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Nature and bioprospecting of haloalkaliphilics: a review. World J Microbiol Biotechnol 2020; 36:66. [DOI: 10.1007/s11274-020-02841-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 04/14/2020] [Indexed: 01/07/2023]
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2
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Varlamov VP, Il'ina AV, Shagdarova BT, Lunkov AP, Mysyakina IS. Chitin/Chitosan and Its Derivatives: Fundamental Problems and Practical Approaches. BIOCHEMISTRY (MOSCOW) 2020; 85:S154-S176. [PMID: 32087058 DOI: 10.1134/s0006297920140084] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this review, we present the data on the natural occurrence of chitin and its partially or fully deacetylated derivative chitosan, as well as their properties, methods of modification, and potential applications of derivatives with bactericidal, fungicidal, and antioxidant activities. The structure and physicochemical characteristics of the polymers, their functions, and features of chitin microbial synthesis and degradation, including the processes occurring in nature, are described. New data on the hydrolytic microorganisms capable of chitin degradation under extreme conditions are presented. Special attention is focused on the effect of physicochemical characteristics of chitosan, including molecular weight, degree of deacetylation, polydispersity index, and number of amino group derivatives (quaternized, succinyl, etc.) on the antimicrobial and antioxidant properties of modified polymers that can be of particular interest for biotechnology, medicine, and agriculture. Analysis of the available literature data confirms the importance of fundamental research to broaden our knowledge on the occurrence of chitin and chitosan in nature, their role in global biosphere cycles, and prospects of applied research aimed at using chitin, chitosan, and their derivatives in various aspects of human activity.
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Affiliation(s)
- V P Varlamov
- Laboratory of Biopolymer Engineering, Institute of Bioengineering, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 117312, Russia.
| | - A V Il'ina
- Laboratory of Biopolymer Engineering, Institute of Bioengineering, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 117312, Russia
| | - B Ts Shagdarova
- Laboratory of Biopolymer Engineering, Institute of Bioengineering, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 117312, Russia
| | - A P Lunkov
- Laboratory of Biopolymer Engineering, Institute of Bioengineering, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 117312, Russia
| | - I S Mysyakina
- Winogradsky Institute of Microbiology, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 117312, Russia
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3
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van Vliet DM, Palakawong Na Ayudthaya S, Diop S, Villanueva L, Stams AJM, Sánchez-Andrea I. Anaerobic Degradation of Sulfated Polysaccharides by Two Novel Kiritimatiellales Strains Isolated From Black Sea Sediment. Front Microbiol 2019; 10:253. [PMID: 30833937 PMCID: PMC6388578 DOI: 10.3389/fmicb.2019.00253] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/30/2019] [Indexed: 12/04/2022] Open
Abstract
The marine environment contains a large diversity of sulfated polysaccharides and other glycopolymers. Saccharolytic microorganisms degrade these compounds through hydrolysis, which includes the hydrolysis of sulfate groups from sugars by sulfatases. Various marine bacteria of the Planctomycetes-Verrucomicrobia-Chlamydia (PVC) superphylum have exceptionally high numbers of sulfatase genes associated with the degradation of sulfated polysaccharides. However, thus far no sulfatase-rich marine anaerobes are known. In this study, we aimed to isolate marine anaerobes using sulfated polysaccharides as substrate. Anoxic enrichment cultures were set up with a mineral brackish marine medium, inoculated with anoxic Black Sea sediment sampled at 2,100 m water depth water and incubated at 15°C (in situ T = 8°C) for several weeks. Community analysis by 16S rRNA gene amplicon sequencing revealed the enrichment of Kiritimatiellaeota clade R76-B128 bacteria in the enrichments with the sulfated polysaccharides fucoidan and iota-carrageenan as substrate. We isolated two strains, F1 and F21, which represent a novel family within the order of the Kiritimatiellales. They were capable of growth on various mono-, di-, and polysaccharides, including fucoidan. The desulfation of iota-carrageenan by strain F21 was confirmed quantitatively by an increase in free sulfate concentration. Strains F1 and F21 represent the first marine sulfatase-rich anaerobes, encoding more sulfatases (521 and 480, 8.0 and 8.4% of all coding sequences, respectively) than any other microorganism currently known. Specific encoded sulfatase subfamilies could be involved in desulfating fucoidan (S1_15, S1_17 and S1_25) and iota-carrageenan (S1_19). Strains F1 and F21 had a sulfatase gene classification profile more similar to aerobic than anaerobic sulfatase-rich PVC bacteria, including Kiritimatiella glycovorans, the only other cultured representative within the Kiritimatiellaeota. Both strains encoded a single anaerobic sulfatase-maturating enzyme which could be responsible for post-translational modification of formylglycine-dependent sulfatases. Strains F1 and F21 are potential anaerobic platforms for future studies on sulfatases and their maturation enzymes.
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Affiliation(s)
- Daan M. van Vliet
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Susakul Palakawong Na Ayudthaya
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
- Thailand Institute of Scientific and Technological Research, Pathum Thani, Thailand
| | - Sally Diop
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ) and Utrecht University, Den Burg, Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
- Centre of Biological Engineering, University of Minho, Braga, Portugal
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4
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Lee CJD, McMullan PE, O'Kane CJ, Stevenson A, Santos IC, Roy C, Ghosh W, Mancinelli RL, Mormile MR, McMullan G, Banciu HL, Fares MA, Benison KC, Oren A, Dyall-Smith ML, Hallsworth JE. NaCl-saturated brines are thermodynamically moderate, rather than extreme, microbial habitats. FEMS Microbiol Rev 2018; 42:672-693. [PMID: 29893835 DOI: 10.1093/femsre/fuy026] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 06/08/2018] [Indexed: 11/12/2022] Open
Abstract
NaCl-saturated brines such as saltern crystalliser ponds, inland salt lakes, deep-sea brines and liquids-of-deliquescence on halite are commonly regarded as a paradigm for the limit of life on Earth. There are, however, other habitats that are thermodynamically more extreme. Typically, NaCl-saturated environments contain all domains of life and perform complete biogeochemical cycling. Despite their reduced water activity, ∼0.755 at 5 M NaCl, some halophiles belonging to the Archaea and Bacteria exhibit optimum growth/metabolism in these brines. Furthermore, the recognised water-activity limit for microbial function, ∼0.585 for some strains of fungi, lies far below 0.755. Other biophysical constraints on the microbial biosphere (temperatures of >121°C; pH > 12; and high chaotropicity; e.g. ethanol at >18.9% w/v (24% v/v) and MgCl2 at >3.03 M) can prevent any cellular metabolism or ecosystem function. By contrast, NaCl-saturated environments contain biomass-dense, metabolically diverse, highly active and complex microbial ecosystems; and this underscores their moderate character. Here, we survey the evidence that NaCl-saturated brines are biologically permissive, fertile habitats that are thermodynamically mid-range rather than extreme. Indeed, were NaCl sufficiently soluble, some halophiles might grow at concentrations of up to 8 M. It may be that the finite solubility of NaCl has stabilised the genetic composition of halophile populations and limited the action of natural selection in driving halophile evolution towards greater xerophilicity. Further implications are considered for the origin(s) of life and other aspects of astrobiology.
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Affiliation(s)
- Callum J D Lee
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Phillip E McMullan
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Callum J O'Kane
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Andrew Stevenson
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Inês C Santos
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Chayan Roy
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Wriddhiman Ghosh
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Rocco L Mancinelli
- BAER Institute, Mail Stop 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Melanie R Mormile
- Department of Biological Sciences, Missouri University of Science and Technology, Rolla, MO 65401, USA
| | - Geoffrey McMullan
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Horia L Banciu
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babes-Bolyai University, 400006 Cluj-Napoca, Romania
| | - Mario A Fares
- Department of Abiotic Stress, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia 46022, Spain.,Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de Valencia (CSIC-UV), Valencia, 46980, Spain.,Department of Genetics, Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Dublin, Ireland
| | - Kathleen C Benison
- Department of Geology and Geography, West Virginia University, Morgantown, WV 26506-6300, USA
| | - Aharon Oren
- Department of Plant & Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat-Ram, Jerusalem 9190401, Israel
| | - Mike L Dyall-Smith
- Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
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Aktuganov GE, Galimzianova NF, Gilvanova EA, Kuzmina LY, Boyko TF, Safina VR, Melentiev AI. Characterization of Chitinase Produced by the Alkaliphilic Bacillus mannanilyticus IB-OR17 B1 Strain. APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683818050022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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6
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Kimbrel JA, Ballor N, Wu YW, David MM, Hazen TC, Simmons BA, Singer SW, Jansson JK. Microbial Community Structure and Functional Potential Along a Hypersaline Gradient. Front Microbiol 2018; 9:1492. [PMID: 30042744 PMCID: PMC6048260 DOI: 10.3389/fmicb.2018.01492] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 06/15/2018] [Indexed: 11/13/2022] Open
Abstract
Salinity is one of the strongest environmental drivers of microbial evolution and community composition. Here we aimed to determine the impact of salt concentrations (2.5, 7.5, and 33.2%) on the microbial community structure of reclaimed saltern ponds near San Francisco, California, and to discover prospective enzymes with potential biotechnological applications. Community compositions were determined by 16S rRNA amplicon sequencing revealing both higher richness and evenness in the pond sediments compared to the water columns. Co-occurrence network analysis additionally uncovered the presence of microbial seed bank communities, potentially primed to respond to rapid changes in salinity. In addition, functional annotation of shotgun metagenomic DNA showed different capabilities if the microbial communities at different salinities for methanogenesis, amino acid metabolism, and carbohydrate-active enzymes. There was an overall shift with increasing salinity in the functional potential for starch degradation, and a decrease in degradation of cellulose and other oligosaccharides. Further, many carbohydrate-active enzymes identified have acidic isoelectric points that have potential biotechnological applications, including deconstruction of biofuel feedstocks under high ionic conditions. Metagenome-assembled genomes (MAGs) of individual halotolerant and halophilic microbes were binned revealing a variety of carbohydrate-degrading potential of individual pond inhabitants.
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Affiliation(s)
- Jeffrey A Kimbrel
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nicholas Ballor
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Yu-Wei Wu
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Biological and Systems Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Maude M David
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Terry C Hazen
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Blake A Simmons
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Biological and Systems Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Steven W Singer
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Biological and Systems Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Janet K Jansson
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
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7
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Proteinivorax hydrogeniformans sp. nov., an anaerobic, haloalkaliphilic bacterium fermenting proteinaceous compounds with high hydrogen production. Antonie van Leeuwenhoek 2017; 111:275-284. [DOI: 10.1007/s10482-017-0949-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 09/20/2017] [Indexed: 10/18/2022]
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8
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Sorokin DY, Kolganova TV, Khijniak TV, Jones BE, Kublanov IV. Diversity of cultivated aerobic poly-hydrolytic bacteria in saline alkaline soils. PeerJ 2017; 5:e3796. [PMID: 28966889 PMCID: PMC5619242 DOI: 10.7717/peerj.3796] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 08/21/2017] [Indexed: 11/25/2022] Open
Abstract
Alkaline saline soils, known also as “soda solonchaks”, represent a natural soda habitat which differs from soda lake sediments by higher aeration and lower humidity. The microbiology of soda soils, in contrast to the more intensively studied soda lakes, remains poorly explored. In this work we investigate the diversity of culturable aerobic haloalkalitolerant bacteria with various hydrolytic activities from soda soils at different locations in Central Asia, Africa, and North America. In total, 179 pure cultures were obtained by using media with various polymers at pH 10 and 0.6 M total Na+. According to the 16S rRNA gene sequence analysis, most of the isolates belonged to Firmicutes and Actinobacteria. Most isolates possessed multiple hydrolytic activities, including endoglucanase, xylanase, amylase and protease. The pH profiling of selected representatives of actinobacteria and endospore-forming bacteria showed, that the former were facultative alkaliphiles, while the latter were mostly obligate alkaliphiles. The hydrolases of selected representatives from both groups were active at a broad pH range from six to 11. Overall, this work demonstrates the presence of a rich hydrolytic bacterial community in soda soils which might be explored further for production of haloalkalistable hydrolases.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Tatiana V Kolganova
- Institute of Bioengineering, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana V Khijniak
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Brian E Jones
- DuPont Industrial Biosciences/Genencor International BV, Leiden, Netherlands
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Immanuel Kant Baltic Federal University, Kaliningrad, Russia
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9
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Sorokin DY, Rakitin AL, Gumerov VM, Beletsky AV, Sinninghe Damsté JS, Mardanov AV, Ravin NV. Phenotypic and Genomic Properties of Chitinispirillum alkaliphilum gen. nov., sp. nov., A Haloalkaliphilic Anaerobic Chitinolytic Bacterium Representing a Novel Class in the Phylum Fibrobacteres. Front Microbiol 2016; 7:407. [PMID: 27065971 PMCID: PMC4814513 DOI: 10.3389/fmicb.2016.00407] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 03/14/2016] [Indexed: 11/18/2022] Open
Abstract
Anaerobic enrichment from sediments of hypersaline alkaline lakes in Wadi el Natrun (Egypt) with chitin resulted in the isolation of a fermentative haloalkaliphilic bacterium, strain ACht6-1, growing exclusively with insoluble chitin as the substrate in a sodium carbonate-based medium at pH 8.5–10.5 and total Na+ concentrations from 0.4 to 1.75 M. The isolate had a Gram-negative cell wall and formed lipid cysts in old cultures. The chitinolytic activity was associated with cells. Analysis of the 4.4 Mb draft genome identified pathways for chitin utilization, particularly, secreted chitinases linked to the cell surface, as well as genes for the hydrolysis of other polysaccharides and fermentation of sugars, while the genes needed for aerobic and anaerobic respiration were absent. Adaptation to a haloalkaliphilic lifestyle was reflected by the gene repertoire encoding sodium rather than proton-dependent membrane-bound ion pumps, including the Rnf-type complex, oxaloacetate decarboxylase, V-type ATPase, and pyrophosphatase. The phylogenetic analysis using 16S rRNA gene and ribosomal proteins indicated that ACht6-1 forms a novel deep lineage at the class level within the bacterial candidate division TG3. Based on phylogenetic, phenotypic and genomic analyses, the novel chitinolytic bacterium is described as Chitinispirillum alkaliphilum gen. nov., sp. nov., within a novel class Chitinispirillia that could be included into the phylum Fibrobacteres.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of SciencesMoscow, Russia; Department of Biotechnology, Delft University of TechnologyDelft, Netherlands
| | - Andrey L Rakitin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Vadim M Gumerov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Jaap S Sinninghe Damsté
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research and and Utrecht UniversityUtrecht, Netherlands; Geochemistry, Department of Earth Sciences, Faculty of Geosciences, Utrecht UniversityUtrecht, Netherlands
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
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10
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Abdul Rahman N, Parks DH, Vanwonterghem I, Morrison M, Tyson GW, Hugenholtz P. A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres. Front Microbiol 2016; 6:1469. [PMID: 26779135 PMCID: PMC4704652 DOI: 10.3389/fmicb.2015.01469] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/07/2015] [Indexed: 12/13/2022] Open
Abstract
The Fibrobacteres has been recognized as a bacterial phylum for over a decade, but little is known about the group beyond its environmental distribution, and characterization of its sole cultured representative genus, Fibrobacter, after which the phylum was named. Based on these incomplete data, it is thought that cellulose hydrolysis, anaerobic metabolism, and lack of motility are unifying features of the phylum. There are also contradicting views as to whether an uncultured sister lineage, candidate phylum TG3, should be included in the Fibrobacteres. Recently, chitin-degrading cultured representatives of TG3 were isolated from a hypersaline soda lake, and the genome of one species, Chitinivibrio alkaliphilus, sequenced and described in detail. Here, we performed a comparative analysis of Fibrobacter succinogenes, C. alkaliphilus and eight near or substantially complete Fibrobacteres/TG3 genomes of environmental populations recovered from termite gut, anaerobic digester, and sheep rumen metagenomes. We propose that TG3 should be amalgamated with the Fibrobacteres phylum based on robust monophyly of the two lineages and shared character traits. Polymer hydrolysis, using a distinctive set of glycoside hydrolases and binding domains, appears to be a prominent feature of members of the Fibrobacteres. Not all members of this phylum are strictly anaerobic as some termite gut Fibrobacteres have respiratory chains adapted to the microaerophilic conditions found in this habitat. Contrary to expectations, flagella-based motility is predicted to be an ancestral and common trait in this phylum and has only recently been lost in F. succinogenes and its relatives based on phylogenetic distribution of flagellar genes. Our findings extend current understanding of the Fibrobacteres and provide an improved basis for further investigation of this phylum.
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Affiliation(s)
- Nurdyana Abdul Rahman
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland Brisbane, QLD, Australia
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland Brisbane, QLD, Australia
| | - Inka Vanwonterghem
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbane, QLD, Australia; Advanced Water Management Center, The University of QueenslandBrisbane, QLD, Australia
| | - Mark Morrison
- Microbial Biology and Metagenomics, The University of Queensland Diamantina Institute, Translational Research Institute Brisbane, QLD, Australia
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland Brisbane, QLD, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbane, QLD, Australia; Genomics and Computational Biology, Institute for Molecular Bioscience, The University of QueenslandBrisbane, QLD, Australia
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11
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Shivlata L, Satyanarayana T. Thermophilic and alkaliphilic Actinobacteria: biology and potential applications. Front Microbiol 2015; 6:1014. [PMID: 26441937 PMCID: PMC4585250 DOI: 10.3389/fmicb.2015.01014] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/07/2015] [Indexed: 11/13/2022] Open
Abstract
Microbes belonging to the phylum Actinobacteria are prolific sources of antibiotics, clinically useful bioactive compounds and industrially important enzymes. The focus of the current review is on the diversity and potential applications of thermophilic and alkaliphilic actinobacteria, which are highly diverse in their taxonomy and morphology with a variety of adaptations for surviving and thriving in hostile environments. The specific metabolic pathways in these actinobacteria are activated for elaborating pharmaceutically, agriculturally, and biotechnologically relevant biomolecules/bioactive compounds, which find multifarious applications.
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12
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Sorokin DY, Banciu HL, Muyzer G. Functional microbiology of soda lakes. Curr Opin Microbiol 2015; 25:88-96. [PMID: 26025021 DOI: 10.1016/j.mib.2015.05.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 04/30/2015] [Accepted: 05/01/2015] [Indexed: 10/23/2022]
Abstract
Soda lakes represent unique permanently haloalkaline system. Despite the harsh conditions, they are inhabited by abundant, mostly prokaryotic, microbial communities. This review summarizes results of studies of main functional groups of the soda lake prokaryotes responsible for carbon, nitrogen and sulfur cycling, including oxygenic and anoxygenic phototrophs, aerobic chemolithotrophs, fermenting and respiring anaerobes. The main conclusion from this work is that the soda lakes are very different from other high-salt systems in respect to microbial richness and activity. The reason for this difference is determined by the major physico-chemical features of two dominant salts - NaCl in neutral saline systems and sodium carbonates in soda lakes, that are influencing the amount of energy required for osmotic adaptation.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia; Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.
| | - Horia L Banciu
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Babeş-Bolyai University, Cluj-Napoca, Romania; Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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13
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Oren A. Halophilic microbial communities and their environments. Curr Opin Biotechnol 2015; 33:119-24. [PMID: 25727188 DOI: 10.1016/j.copbio.2015.02.005] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 01/04/2015] [Accepted: 02/13/2015] [Indexed: 10/23/2022]
Abstract
Use of culture-independent studies have greatly increased our understanding of the microbiology of hypersaline lakes (the Dead Sea, Great Salt Lake) and saltern ponds in recent years. Exciting new information has become available on the microbial processes in Antarctic lakes and in deep-sea brines. These studies led to the recognition of many new lineages of microorganisms not yet available for study in culture, and their cultivation in the laboratory is now a major challenge. Studies of the metabolic potentials of different halophilic microorganisms, Archaea as well as Bacteria, shed light on the possibilities and the limitations of life at high salt concentrations, and also show their potential for applications in bioremediation.
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Affiliation(s)
- Aharon Oren
- Department of Plant & Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat-Ram, Jerusalem 91904, Israel.
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14
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Johnson-Rollings AS, Wright H, Masciandaro G, Macci C, Doni S, Calvo-Bado LA, Slade SE, Vallin Plou C, Wellington EMH. Exploring the functional soil-microbe interface and exoenzymes through soil metaexoproteomics. THE ISME JOURNAL 2014; 8:2148-50. [PMID: 25036924 PMCID: PMC4184004 DOI: 10.1038/ismej.2014.130] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 06/03/2014] [Indexed: 01/06/2023]
Abstract
Functionally important proteins at the interface of cell and soil are of potentially low abundance when compared with commonly recovered intracellular proteins. A novel approach was developed and used to extract the metaexoproteome, the subset of proteins found outside the cell, in the context of a soil enriched with the nitrogen-containing recalcitrant polymer chitin. The majority of proteins recovered was of bacterial origin and localized to the outer membrane or extracellular milieu. A wide variety of transporter proteins were identified, particularly those associated with amino-acid and phosphate uptake. The metaexoproteome extract retained chitinolytic activity and we were successful in detecting Nocardiopsis-like chitinases that correlated with the glycoside hydrolase family 18 (GH18) chi gene data and metataxonomic analysis. Nocardiopsis-like chitinases appeared to be solely responsible for chitinolytic activity in soil. This is the first study to detect and sequence bacterial exoenzymes with proven activity in the soil enzyme pool.
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Affiliation(s)
| | - Helena Wright
- School of Life Sciences, University of Warwick, Coventry, UK
| | | | - Cristina Macci
- Istituto per lo Studio degli Ecosistemi, CNR, Pisa, Italy
| | - Serena Doni
- Istituto per lo Studio degli Ecosistemi, CNR, Pisa, Italy
| | | | - Susan E Slade
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Carlos Vallin Plou
- Grupo de Biotecnología, CEIEB, IFAL, Universidad de La Habana, Havana, Cuba
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15
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Sorokin DY, Berben T, Melton ED, Overmars L, Vavourakis CD, Muyzer G. Microbial diversity and biogeochemical cycling in soda lakes. Extremophiles 2014; 18:791-809. [PMID: 25156418 PMCID: PMC4158274 DOI: 10.1007/s00792-014-0670-9] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 06/26/2014] [Indexed: 01/26/2023]
Abstract
Soda lakes contain high concentrations of sodium carbonates resulting in a stable elevated pH, which provide a unique habitat to a rich diversity of haloalkaliphilic bacteria and archaea. Both cultivation-dependent and -independent methods have aided the identification of key processes and genes in the microbially mediated carbon, nitrogen, and sulfur biogeochemical cycles in soda lakes. In order to survive in this extreme environment, haloalkaliphiles have developed various bioenergetic and structural adaptations to maintain pH homeostasis and intracellular osmotic pressure. The cultivation of a handful of strains has led to the isolation of a number of extremozymes, which allow the cell to perform enzymatic reactions at these extreme conditions. These enzymes potentially contribute to biotechnological applications. In addition, microbial species active in the sulfur cycle can be used for sulfur remediation purposes. Future research should combine both innovative culture methods and state-of-the-art 'meta-omic' techniques to gain a comprehensive understanding of the microbes that flourish in these extreme environments and the processes they mediate. Coupling the biogeochemical C, N, and S cycles and identifying where each process takes place on a spatial and temporal scale could unravel the interspecies relationships and thereby reveal more about the ecosystem dynamics of these enigmatic extreme environments.
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Affiliation(s)
- Dimitry Y. Sorokin
- Winogradsky Institute of Microbiology, RAS, Moscow, Russia
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Tom Berben
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Emily Denise Melton
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Lex Overmars
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Charlotte D. Vavourakis
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Gerard Muyzer
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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16
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Bacterial chitin utilization at halophilic conditions. Extremophiles 2013; 18:243-8. [PMID: 24306781 DOI: 10.1007/s00792-013-0611-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 11/14/2013] [Indexed: 10/26/2022]
Abstract
Chitin is a dominant structural polymer produced in large amounts by brine shrimp Artemia in hypersaline lakes. Microbiological analysis of chitin utilization as a growth substrate in hypersaline chloride-sulfate lakes in the south Kulunda Steppe (Altai, Russia) revealed two groups of bacteria able to grow on chitin at moderate salinity. Under aerobic conditions, an enrichment culture was obtained at 2 M NaCl. Further purification resulted in the isolation of strains HCh1 and strain HCh2, identified as representatives of the genera Saccharospirillum and Arhodomonas (both in the Gammaproteobacteria). The chitin-utilizing potential has not been previously recognized in these genera. The Saccharospirillum sp. strain HCh1 grew on chitin within the salinity range from 0.5 to 3.25 M NaCl (optimum at 1 M), while Arhodomonas sp. strain HCh2 grew up to 2.5 M NaCl but had a higher salt optimum at 1.5 M. Anaerobic enrichments grew with chitin at 2 and 4 M NaCl, but growth in the latter was extremely slow and the culture eventually lost viability. The enrichment at 2 M NaCl resulted in the isolation of strain HCh-An1, identified as a distant new species of the genus Orenia in the clostridial order Halanaerobiales. It was able to grow on chitin within a salinity range from 1.0 to 2.5 M NaCl (optimum at 1.5 M). The strain is proposed as a new species of the genus Orenia-O. chitinitropha.
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17
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Sorokin DY, Gumerov VM, Rakitin AL, Beletsky AV, Damsté JSS, Muyzer G, Mardanov AV, Ravin NV. Genome analysis of Chitinivibrio alkaliphilus gen. nov., sp. nov., a novel extremely haloalkaliphilic anaerobic chitinolytic bacterium from the candidate phylum Termite Group 3. Environ Microbiol 2013; 16:1549-65. [PMID: 24112708 DOI: 10.1111/1462-2920.12284] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 07/29/2013] [Accepted: 09/09/2013] [Indexed: 11/30/2022]
Abstract
Anaerobic enrichments from hypersaline soda lakes with chitin as substrate yielded five closely related anaerobic haloalkaliphilic isolates growing on insoluble chitin by fermentation at pH 10 and salinities up to 3.5 M. The chitinolytic activity was exclusively cell associated. To better understand the biology and evolutionary history of this novel bacterial lineage, the genome of the type strain ACht1 was sequenced. Analysis of the 2.6 Mb draft genome revealed enzymes of chitin-degradation pathways, including secreted cell-bound chitinases. The reconstructed central metabolism revealed pathways enabling the fermentation of polysaccharides, while it lacks the genes needed for aerobic or anaerobic respiration. The Rnf-type complex, oxaloacetate decarboxylase and sodium-transporting V-type adenosine triphosphatase were identified among putative membrane-bound ion pumps. According to 16S ribosomal RNA analysis, the isolates belong to the candidate phylum Termite Group 3, representing its first culturable members. Phylogenetic analysis using ribosomal proteins and taxonomic distribution analysis of the whole proteome supported a class-level classification of ACht1 most probably affiliated to the phylum Fibribacteres. Based on phylogenetic, phenotypic and genomic analyses, the novel bacteria are proposed to be classified as Chitinivibrio alkaliphilus gen. nov., sp. nov., within a novel class Chitinivibrione.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-let Oktyabrya, bld. 7-2, 117312, Moscow, Russia; Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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18
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Adaptation in Haloalkaliphiles and Natronophilic Bacteria. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2013. [DOI: 10.1007/978-94-007-6488-0_5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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