. The machinery of oxidative phosphorylation in H. elongata and C. salexigens differs greatly from that of non-halophilic organisms, and electron flow can occur from quinone to oxygen along four alternative routes. Two of these pathways via cytochrome bo' and cytochrome bd quinol oxidases seem to be upregulated in salt stressed cells. Among the most highly regulated genes in H. elongata and C. salexigens are those encoding chemotaxis and motility proteins, with genes for chemotaxis and flagellar assembly severely downregulated at low salt concentrations. We also compared transcripts at low and high-salt stress (low growth rate) with transcripts at optimal salt concentration and found that the majority of regulated genes were down-regulated in stressed cells, including many genes involved in carbohydrate metabolism, while ribosome synthesis was up-regulated, which is in contrast to what is known from non-halophiles at slow growth. Finally, comparing the acidity of the cytoplasmic proteomes of non-halophiles, extreme halophiles and moderate halophiles suggests adaptation to an increased cytoplasmic ion concentration of H. elongata. Taken together, these results lead us to propose a model for salt tolerance in H. elongata where ion accumulation plays a greater role in salt tolerance than previously assumed.
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Affiliation(s)
- Karina Hobmeier
- Systems Biotechnology, Technical University of Munich, Garching, Germany
| | - Martina Cantone
- Systems Biotechnology, Technical University of Munich, Garching, Germany
| | - Quynh Anh Nguyen
- Systems Biotechnology, Technical University of Munich, Garching, Germany
| | | | - Andreas Kremling
- Systems Biotechnology, Technical University of Munich, Garching, Germany
| | - Hans Jörg Kunte
- Division Biodeterioration and Reference Organisms, Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
| | - Friedhelm Pfeiffer
- Computational Biology Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Alberto Marin-Sanguino
- Systems Biotechnology, Technical University of Munich, Garching, Germany.,Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
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Imhoff JF, Kyndt JA, Meyer TE. Genomic Comparison, Phylogeny and Taxonomic Reevaluation of the Ectothiorhodospiraceae and Description of Halorhodospiraceae fam. nov. and Halochlorospira gen. nov. Microorganisms 2022; 10:microorganisms10020295. [PMID: 35208750 PMCID: PMC8877833 DOI: 10.3390/microorganisms10020295] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/12/2022] [Accepted: 01/23/2022] [Indexed: 12/29/2022] Open
Abstract
The Ectothiorhodospiraceae family represents purple sulfur bacteria of the Gammaproteobacteria found primarily in alkaline soda lakes of moderate to extremely high salinity. The main microscopically visible characteristic separating them from the Chromatiaceae is the excretion of the intermediate elemental sulfur formed during oxidation of sulfide prior to complete oxidation to sulfate rather than storing it in the periplasm. We present a comparative study of 38 genomes of all species of phototrophic Ectothiorhodospiraceae. We also include a comparison with those chemotrophic bacteria that have been assigned to the family previously and critically reevaluate this assignment. The data demonstrate the separation of Halorhodospira species in a major phylogenetic branch distant from other Ectothiorhodospiraceae and support their separation into a new family, for which the name Halorhodospiraceae fam. nov. is proposed. In addition, the green-colored, bacteriochlorophyll-containing species Halorhodospira halochloris and Halorhodospira abdelmalekii were transferred to the new genus Halochlorospira gen. nov. of this family. The data also enable classification of several so far unclassified isolates and support the separation of Ectothiorhodospira shaposhnikovii and Ect. vacuolata as well as Ect. mobilis and Ect. marismortui as distinct species.
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Affiliation(s)
- Johannes F. Imhoff
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
- Correspondence:
| | - John A. Kyndt
- College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA;
| | - Terrance E. Meyer
- Department of Biochemistry, University of Arizona, Tucson, AZ 85721, USA;
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6
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Tirumalai MR, Anane-Bediakoh D, Rajesh S, Fox GE. Net Charges of the Ribosomal Proteins of the S10 and spc Clusters of Halophiles Are Inversely Related to the Degree of Halotolerance. Microbiol Spectr 2021; 9:e0178221. [PMID: 34908470 PMCID: PMC8672879 DOI: 10.1128/spectrum.01782-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/24/2021] [Indexed: 11/20/2022] Open
Abstract
Net positive charge(s) on ribosomal proteins (r-proteins) have been reported to influence the assembly and folding of ribosomes. A high percentage of r-proteins from extremely halophilic archaea are known to be acidic or even negatively charged. Those proteins that remain positively charged are typically far less positively charged. Here, the analysis is extended to non-archaeal halophilic bacteria, eukaryotes, and halotolerant archaea. The net charges (pH 7.4) of the r-proteins that comprise the S10-spc operon/cluster from individual microbial and eukaryotic genomes were estimated and intercompared. It was observed that, as a general rule, the net charges of individual proteins remained mostly basic as the salt tolerance of the bacterial strains increased from 5 to 15%. The most striking exceptions were the extremely halophilic bacterial strains, Salinibacter ruber SD01, Acetohalobium arabaticum DSM 5501 and Selenihalanaerobacter shriftii ATCC BAA-73, which are reported to require a minimum of 18% to 21% salt for their growth. All three strains have higher numbers of acidic S10-spc cluster r-proteins than what is seen in the moderate halophiles or the halotolerant strains. Of the individual proteins, only uL2 never became acidic. uS14 and uL16 also seldom became acidic. The net negative charges on several of the S10-spc cluster r-proteins are a feature generally shared by all extremely halophilic archaea and bacteria. The S10-spc cluster r-proteins of halophilic fungi and algae (eukaryotes) were exceptions: these were positively charged despite the halophilicity of the organisms. IMPORTANCE The net charges (at pH 7.4) of the ribosomal proteins (r-proteins) that comprise the S10-spc cluster show an inverse relationship with the halophilicity/halotolerance levels in both bacteria and archaea. In non-halophilic bacteria, the S10-spc cluster r-proteins are generally basic (positively charged), while the rest of the proteomes in these strains are generally acidic. On the other hand, the whole proteomes of the extremely halophilic strains are overall negatively charged, including the S10-spc cluster r-proteins. Given that the distribution of charged residues in the ribosome exit tunnel influences cotranslational folding, the contrasting charges observed in the S10-spc cluster r-proteins have potential implications for the rate of passage of these proteins through the ribosomal exit tunnel. Furthermore, the universal protein uL2, which lies in the oldest part of the ribosome, is always positively charged irrespective of the strain/organism it belongs to. This has implications for its role in the prebiotic context.
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Affiliation(s)
- Madhan R. Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | | | - Sidharth Rajesh
- Clements High School (Class of 2023), Fort Bend Independent School District, Sugar Land, Texas, USA
| | - George E. Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
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7
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Yakimov MM, Merkel AY, Gaisin VA, Pilhofer M, Messina E, Hallsworth JE, Klyukina AA, Tikhonova EN, Gorlenko VM. Cultivation of a vampire: 'Candidatus Absconditicoccus praedator'. Environ Microbiol 2021; 24:30-49. [PMID: 34750952 DOI: 10.1111/1462-2920.15823] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 12/12/2022]
Abstract
Halorhodospira halophila, one of the most-xerophilic halophiles, inhabits biophysically stressful and energetically expensive, salt-saturated alkaline brines. Here, we report an additional stress factor that is biotic: a diminutive Candidate-Phyla-Radiation bacterium, that we named 'Ca. Absconditicoccus praedator' M39-6, which predates H. halophila M39-5, an obligately photosynthetic, anaerobic purple-sulfur bacterium. We cultivated this association (isolated from the hypersaline alkaline Lake Hotontyn Nur, Mongolia) and characterized their biology. 'Ca. Absconditicoccus praedator' is the first stably cultivated species from the candidate class-level lineage Gracilibacteria (order-level lineage Absconditabacterales). Its closed-and-curated genome lacks genes for the glycolytic, pentose phosphate- and Entner-Doudoroff pathways which would generate energy/reducing equivalents and produce central carbon currencies. Therefore, 'Ca. Absconditicoccus praedator' is dependent on host-derived building blocks for nucleic acid-, protein-, and peptidoglycan synthesis. It shares traits with (the uncultured) 'Ca. Vampirococcus lugosii', which is also of the Gracilibacteria lineage. These are obligate parasitic lifestyle, feeding on photosynthetic anoxygenic Gammaproteobacteria, and absorption of host cytoplasm. Commonalities in their genomic composition and structure suggest that the entire Absconditabacterales lineage consists of predatory species which act to cull the populations of their respective host bacteria. Cultivation of vampire : host associations can shed light on unresolved aspects of their metabolism and ecosystem dynamics at life-limiting extremes.
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Affiliation(s)
| | - Alexander Y Merkel
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Vasil A Gaisin
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Martin Pilhofer
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Enzo Messina
- Institute for Marine Biological Resources and Biotechnology, IRBIM-CNR, Messina, Italy
| | - John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Alexandra A Klyukina
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina N Tikhonova
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir M Gorlenko
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
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8
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A potassium chloride to glycine betaine osmoprotectant switch in the extreme halophile Halorhodospira halophila. Sci Rep 2020; 10:3383. [PMID: 32098991 PMCID: PMC7042295 DOI: 10.1038/s41598-020-59231-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 12/10/2019] [Indexed: 11/08/2022] Open
Abstract
Halophiles utilize two distinct osmoprotection strategies. The accumulation of organic compatible solutes such as glycine betaine does not perturb the functioning of cytoplasmic components, but represents a large investment of energy and carbon. KCl is an energetically attractive alternative osmoprotectant, but requires genome-wide modifications to establish a highly acidic proteome. Most extreme halophiles are optimized for the use of one of these two strategies. Here we examine the extremely halophilic Proteobacterium Halorhodospira halophila and report that medium K+ concentration dramatically alters its osmoprotectant use. When grown in hypersaline media containing substantial K+ concentrations, H. halophila accumulates molar concentrations of KCl. However, at limiting K+ concentrations the organism switches to glycine betaine as its major osmoprotectant. In contrast, the closely related organism Halorhodospira halochloris is limited to using compatible solutes. H. halophila performs both de novo synthesis and uptake of glycine betaine, matching the biosynthesis and transport systems encoded in its genome. The medium K+ concentration (~10 mM) at which the KCl to glycine betaine osmoprotectant switch in H. halophila occurs is near the K+ content of the lake from which it was isolated, supporting an ecological relevance of this osmoprotectant strategy.
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9
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Nash MV, Anesio AM, Barker G, Tranter M, Varliero G, Eloe-Fadrosh EA, Nielsen T, Turpin-Jelfs T, Benning LG, Sánchez-Baracaldo P. Metagenomic insights into diazotrophic communities across Arctic glacier forefields. FEMS Microbiol Ecol 2019; 94:5036517. [PMID: 29901729 PMCID: PMC6054269 DOI: 10.1093/femsec/fiy114] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 06/11/2018] [Indexed: 11/30/2022] Open
Abstract
Microbial nitrogen fixation is crucial for building labile nitrogen stocks and facilitating higher plant colonisation in oligotrophic glacier forefield soils. Here, the diazotrophic bacterial community structure across four Arctic glacier forefields was investigated using metagenomic analysis. In total, 70 soil metagenomes were used for taxonomic interpretation based on 185 nitrogenase (nif) sequences, extracted from assembled contigs. The low number of recovered genes highlights the need for deeper sequencing in some diverse samples, to uncover the complete microbial populations. A key group of forefield diazotrophs, found throughout the forefields, was identified using a nifH phylogeny, associated with nifH Cluster I and III. Sequences related most closely to groups including Alphaproteobacteria, Betaproteobacteria, Cyanobacteria and Firmicutes. Using multiple nif genes in a Last Common Ancestor analysis revealed a diverse range of diazotrophs across the forefields. Key organisms identified across the forefields included Nostoc, Geobacter, Polaromonas and Frankia. Nitrogen fixers that are symbiotic with plants were also identified, through the presence of root associated diazotrophs, which fix nitrogen in return for reduced carbon. Additional nitrogen fixers identified in forefield soils were metabolically diverse, including fermentative and sulphur cycling bacteria, halophiles and anaerobes.
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Affiliation(s)
- Maisie V Nash
- School of Geographical Sciences, University of Bristol, UK
| | | | - Gary Barker
- School of Life Sciences, University of Bristol, UK
| | - Martyn Tranter
- School of Geographical Sciences, University of Bristol, UK
| | | | | | - Torben Nielsen
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, US
| | | | - Liane G Benning
- GFZ German Research Centre for Geosciences, Telegrafenenberg, 14473 Potsdam, Germany.,School of Earth and Environment, University of Leeds, LS2 9JT, Leeds, UK.,Department of Earth Sciences, Free University of Berlin, Malteserstr, 74-100, Building A, 12249, Berlin, Germany
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10
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Ospino MC, Kojima H, Fukui M. Arsenite Oxidation by a Newly Isolated Betaproteobacterium Possessing arx Genes and Diversity of the arx Gene Cluster in Bacterial Genomes. Front Microbiol 2019; 10:1210. [PMID: 31191509 PMCID: PMC6549141 DOI: 10.3389/fmicb.2019.01210] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/13/2019] [Indexed: 12/21/2022] Open
Abstract
Microbes play essential roles in arsenic transformation in the environment. Microbial arsenite oxidation is catalyzed by either of two distantly related arsenite oxidases, referred to as AIO and ARX. The arx genes encoding ARX and its regulatory proteins were originally defined in the genomes of gammaproteobacteria isolated from an alkaline soda lake. The arx gene cluster has been identified in a limited number of bacteria, predominantly in gammaproteobacteria isolated from lakes characterized by high pH and high salinity. In the present study, a novel arsenite-oxidizing betaproteobacterium, strain M52, was isolated from a hot spring microbial mat. The strain oxidized arsenite under both microaerophilic and nitrate-reducing conditions at nearly neutral pH. Genome analysis revealed that the strain possesses the arx gene cluster in its genome and lacks genes encoding AIO. Inspection of the bacterial genomes available in the GenBank database revealed that the presence of this gene cluster is restricted to genomes of Proteobacteria, mainly in the classes Gammaproteobacteria and Betaproteobacteria. In these genomes, the structure of the gene cluster was generally well-conserved, but genes for regulatory proteins were lacking in genomes of strains belonging to a specific lineage. Phylogenetic analysis suggested that ARX encoded in the genomes can be divided into three groups, and strain M52 belongs to a group specific for organisms living in low-salt environments. The ArxA protein encoded in the genome of strain M52 was characterized by the presence of a long insertion, which was specifically observed in the same group of ARX. In clone library analyses with a newly designed primer pair, a diverse ArxA sequence with a long insertion was detected in samples of lake water and hot spring microbial mat, characterized by low salinity and a nearly neutral pH. Among the isolated bacterial strains whose arsenite oxidation has been demonstrated, strain M52 is the first betaproteobacterium that possesses the arx genes, the first strain encoding ARX of the group specific for low-salt environments, and the first organism possessing the gene encoding ArxA with a long insertion.
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Affiliation(s)
| | - Hisaya Kojima
- The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Manabu Fukui
- The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
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11
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Shrestha N, Chilkoor G, Vemuri B, Rathinam N, Sani RK, Gadhamshetty V. Extremophiles for microbial-electrochemistry applications: A critical review. BIORESOURCE TECHNOLOGY 2018; 255:318-330. [PMID: 29433771 DOI: 10.1016/j.biortech.2018.01.151] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/30/2018] [Accepted: 01/31/2018] [Indexed: 06/08/2023]
Abstract
Extremophiles, notably archaea and bacteria, offer a good platform for treating industrial waste streams that were previously perceived as hostile to the model organisms in microbial electrochemical systems (MESs). Here we present a critical overview of the fundamental and applied biology aspects of halophiles and thermophiles in MESs. The current study suggests that extremophiles enable the MES operations under a seemingly harsh conditions imposed by the physical (pressure, radiation, and temperature) and geochemical extremes (oxygen levels, pH, and salinity). We highlight a need to identify the underpinning mechanisms that define the exceptional electrocatalytic performance of extremophiles in MESs.
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Affiliation(s)
- Namita Shrestha
- Civil and Environmental Engineering, South Dakota School of Mines and Technology, 501 E Saint Joseph Blvd, Rapid City, SD 57701, United States
| | - Govinda Chilkoor
- Civil and Environmental Engineering, South Dakota School of Mines and Technology, 501 E Saint Joseph Blvd, Rapid City, SD 57701, United States
| | - Bhuvan Vemuri
- Civil and Environmental Engineering, South Dakota School of Mines and Technology, 501 E Saint Joseph Blvd, Rapid City, SD 57701, United States
| | - Navanietha Rathinam
- Chemical and Biological Engineering, South Dakota School of Mines and Technology, 501 E Saint Joseph Blvd, Rapid City, SD 57701, United States
| | - Rajesh K Sani
- Chemical and Biological Engineering, South Dakota School of Mines and Technology, 501 E Saint Joseph Blvd, Rapid City, SD 57701, United States
| | - Venkataramana Gadhamshetty
- Civil and Environmental Engineering, South Dakota School of Mines and Technology, 501 E Saint Joseph Blvd, Rapid City, SD 57701, United States; Surface Engineering Research Center, South Dakota School of Mines and Technology, 501 E Saint Joseph Blvd, Rapid City, SD 57701, United States.
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12
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Wu G, Huang L, Jiang H, Peng Y, Guo W, Chen Z, She W, Guo Q, Dong H. Thioarsenate Formation Coupled with Anaerobic Arsenite Oxidation by a Sulfate-Reducing Bacterium Isolated from a Hot Spring. Front Microbiol 2017; 8:1336. [PMID: 28769902 PMCID: PMC5509915 DOI: 10.3389/fmicb.2017.01336] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 06/30/2017] [Indexed: 11/18/2022] Open
Abstract
Thioarsenates are common arsenic species in sulfidic geothermal waters, yet little is known about their biogeochemical traits. In the present study, a novel sulfate-reducing bacterial strain Desulfotomaculum TC-1 was isolated from a sulfidic hot spring in Tengchong geothermal area, Yunnan Province, China. The arxA gene, encoding anaerobic arsenite oxidase, was successfully amplified from the genome of strain TC-1, indicating it has a potential ability to oxidize arsenite under anaerobic condition. In anaerobic arsenite oxidation experiments inoculated with strain TC-1, a small amount of arsenate was detected in the beginning but became undetectable over longer time. Thioarsenates (AsO4-xSx2- with x = 1-4) formed with mono-, di- and tri-thioarsenates being dominant forms. Tetrathioarsenate was only detectable at the end of the experiment. These results suggest that thermophilic microbes might be involved in the formation of thioarsenates and provide a possible explanation for the widespread distribution of thioarsenates in terrestrial geothermal environments.
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Affiliation(s)
- Geng Wu
- State Key Laboratory of Biogeology and Environmental Geology, China University of GeosciencesWuhan, China
| | - Liuqin Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of GeosciencesWuhan, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of GeosciencesWuhan, China
| | - Yue’e Peng
- State Key Laboratory of Biogeology and Environmental Geology, China University of GeosciencesWuhan, China
| | - Wei Guo
- State Key Laboratory of Biogeology and Environmental Geology, China University of GeosciencesWuhan, China
| | - Ziyu Chen
- State Key Laboratory of Biogeology and Environmental Geology, China University of GeosciencesWuhan, China
| | - Weiyu She
- State Key Laboratory of Biogeology and Environmental Geology, China University of GeosciencesWuhan, China
| | - Qinghai Guo
- State Key Laboratory of Biogeology and Environmental Geology, China University of GeosciencesWuhan, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of GeosciencesBeijing, China
- Department of Geology and Environmental Earth Science, Miami University, OxfordOH, United States
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13
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part V. {[Fe4S4](SCysγ)4} proteins. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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14
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Insights from the metagenome of an acid salt lake: the role of biology in an extreme depositional environment. PLoS One 2015; 10:e0122869. [PMID: 25923206 PMCID: PMC4414474 DOI: 10.1371/journal.pone.0122869] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 02/24/2015] [Indexed: 12/31/2022] Open
Abstract
The extremely acidic brine lakes of the Yilgarn Craton of Western Australia are home to some of the most biologically challenging waters on Earth. In this study, we employed metagenomic shotgun sequencing to generate a microbial profile of the depositional environment associated with the sulfur-rich sediments of one such lake. Of the 1.5 M high-quality reads generated, 0.25 M were mapped to protein features, which in turn provide new insights into the metabolic function of this community. In particular, 45 diverse genes associated with sulfur metabolism were identified, the majority of which were linked to either the conversion of sulfate to adenylylsulfate and the subsequent production of sulfide from sulfite or the oxidation of sulfide, elemental sulfur, and thiosulfate via the sulfur oxidation (Sox) system. This is the first metagenomic study of an acidic, hypersaline depositional environment, and we present evidence for a surprisingly high level of microbial diversity. Our findings also illuminate the possibility that we may be meaningfully underestimating the effects of biology on the chemistry of these sulfur-rich sediments, thereby influencing our understanding of past geobiological conditions that may have been present on Earth as well as early Mars.
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15
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Batista-García RA, Balcázar-López E, Miranda-Miranda E, Sánchez-Reyes A, Cuervo-Soto L, Aceves-Zamudio D, Atriztán-Hernández K, Morales-Herrera C, Rodríguez-Hernández R, Folch-Mallol J. Characterization of lignocellulolytic activities from a moderate halophile strain of Aspergillus caesiellus isolated from a sugarcane bagasse fermentation. PLoS One 2014; 9:e105893. [PMID: 25162614 PMCID: PMC4146556 DOI: 10.1371/journal.pone.0105893] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 07/25/2014] [Indexed: 01/31/2023] Open
Abstract
A moderate halophile and thermotolerant fungal strain was isolated from a sugarcane bagasse fermentation in the presence of 2 M NaCl that was set in the laboratory. This strain was identified by polyphasic criteria as Aspergillus caesiellus. The fungus showed an optimal growth rate in media containing 1 M NaCl at 28°C and could grow in media added with up to 2 M NaCl. This strain was able to grow at 37 and 42°C, with or without NaCl. A. caesiellus H1 produced cellulases, xylanases, manganese peroxidase (MnP) and esterases. No laccase activity was detected in the conditions we tested. The cellulase activity was thermostable, halostable, and no differential expression of cellulases was observed in media with different salt concentrations. However, differential band patterns for cellulase and xylanase activities were detected in zymograms when the fungus was grown in different lignocellulosic substrates such as wheat straw, maize stover, agave fibres, sugarcane bagasse and sawdust. Optimal temperature and pH were similar to other cellulases previously described. These results support the potential of this fungus to degrade lignocellulosic materials and its possible use in biotechnological applications.
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Affiliation(s)
- Ramón Alberto Batista-García
- Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Edgar Balcázar-López
- Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Estefan Miranda-Miranda
- Centro Nacional de Investigación Disciplinaria en Parasitología Veterinaria, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Cuernavaca, Morelos, Mexico
| | - Ayixón Sánchez-Reyes
- Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Laura Cuervo-Soto
- Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Denise Aceves-Zamudio
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Karina Atriztán-Hernández
- Facultad de Ciencias Biológicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Catalina Morales-Herrera
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Rocío Rodríguez-Hernández
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Jorge Folch-Mallol
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
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16
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Singh KS, Kirksey J, Hoff WD, Deole R. Draft Genome Sequence of the Extremely Halophilic Phototrophic Purple Sulfur Bacterium Halorhodospira halochloris. J Genomics 2014; 2:118-20. [PMID: 25057327 PMCID: PMC4105433 DOI: 10.7150/jgen.9123] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Halorhodospira halochloris is an extremely halophilic bacterium isolated from hypersaline Wadi Nantrun lakes in Egypt. Here we report the draft genome sequence of this gammaproteobacteria (GI number: 589289709, GenBank Accession number: CP007268). The 3.5-Mb genome encodes for photosynthesis and biosynthesis of organic osmoprotectants. Comparison with the genome of H.halophila promises to yield insights into the evolution of halophilic adaptations.
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Affiliation(s)
- Kumar Saurabh Singh
- 1. School of Biosciences and Veterinary Medicine, University of Camerino, 62032 CAMERINO (MC) ITALY
| | - Jared Kirksey
- 2. Department of Natural Sciences, Northeastern State University, Broken Arrow, OK, USA
| | - Wouter D Hoff
- 3. Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Ratnakar Deole
- 2. Department of Natural Sciences, Northeastern State University, Broken Arrow, OK, USA
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17
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Wee SK, Burns JL, DiChristina TJ. Identification of a molecular signature unique to metal-reducingGammaproteobacteria. FEMS Microbiol Lett 2013; 350:90-9. [DOI: 10.1111/1574-6968.12304] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 10/08/2013] [Accepted: 10/11/2013] [Indexed: 11/30/2022] Open
Affiliation(s)
- Seng K. Wee
- School of Biology; Georgia Institute of Technology; Atlanta GA USA
| | - Justin L. Burns
- School of Biology; Georgia Institute of Technology; Atlanta GA USA
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