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Rizzo C, Arcadi E, Calogero R, Ciro Rappazzo A, Caruso G, Maimone G, Lo Giudice A, Romeo T, Andaloro F. Deciphering the evolvement of microbial communities from hydrothermal vent sediments in a global change perspective. ENVIRONMENTAL RESEARCH 2024; 240:117514. [PMID: 37890823 DOI: 10.1016/j.envres.2023.117514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/17/2023] [Accepted: 10/24/2023] [Indexed: 10/29/2023]
Abstract
Microbial communities first respond to changes of external environmental conditions. Observing the microbial responses to environmental changes in terms of taxonomic and functional biodiversity is therefore of great interest, particularly in extreme environments, where the already extreme conditions can become even harsher. In this study, sediment samples from three different shallow hydrothermal vents in Levante Bay (Vulcano Island, Aeolian Islands, Italy) were used to set up microcosm experiments with the aim to explore the microbial dynamics under changing conditions of pH and redox potential over a 90-days period. The leading hypothesis was to establish under microcosm conditions whether the starting microbial communities of the sediments evolved differently depending on their origin. To profile the dynamics of microbial populations over time, biodiversity, enzymatic profile, total cell abundance estimations, total/respiring cell ratio were estimated by using different approaches. An evident change in the microbial community structure was observed, mainly in the microcosm containing the sediment from the most acidified site, which was characterized by a highly diversified microbial community (in prevalence composed of Thermotoga, Desulfobacterota, Planctomycetota, Synergistota and Deferribacterota). An increase in microbial resistant forms (e.g., spore-forming species) with anaerobic metabolism was detected in all experimental conditions. Differential physiological responses characterized the sedimentary microbial communities. Proteolytic activity appeared to be stimulated under microcosm conditions, whereas the alkaline phosphatase activity was significantly depressed at low pH values, like those that were measured at the station showing intermediate pH-conditions. The results confirmed a differential response of microbial communities depending on the starting environmental conditions.
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Affiliation(s)
- Carmen Rizzo
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn-, Sicily Marine Centre, Villa Pace, Contrada Porticatello 29, 98167, Messina, Italy; Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122, Messina, Italy.
| | - Erika Arcadi
- StazioneZoologica Anton Dohrn, Sicily Marine Centre, Department of Biology and Evolution of Marine Organisms, Villa Pace, Contrada Porticatello 29, 98167, Messina, Italy.
| | - Rosario Calogero
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Contrada Porticatello, 29, 98167 Messina, Italy
| | - Alessandro Ciro Rappazzo
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122, Messina, Italy; Campus Scientifico, Ca' Foscari University of Venice, Italy
| | - Gabriella Caruso
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122, Messina, Italy
| | - Giovanna Maimone
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122, Messina, Italy
| | - Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata S. Raineri 86, 98122, Messina, Italy
| | - Teresa Romeo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Contrada Porticatello, 29, 98167, Messina, Italy; National Institute for Environmental Protection and Research, Via Dei Mille 46, 98057, Milazzo, Italy
| | - Franco Andaloro
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Lungomare Cristoforo Colombo, 4521 Palermo, Italy
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Hominibacterium faecale gen. nov., sp. nov., an anaerobic l-arginine-degrading bacterium isolated from human feces. Arch Microbiol 2023; 205:33. [DOI: 10.1007/s00203-022-03365-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
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3
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Akram F, Haq IU, Shah FI, Aqeel A, Ahmed Z, Mir AS, Qureshi SS, Raja SI. Genus Thermotoga: A valuable home of multifunctional glycoside hydrolases (GHs) for industrial sustainability. Bioorg Chem 2022; 127:105942. [PMID: 35709577 DOI: 10.1016/j.bioorg.2022.105942] [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] [Received: 12/31/2021] [Revised: 06/04/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022]
Abstract
Nature is a dexterous and prolific chemist for cataloging a number of hostile niches that are the ideal residence of various thermophiles. Apart from having other species, these subsurface environments are considered a throne of bacterial genus Thermotoga. The genome sequence of Thermotogales encodes complex and incongruent clusters of glycoside hydrolases (GHs), which are superior to their mesophilic counterparts and play a prominent role in various applications due to their extreme intrinsic stability. They have a tremendous capacity to use a wide variety of simple and multifaceted carbohydrates through GHs, formulate fermentative hydrogen and bioethanol at extraordinary yield, and catalyze high-temperature reactions for various biotechnological applications. Nevertheless, no stringent rules exist for the thermo-stabilization of biocatalysts present in the genus Thermotoga. These enzymes endure immense attraction in fundamental aspects of how these polypeptides attain and stabilize their distinctive three-dimensional (3D) structures to accomplish their physiological roles. Moreover, numerous genome sequences from Thermotoga species have revealed a significant fraction of genes most closely related to those of archaeal species, thus firming a staunch belief of lateral gene transfer mechanism. However, the question of its magnitude is still in its infancy. In addition to GHs, this genus is a paragon of encapsulins which carry pharmacological and industrial significance in the field of life sciences. This review highlights an intricate balance between the genomic organizations, factors inducing the thermostability, and pharmacological and industrial applications of GHs isolated from genus Thermotoga.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan.
| | - Ikram Ul Haq
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan; Pakistan Academy of Science, Islamabad, Pakistan
| | - Fatima Iftikhar Shah
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Amna Aqeel
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Zeeshan Ahmed
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Azka Shahzad Mir
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Sumbal Sajid Qureshi
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Saleha Ibadat Raja
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
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Lanzilli M, Esercizio N, Vastano M, Xu Z, Nuzzo G, Gallo C, Manzo E, Fontana A, d’Ippolito G. Effect of Cultivation Parameters on Fermentation and Hydrogen Production in the Phylum Thermotogae. Int J Mol Sci 2020; 22:ijms22010341. [PMID: 33396970 PMCID: PMC7795431 DOI: 10.3390/ijms22010341] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 01/19/2023] Open
Abstract
The phylum Thermotogae is composed of a single class (Thermotogae), 4 orders (Thermotogales, Kosmotogales, Petrotogales, Mesoaciditogales), 5 families (Thermatogaceae, Fervidobacteriaceae, Kosmotogaceae, Petrotogaceae, Mesoaciditogaceae), and 13 genera. They have been isolated from extremely hot environments whose characteristics are reflected in the metabolic and phenotypic properties of the Thermotogae species. The metabolic versatility of Thermotogae members leads to a pool of high value-added products with application potentials in many industry fields. The low risk of contamination associated with their extreme culture conditions has made most species of the phylum attractive candidates in biotechnological processes. Almost all members of the phylum, especially those in the order Thermotogales, can produce bio-hydrogen from a variety of simple and complex sugars with yields close to the theoretical Thauer limit of 4 mol H2/mol consumed glucose. Acetate, lactate, and L-alanine are the major organic end products. Thermotagae fermentation processes are influenced by various factors, such as hydrogen partial pressure, agitation, gas sparging, culture/headspace ratio, inoculum, pH, temperature, nitrogen sources, sulfur sources, inorganic compounds, metal ions, etc. Optimization of these parameters will help to fully unleash the biotechnological potentials of Thermotogae and promote their applications in industry. This article gives an overview of how these operational parameters could impact Thermotogae fermentation in terms of sugar consumption, hydrogen yields, and organic acids production.
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Affiliation(s)
- Mariamichela Lanzilli
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; (M.L.); (N.E.); (M.V.); (G.N.); (C.G.); (E.M.); (A.F.)
| | - Nunzia Esercizio
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; (M.L.); (N.E.); (M.V.); (G.N.); (C.G.); (E.M.); (A.F.)
| | - Marco Vastano
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; (M.L.); (N.E.); (M.V.); (G.N.); (C.G.); (E.M.); (A.F.)
| | - Zhaohui Xu
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA;
| | - Genoveffa Nuzzo
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; (M.L.); (N.E.); (M.V.); (G.N.); (C.G.); (E.M.); (A.F.)
| | - Carmela Gallo
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; (M.L.); (N.E.); (M.V.); (G.N.); (C.G.); (E.M.); (A.F.)
| | - Emiliano Manzo
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; (M.L.); (N.E.); (M.V.); (G.N.); (C.G.); (E.M.); (A.F.)
| | - Angelo Fontana
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; (M.L.); (N.E.); (M.V.); (G.N.); (C.G.); (E.M.); (A.F.)
| | - Giuliana d’Ippolito
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; (M.L.); (N.E.); (M.V.); (G.N.); (C.G.); (E.M.); (A.F.)
- Correspondence: ; Tel.: +39-081-8675096
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Lv XM, Yang M, Dai LR, Tu B, Chang C, Huang Y, Deng Y, Lawson PA, Zhang H, Cheng L, Tang YQ. Zhaonella formicivorans gen. nov., sp. nov., an anaerobic formate-utilizing bacterium isolated from Shengli oilfield, and proposal of four novel families and Moorellales ord. nov. in the phylum Firmicutes. Int J Syst Evol Microbiol 2020; 70:3361-3373. [DOI: 10.1099/ijsem.0.004178] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A novel obligately anaerobic, thermophilic and formate-utilizing bacterium K32T was isolated from Shengli oilfield of China. Cells were straight rods (0.4–0.8 µm × 2.5–8.0 µm), Gram-stain-positive, non-spore-forming and slightly motile. Optimum growth occurred with pH of 7 and 0.5 g l–1 NaCl under temperature of 55–60 °C. Nitrate could be reduced into nitrite, syntrophic formate oxidation to methane and carbon dioxide occurred when co-culturing strain K32T and
Methanothermobacter thermautotrophicus
ΔH. The main cellular fatty acids were iso-C15 : 0 (24.0 %), anteiso-C15 : 0 (21.7 %), C16 : 0 (12.7 %) and C14 : 0 (10.8 %), and the main polar lipid was phosphatidylglycerol. The G+C content of the genomic DNA was 46.3 mol%. The 16S rRNA gene sequence of K32T shared ≤90.4 % of sequence similarity to closest type strains of
Desulfitibacter alkalitolerans
,
Calderihabitans maritimus
and members of the genus
Moorella
. Based on the phenotypic, biochemical and genotypic characterization, Zhaonella formicivorans gen. nov., sp. nov. is proposed with K32T (=CCAM 584T =DSM 107278T=CGMCC1.5297T) as the type strain, which is the first representative of Zhaonellaceae fam. nov. In addition, the order Thermoanaerobacterales and family
Peptococcaceae
were reclassified, and three novel families in the novel order of Moorellales ord. nov. were also proposed.
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Affiliation(s)
- Xiao-meng Lv
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
- Institute of New Energy and Low-Carbon Technology, Sichuan University, Chengdu, 610065, PR China
| | - Min Yang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
- Institute of New Energy and Low-Carbon Technology, Sichuan University, Chengdu, 610065, PR China
| | - Li-rong Dai
- China Collection of Anaerobic microorganisms, Chengdu 610041, PR China
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Bo Tu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Chen Chang
- China Collection of Anaerobic microorganisms, Chengdu 610041, PR China
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Yan Huang
- China Collection of Anaerobic microorganisms, Chengdu 610041, PR China
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Yu Deng
- China Collection of Anaerobic microorganisms, Chengdu 610041, PR China
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Paul A. Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Hui Zhang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
- China Collection of Anaerobic microorganisms, Chengdu 610041, PR China
| | - Yue-qin Tang
- Institute of New Energy and Low-Carbon Technology, Sichuan University, Chengdu, 610065, PR China
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6
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Description of Biomaibacter acetigenes gen. nov., sp. nov., and proposal of Thermosediminibacterales ord. nov. containing two novel families of Tepidanaerobacteraceae fam. nov. and Thermosediminibacteraceae fam. nov. Int J Syst Evol Microbiol 2019; 69:3891-3902. [DOI: 10.1099/ijsem.0.003701] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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7
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Wu K, Dai L, Tu B, Zhang X, Zhang H, Deng Y, Lawson PA, Cheng L. Gudongella oleilytica gen. nov., sp. nov., an aerotorelant bacterium isolated from Shengli oilfield and validation of family Tissierellaceae. Int J Syst Evol Microbiol 2019; 70:951-957. [PMID: 31751197 DOI: 10.1099/ijsem.0.003854] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive, rod shaped and anaerobic bacterium, designated as W6T, was isolated from Shengli oilfield in China. Strain W6T was observed to grow from 20 to 45 °C with pH 6.5-9.0 (optimally at 40 °C and pH of 7.5) and without addition of NaCl. The major cellular fatty acids were iso-C15 : 0 (29.1%), C14 : 0 (27.0%) and C16 : 0 (12.2%), and the main polar lipids were lipids (L) and aminolipids (AL). The DNA G+C content is 42.9 mol%. Based on 16S rRNA gene sequence analysis, strain W6T showed highest similarities to Tissierella creatinini DSM 9508T (94.9%) and Soehngenia saccharolytica DSM 12858T (94.1%). The morphological, physiological, biochemical, phylogenetic and phylogenomic analyses demonstrated strain W6T (CCAM 534T=DSM 28124T=CGMCC 1.5291T) represents a novel species in a new genus, for which the name Gudongella oleilytica gen. nov. sp. nov. is proposed. The family Tissierellaceae is proposed as a new family containing the genera Anaerosalibacter, Gudongella, Keratinibaculum, Soehngenia, Sporanaerobacter, Tepidimicrobium, Tissierella, Urmitella and species Clostridium ultunense based on the phylogenetic and phylogenomic analyses.
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Affiliation(s)
- Kejia Wu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China.,Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, PR China
| | - Lirong Dai
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China.,Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, PR China
| | - Bo Tu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China.,Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, PR China
| | - Xue Zhang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China.,Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, PR China
| | - Hui Zhang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China.,Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, PR China
| | - Yu Deng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China.,Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, PR China
| | - Paul A Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China.,Center for Anaerobic Microbial Resources of Sichuan Province, Chengdu, PR China
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Zhang X, Tu B, Dai LR, Lawson PA, Zheng ZZ, Liu LY, Deng Y, Zhang H, Cheng L. Petroclostridium xylanilyticum gen. nov., sp. nov., a xylan-degrading bacterium isolated from an oilfield, and reclassification of clostridial cluster III members into four novel genera in a new Hungateiclostridiaceae fam. nov. Int J Syst Evol Microbiol 2018; 68:3197-3211. [DOI: 10.1099/ijsem.0.002966] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Xue Zhang
- 1Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Bo Tu
- 1Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Li-rong Dai
- 1Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Paul A. Lawson
- 2Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Zhen-zhen Zheng
- 1Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Lai-Yan Liu
- 1Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Yu Deng
- 1Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Hui Zhang
- 1Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Lei Cheng
- 1Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
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Fitamo T, Treu L, Boldrin A, Sartori C, Angelidaki I, Scheutz C. Microbial population dynamics in urban organic waste anaerobic co-digestion with mixed sludge during a change in feedstock composition and different hydraulic retention times. WATER RESEARCH 2017; 118:261-271. [PMID: 28456109 DOI: 10.1016/j.watres.2017.04.012] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/22/2017] [Accepted: 04/04/2017] [Indexed: 05/27/2023]
Abstract
Microbial communities play an essential role in the biochemical pathways of anaerobic digestion processes. The correlations between microorganisms' relative abundance and anaerobic digestion process parameters were investigated, by considering the effect of different feedstock compositions and hydraulic retention times (HRTs). Shifts in microbial diversity and changes in microbial community richness were observed by changing feedstock composition from mono-digestion of mixed sludge to co-digestion of food waste, grass clippings and garden waste with mixed sludge at HRT of 30, 20, 15 and 10 days. Syntrophic acetate oxidation along with hydrogenotrophic methanogenesis, mediated by Methanothermobacter, was found to be the most prevalent methane formation pathway, with the only exception of 10 days' HRT, in which Methanosarcina was the most dominant archaea. Significantly, the degradation of complex organic polymers was found to be the most active process, performed by members of S1 (Thermotogales), Thermonema and Lactobacillus in a reactor fed with a high share of food waste. Conversely, Thermacetogenium, Anaerobaculum, Ruminococcaceae, Porphyromonadaceae and the lignocellulosic-degrading Clostridium were the significantly more abundant bacteria in the reactor fed with an increased share of lignocellulosic biomass in the form of grass clippings and garden waste. Finally, microbes belonging to Coprothermobacter, Syntrophomonas and Clostridium were correlated significantly with the specific methane yield obtained in both reactors.
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Affiliation(s)
- Temesgen Fitamo
- Department of Environmental Engineering, Technical University of Denmark, Miljoevej, Building 115, DK-2800, Kongens Lyngby, Denmark.
| | - Laura Treu
- Department of Environmental Engineering, Technical University of Denmark, Miljoevej, Building 115, DK-2800, Kongens Lyngby, Denmark; Department of Agronomy, Food, Natural Resources, Animal and Environment (DAFNAE), viale dell'Università, 16, 35020, Legnaro, Padova, Italy
| | - Alessio Boldrin
- Department of Environmental Engineering, Technical University of Denmark, Miljoevej, Building 115, DK-2800, Kongens Lyngby, Denmark
| | - Cristina Sartori
- Department of Agronomy, Food, Natural Resources, Animal and Environment (DAFNAE), viale dell'Università, 16, 35020, Legnaro, Padova, Italy
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, Miljoevej, Building 115, DK-2800, Kongens Lyngby, Denmark
| | - Charlotte Scheutz
- Department of Environmental Engineering, Technical University of Denmark, Miljoevej, Building 115, DK-2800, Kongens Lyngby, Denmark
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Ju F, Lau F, Zhang T. Linking Microbial Community, Environmental Variables, and Methanogenesis in Anaerobic Biogas Digesters of Chemically Enhanced Primary Treatment Sludge. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:3982-3992. [PMID: 28240534 DOI: 10.1021/acs.est.6b06344] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Understanding the influences of biotic and abiotic factors on microbial community structure and methanogenesis are important for its engineering and ecological significance. In this study, four biogas digesters were supplied with the same inoculum and feeding sludge but operated at different sludge retention time (7 to 16 days) and organic loading rates for 90 days to determine the relative influence of biotic and environmental factors on the microbial community assembly and methanogenic performance. Despite different operational parameters, all digester communities were dominated by Bacteroidales, Clostridiales, and Thermotogales and followed the same trend of population dynamics over time. Network and multivariate analyses suggest that deterministic factors, including microbial competition (involving Bacteroidales spp.), niche differentiation (e.g., within Clostridiales spp.), and periodic microbial immigration (from feed sludge), are the key drivers of microbial community assembly and dynamics. A yet-to-be-cultured phylotype of Bacteroidales (GenBank ID: GU389558.1 ) is implicated as a strong competitor for carbohydrates. Moreover, biogas-producing rate and methane content were significantly related with the abundances of functional populations rather than any operational or physicochemical parameter, revealing microbiological mediation of methanogenesis. Combined, this study enriches our understandings of biological and environmental drivers of microbial community assembly and performance in anaerobic digesters.
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Affiliation(s)
- Feng Ju
- Environmental Biotechnology Lab, The University of Hong Kong , Hong Kong SAR, China
| | - Frankie Lau
- Drainage Services Department, The Government of the Hong Kong Special Administrative Region , Hong Kong SAR, China
| | - Tong Zhang
- Environmental Biotechnology Lab, The University of Hong Kong , Hong Kong SAR, China
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11
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Itoh T, Onishi M, Kato S, Iino T, Sakamoto M, Kudo T, Takashina T, Ohkuma M. Athalassotoga saccharophila gen. nov., sp. nov., isolated from an acidic terrestrial hot spring, and proposal of Mesoaciditogales ord. nov. and Mesoaciditogaceae fam. nov. in the phylum Thermotogae. Int J Syst Evol Microbiol 2016; 66:1045-1051. [DOI: 10.1099/ijsem.0.000833] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Takashi Itoh
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Masafumi Onishi
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
- Graduate School of Life Sciences, Toyo University, Oura, Gunma 374-0193, Japan
| | - Shingo Kato
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Takao Iino
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Mitsuo Sakamoto
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Tomonori Takashina
- Graduate School of Life Sciences, Toyo University, Oura, Gunma 374-0193, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
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12
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Pollo SM, Zhaxybayeva O, Nesbø CL. Insights into thermoadaptation and the evolution of mesophily from the bacterial phylum Thermotogae. Can J Microbiol 2015. [DOI: 10.1139/cjm-2015-0073] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Thermophiles are extremophiles that grow optimally at temperatures >45 °C. To survive and maintain function of their biological molecules, they have a suite of characteristics not found in organisms that grow at moderate temperature (mesophiles). At the cellular level, thermophiles have mechanisms for maintaining their membranes, nucleic acids, and other cellular structures. At the protein level, each of their proteins remains stable and retains activity at temperatures that would denature their mesophilic homologs. Conversely, cellular structures and proteins from thermophiles may not function optimally at moderate temperatures. These differences between thermophiles and mesophiles presumably present a barrier for evolutionary transitioning between the 2 lifestyles. Therefore, studying closely related thermophiles and mesophiles can help us determine how such lifestyle transitions may happen. The bacterial phylum Thermotogae contains hyperthermophiles, thermophiles, mesophiles, and organisms with temperature ranges wide enough to span both thermophilic and mesophilic temperatures. Genomic, proteomic, and physiological differences noted between other bacterial thermophiles and mesophiles are evident within the Thermotogae. We argue that the Thermotogae is an ideal group of organisms for understanding of the response to fluctuating temperature and of long-term evolutionary adaptation to a different growth temperature range.
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Affiliation(s)
- Stephen M.J. Pollo
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
| | - Olga Zhaxybayeva
- Department of Biological Sciences and Department of Computer Science, Dartmouth College, 78 College Street, Hanover, NH 03755, USA
| | - Camilla L. Nesbø
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway
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13
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Kanoksilapatham W, Keawram P, Gonzalez JM, Robb FT. Isolation, characterization, and survival strategies of Thermotoga sp. strain PD524, a hyperthermophile from a hot spring in Northern Thailand. Extremophiles 2015; 19:853-61. [PMID: 26101016 DOI: 10.1007/s00792-015-0761-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/26/2015] [Indexed: 11/30/2022]
Abstract
A hyperthermophilic Thermotoga sp. strain PD524 was isolated from a hot spring in Northern Thailand. Cells were long-curved rods (0.5-0.6 × 2.5-10 μm) surrounded by a typical outer membrane toga. Strain PD524 is aero-tolerant at 4 °C but is aero-sensitive at 80 °C. A heat resistant subpopulation was observed in late-stationary phase. Cells from late-stationary phase were revealed remarkably less sensitive to 0.001 % SDS treatment than cells from exponential phase. The temperature range for growth was 70-85 °C (opt. temp. 80 °C), pH range was 6-8.5 (opt. pH 7.5-8.0), and NaCl range of 0 to <10 g/L (opt. 0.5 g/L). Glucose, sucrose, maltose, fructose, xylose, mannose, arabinose, trehalose, starch, and cellobiose were utilized as growth substrates. Growth was inhibited by S(o). Growth yield was stimulated by SO 4 (=) but not by S2O 3 (=) and NO3 (-). Analysis of 16S rRNA gene sequence (KF164213) of strain PD524 revealed closest similarity (96 %) to Thermotoga maritima MSB8(T), T. neapolitana NES(T), T. petrophila RKU-1(T), and T. naphthophila RKU-10(T).
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Affiliation(s)
- Wirojne Kanoksilapatham
- Department of Microbiology, Faculty of Science, Silpakorn University, Nakhon Pathom, 73000, Thailand,
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14
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Microbial community composition and dynamics in high-temperature biogas reactors using industrial bioethanol waste as substrate. Appl Microbiol Biotechnol 2014; 98:9095-106. [DOI: 10.1007/s00253-014-5906-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 06/19/2014] [Accepted: 06/20/2014] [Indexed: 12/31/2022]
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15
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Göker M, Spring S, Scheuner C, Anderson I, Zeytun A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Genome sequence of the Thermotoga thermarum type strain (LA3(T)) from an African solfataric spring. Stand Genomic Sci 2014; 9:1105-17. [PMID: 25197486 PMCID: PMC4148951 DOI: 10.4056/sigs.3016383] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Thermotoga thermarum Windberger et al. 1989 is a member to the genomically well characterized genus Thermotoga in the phylum 'Thermotogae'. T. thermarum is of interest for its origin from a continental solfataric spring vs. predominantly marine oil reservoirs of other members of the genus. The genome of strain LA3T also provides fresh data for the phylogenomic positioning of the (hyper-)thermophilic bacteria. T. thermarum strain LA3(T) is the fourth sequenced genome of a type strain from the genus Thermotoga, and the sixth in the family Thermotogaceae to be formally described in a publication. Phylogenetic analyses do not reveal significant discrepancies between the current classification of the group, 16S rRNA gene data and whole-genome sequences. Nevertheless, T. thermarum significantly differs from other Thermotoga species regarding its iron-sulfur cluster synthesis, as it contains only a minimal set of the necessary proteins. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,039,943 bp long chromosome with its 2,015 protein-coding and 51 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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Affiliation(s)
- Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Stefan Spring
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Carmen Scheuner
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Iain Anderson
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Ahmet Zeytun
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Hope Tice
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Cliff Han
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Lynne A Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Ioanna Pagani
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Krishna Palaniappan
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Loren Hauser
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Yun-Juan Chang
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Cynthia D Jeffries
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Manfred Rohde
- HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - John C Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - James Bristow
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Jonathan A Eisen
- DOE Joint Genome Institute, Walnut Creek, California, USA ; University of California Davis Genome Center, Davis, California, USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Philip Hugenholtz
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Alla Lapidus
- Theodosius Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia ; Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia
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16
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Purwasena IA, Sugai Y, Sasaki K. Petrotoga japonica sp. nov., a thermophilic, fermentative bacterium isolated from Yabase Oilfield in Japan. Arch Microbiol 2014; 196:313-21. [PMID: 24604301 DOI: 10.1007/s00203-014-0972-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 02/21/2014] [Accepted: 02/24/2014] [Indexed: 11/25/2022]
Abstract
A gram-negative, motile, fermentative, thermophilic bacterium, designated AR80(T), was isolated from a high-temperature oil reservoir in Yabase Oilfield in Akita, Japan. Cells were rod-shaped, motile by means of polar flagella, and formed circular, convex, white colonies. The strain grew at 40-65 °C (optimum 60 °C), 0.5-9 % (w/v) NaCl (optimum 0.5-1 %), pH 6-9 (optimum pH 7.5), and elemental sulfur or thiosulfate serves as terminal electron acceptor. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain AR80(T) belonged to the genus Petrotoga and shared approximately 94.5 % sequence similarity with the type species of this genus. The G + C content of genomic DNA was 32.4 mol% while the value of DNA-DNA hybridization between the closest relative species Petrotoga miotherma and AR80(T) was 58.1 %. The major cellular fatty acids of strain AR80(T) consisted of 18:1 w9c, 16:0, and 16:1 w9c. Based on genetic and phenotypic properties, strain AR80(T) was different with other identified Petrotoga species and represents as a novel species, for which the name Petrotoga japonica sp. nov. is proposed. The type strain is AR80(T) (=NBRC 108752(T) = KCTC 15103(T) = HUT 8122(T)).
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MESH Headings
- Bacterial Typing Techniques
- Base Composition
- DNA, Bacterial/genetics
- Fatty Acids/chemistry
- Fermentation
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/classification
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/genetics
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/isolation & purification
- Hot Temperature
- Japan
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Oil and Gas Fields/microbiology
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Thiosulfates/metabolism
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Affiliation(s)
- Isty Adhitya Purwasena
- School of Life Science and Technology, Bandung Institute of Technology, Ganesha 10, Bandung, West Java, 40132, Indonesia,
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17
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Members of the Order Thermotogales: From Microbiology to Hydrogen Production. MICROBIAL BIOENERGY: HYDROGEN PRODUCTION 2014. [DOI: 10.1007/978-94-017-8554-9_9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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18
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Kosmotoga pacifica sp. nov., a thermophilic chemoorganoheterotrophic bacterium isolated from an East Pacific hydrothermal sediment. Extremophiles 2013; 18:81-8. [DOI: 10.1007/s00792-013-0596-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 10/30/2013] [Indexed: 10/26/2022]
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19
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Bhandari V, Gupta RS. Molecular signatures for the phylum (class) Thermotogae and a proposal for its division into three orders (Thermotogales, Kosmotogales ord. nov. and Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov., Kosmotogaceae fam. nov. and Petrotogaceae fam. nov.) and a new genus Pseudothermotoga gen. nov. with five new combinations. Antonie van Leeuwenhoek 2013; 105:143-68. [PMID: 24166034 DOI: 10.1007/s10482-013-0062-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 10/21/2013] [Indexed: 10/26/2022]
Abstract
All species from the phylum Thermotogae, class Thermotogae, are currently part of a single family, Thermotogaceae. Using genomic data from 17 Thermotogae species, detailed phylogenetic and comparative genomic analyses were carried out to understand their evolutionary relationships and identify molecular markers that are indicative of species relationships within the phylum. In the 16S rRNA gene tree and phylogenetic trees based upon two different large sets of proteins, members of the phylum Thermotogae formed a number of well-resolved clades. Character compatibility analysis on the protein sequence data also recovered a single largest clique that exhibited similar topology to the protein trees and where all nodes were supported by multiple compatible characters. Comparative genomic analyses have identified 85 molecular markers, in the form of conserved signature indels (CSIs), which are specific for different observed clades of Thermotogae at multiple phylogenetic depths. Eleven of these CSIs were specific for the phylum Thermotogae whereas nine others supported a clade comprising of the genera Thermotoga, Thermosipho and Fervidobacterium. Ten other CSIs provided evidence that the genera Thermosipho and Fervidobacterium shared a common ancestor exclusive of the other Thermotogae and four and eight CSIs in other proteins were specific for the genera Thermosipho and Fervidobacterium, respectively. Two other deep branching clades, one consisting of the genera Kosmotoga and Mesotoga and the other comprising of the genera Petrotoga and Marinitoga, were also supported by multiple CSIs. Based upon the consistent branching of the Thermotogae species using different phylogenetic approaches, and numerous identified CSIs supporting the distinctness of different clades, it is proposed that the class Thermotogae should be divided into three orders (Thermotogales, Kosmotogales ord. nov. and Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov., Kosmotogaceae fam. nov. and Petrotogaceae fam. nov.). Additionally, the results of our phylogenetic/compatibility studies along with the species distribution patterns of 22 identified CSIs, provide compelling evidence that the current genus Thermotoga is comprised of two evolutionary distinct groups and that it should be divided into two genera. It is proposed that the emended genus Thermotoga should retain only the species Thermotoga maritima, Tt. neapolitana, Tt. petrophila, Tt. naphthophila, Thermotoga sp. EMP, Thermotoga sp. A7A and Thermotoga sp. RQ2 while the other Thermotoga species (viz. Tt. lettingae, Tt. thermarum, Tt. elfii, Tt. subterranean and Tt. hypogea) be transferred to a new genus, Pseudothermotoga gen. nov.
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Affiliation(s)
- Vaibhav Bhandari
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
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20
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Starting Up Microbial Enhanced Oil Recovery. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 142:1-94. [DOI: 10.1007/10_2013_256] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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21
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Ben Hania W, Godbane R, Postec A, Hamdi M, Ollivier B, Fardeau ML. Defluviitoga tunisiensis gen. nov., sp. nov., a thermophilic bacterium isolated from a mesothermic and anaerobic whey digester. Int J Syst Evol Microbiol 2012; 62:1377-1382. [DOI: 10.1099/ijs.0.033720-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain SulfLac1T, a thermophilic, anaerobic and slightly halophilic, rod-shaped bacterium with a sheath-like outer structure (toga), was isolated from a whey digester in Tunisia. The strain’s non-motile cells measured 3–30×1 µm and appeared singly, in pairs or as long chains. The novel strain reduced thiosulfate and elemental sulfur, but not sulfate or sulfite, into sulfide. It grew at 37–65 °C (optimum 55 °C), at pH 6.5–7.9 (optimum pH 6.9) and with 0.2–3 % (w/v) NaCl (optimum 0.5 %). The G+C content of the strain’s genomic DNA was 33.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SulfLac1T was most closely related to
Petrotoga mobilis
(91.4 % sequence similarity). Based on phenotypic, phylogenetic and chemotaxonomic evidence, strain SulfLac1T represents a novel species of a new genus within the order
Thermotogales
, for which the name Defluviitoga tunisiensis gen. nov., sp. nov. is proposed. The type strain of the type species is SulfLac1T ( = DSM 23805T = JCM 17210T).
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Affiliation(s)
- Wajdi Ben Hania
- Laboratoire d’Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie, Centre Urbain Nord, BP 676, 1080 Tunis, Tunisia
- Laboratoire de Microbiologie H10, UMR 235, Aix-Marseille Univ., Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Ramzi Godbane
- Laboratoire d’Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie, Centre Urbain Nord, BP 676, 1080 Tunis, Tunisia
- Laboratoire de Microbiologie H10, UMR 235, Aix-Marseille Univ., Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Anne Postec
- Laboratoire de Microbiologie H10, UMR 235, Aix-Marseille Univ., Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Moktar Hamdi
- Laboratoire d’Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie, Centre Urbain Nord, BP 676, 1080 Tunis, Tunisia
| | - Bernard Ollivier
- Laboratoire de Microbiologie H10, UMR 235, Aix-Marseille Univ., Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Marie-Laure Fardeau
- Laboratoire de Microbiologie H10, UMR 235, Aix-Marseille Univ., Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
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22
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Dahle H, Hannisdal B, Steinsbu BO, Ommedal H, Einen J, Jensen S, Larsen O, Ovreås L, Norland S. Evolution of temperature optimum in Thermotogaceae and the prediction of trait values of uncultured organisms. Extremophiles 2011; 15:509-16. [PMID: 21638056 PMCID: PMC3119804 DOI: 10.1007/s00792-011-0381-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Accepted: 05/20/2011] [Indexed: 11/28/2022]
Abstract
Quantitative characterization of the mode and rate of phenotypic evolution is rarely applied to prokaryotes. Here, we present an analysis of temperature optimum (Topt) evolution in the thermophilic family Thermotogaceae, which has a large number of cultured representatives. We use log-rate-interval analysis to show that Topt evolution in Thermotogaceae is consistent with a Brownian motion (BM) evolutionary model. The properties of the BM model are used to a establish confidence intervals on the unknown phenotypic trait value of an uncultured organism, given its distance to a close relative with known trait value. Cross-validation by bootstrapping indicates that the predictions are robust.
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Affiliation(s)
- Håkon Dahle
- Centre for Geobiology, University of Bergen, Allegaten, Norway.
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23
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Phylogeny and molecular signatures for the phylum Thermotogae and its subgroups. Antonie van Leeuwenhoek 2011; 100:1-34. [DOI: 10.1007/s10482-011-9576-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Accepted: 03/11/2011] [Indexed: 11/25/2022]
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24
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Nunoura T, Hirai M, Imachi H, Miyazaki M, Makita H, Hirayama H, Furushima Y, Yamamoto H, Takai K. Kosmotoga arenicorallina sp. nov. a thermophilic and obligately anaerobic heterotroph isolated from a shallow hydrothermal system occurring within a coral reef, southern part of the Yaeyama Archipelago, Japan, reclassification of Thermococcoides shengliensis as Kosmotoga shengliensis comb. nov., and emended description of the genus Kosmotoga. Arch Microbiol 2010; 192:811-9. [PMID: 20694719 DOI: 10.1007/s00203-010-0611-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2010] [Revised: 07/20/2010] [Accepted: 07/26/2010] [Indexed: 11/28/2022]
Abstract
A novel thermophilic and sulfur-reducing bacterium, strain S304(T), was isolated from the Taketomi submarine hot spring shallow hydrothermal field located at southern part of the Yaeyama Archipelago, Japan. The cells were non-motile short thick rods or oval cocci 1.1-2.7 μm in length and 1.1-1.9 μm in width. Strain S304(T) was an obligately anaerobic heterotroph and sulfur reduction stimulates growth. Growth was observed between 50-65°C (optimum 60°C), pH 6.2-8.0 (optimum pH 7.1), 1.0-6.0% NaCl concentration (optimum 3.0%). The fatty acid composition was C(16:0) (71.4%), C(18:0) (20.9%) and C(18:1) (7.7%). The G + C content of genomic DNA was 40.8 mol%. The 16S rRNA gene sequence analysis indicated that strain S304(T) belonged to the genus Kosmotoga. Based on physiological and phylogenetic features of a new isolate, we propose new species in the genus Kosmotoga: the type strain of Kosmotoga arenicorallina sp. nov is S304(T) (=JCM 15790(T) = DSM22549(T)). Thermococcoides shengliensis 2SM-2(T) is phylogenetically associated with Kosmotoga olearia 14.5.1(T). Based on the phylogenetic relationship between Thermococcoides shengliensis 2SM-2(T) and Kosmotoga olearia 14.5.1(T), we propose the reclassification of Thermococcoides shengliensis as Kosmotoga shengliensis comb. nov. (type strain 2SM-2(T)). In addition, an emended description of the genus Kosmotoga is proposed.
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Affiliation(s)
- Takuro Nunoura
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology, Yokosuka, Japan.
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