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Böer T, Schüler MA, Lüschen A, Eysell L, Dröge J, Heinemann M, Engelhardt L, Basen M, Daniel R, Poehlein A. Isolation and characterization of novel acetogenic strains of the genera Terrisporobacter and Acetoanaerobium. Front Microbiol 2024; 15:1426882. [PMID: 39021630 PMCID: PMC11253131 DOI: 10.3389/fmicb.2024.1426882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 06/13/2024] [Indexed: 07/20/2024] Open
Abstract
Due to their metabolic versatility in substrate utilization, acetogenic bacteria represent industrially significant production platforms for biotechnological applications such as syngas fermentation, microbial electrosynthesis or transformation of one-carbon substrates. However, acetogenic strains from the genera Terrisporobacter and Acetoanaerobium remained poorly investigated for biotechnological applications. We report the isolation and characterization of four acetogenic Terrisporobacter strains and one Acetoanaerobium strain. All Terrisporobacter isolates showed a characteristic growth pattern under a H2 + CO2 atmosphere. An initial heterotrophic growth phase was followed by a stationary growth phase, where continuous acetate production was indicative of H2-dependent acetogenesis. One of the novel Terrisporobacter isolates obtained from compost (strain COMT) additionally produced ethanol besides acetate in the stationary growth phase in H2-supplemented cultures. Genomic and physiological characterizations showed that strain COMT represented a novel Terrisporobacter species and the name Terrisporobacter vanillatitrophus is proposed (=DSM 116160T = CCOS 2104T). Phylogenomic analysis of the novel isolates and reference strains implied the reclassification of the T. petrolearius/T. hibernicus phylogenomic cluster to the species T. petrolearius and of the A. noterae/A. sticklandii phylogenomic cluster to the species A. sticklandii. Furthermore, we provide first insights into active prophages of acetogens from the genera Terrisporobacter and Acetoanaerobium.
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Affiliation(s)
- Tim Böer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Miriam Antonia Schüler
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Alina Lüschen
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Lena Eysell
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Jannina Dröge
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Melanie Heinemann
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Lisa Engelhardt
- Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Mirko Basen
- Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
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Postec A, Galès G, Prime AH, Bartoli M, Price RE, Vandecasteele C, Erauso G. Marinitoga aeolica sp. nov., a novel thermophilic anaerobic heterotroph isolated from a shallow hydrothermal field of Panarea Island in the Aeolian archipelago, Italy. Int J Syst Evol Microbiol 2023; 73. [PMID: 38015056 DOI: 10.1099/ijsem.0.006186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
A novel thermophilic strain, designated BP5-C20AT, was isolated from the shallow hydrothermal field of the Panarea island in the Aeolian archipelago close to Sicily, Italy. Cells are motile rods surrounded with a 'toga', Gram-stain-negative and display a straight to curved morphology during the exponential phase. Strain BP5-C20AT is thermophilic (optimum 55 °C), moderately acidophilic (optimum pH 5.6) and halotolerant (optimum 25 g l-1 NaCl). It can use yeast extract, peptone and tryptone. It uses the following carbohydrates: cellobiose, fructose, glucose, maltose, starch, sucrose and xylan. Elemental sulphur is used as an electron acceptor and reduced to hydrogen sulphide. The predominant cellular fatty acid is C16 : 0. Phylogenetic analysis showed that strain BP5-C20AT shared 97.3 % 16S rRNA gene sequence identity with the closest related species Marinitoga lauensis LG1T. The complete genome of strain BP5-C20AT is 2.44 Mb in size with a G+C content of 27.3 mol%. The dDDH and ANI values between the genomes of strains BP5-C20AT and M. lauensis LG1T are 31.0 and 85.70% respectively. Finally, from its physiological, metabolic and genomic characteristics, strain BP5-C20AT (=DSM 112332T=JCM 39183 T) is proposed as representative of a novel species of the genus Marinitoga named Marinitoga aeolica sp. nov. and belonging to the order Petrotogales, in the phylum Thermotogota.
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Affiliation(s)
- Anne Postec
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Grégoire Galès
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Anne-Hélène Prime
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Manon Bartoli
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Roy E Price
- Stony Brook University, SoMAS Stony Brook, New York 11794, USA
| | - Céline Vandecasteele
- INRAE, US 1426, GeT-PlaGe, Genotoul, France Genomique, Université Fédérale de Toulouse, Castanet-Tolosan, France
| | - Gaël Erauso
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
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Popall RM, Postec A, Lecoeuvre A, Quéméneur M, Erauso G. Metabolic challenges and key players in serpentinite-hosted microbial ecosystems. Front Microbiol 2023; 14:1197823. [PMID: 37555067 PMCID: PMC10404738 DOI: 10.3389/fmicb.2023.1197823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/29/2023] [Indexed: 08/10/2023] Open
Abstract
Serpentinite-hosted systems are amongst the most challenging environments for life on Earth. Serpentinization, a geochemical alteration of exposed ultramafic rock, produces hydrothermal fluids enriched in abiotically derived hydrogen (H2), methane (CH4), and small organic molecules. The hyperalkaline pH of these fluids poses a great challenge for metabolic energy and nutrient acquisition, curbing the cellular membrane potential and limiting electron acceptor, carbon, and phosphorous availability. Nevertheless, serpentinization supports the growth of diverse microbial communities whose metabolic make-up might shed light on the beginning of life on Earth and potentially elsewhere. Here, we outline current hypotheses on metabolic energy production, carbon fixation, and nutrient acquisition in serpentinizing environments. A taxonomic survey is performed for each important metabolic function, highlighting potential key players such as H2 and CH4 cycling Serpentinimonas, Hydrogenophaga, Methanobacteriales, Methanosarcinales, and novel candidate phyla. Methodological biases of the available data and future approaches are discussed.
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Affiliation(s)
| | | | | | | | - Gaël Erauso
- Aix-Marseille Univ, Univ Toulon, CNRS, IRD, MIO, Marseille, France
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Ma Y, You F, Parry D, Urban A, Huang L. Adaptive growth and acidogenic fermentation performance of haloalkaliphilic bacterial communities enriched from biofilms colonising strongly alkaline and saline bauxite residue. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159131. [PMID: 36183768 DOI: 10.1016/j.scitotenv.2022.159131] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
The present study aimed to characterise the adaptive growth and acidogenic fermentation performance of haloalkaliphilic bacteria sourced from field biofilms colonising seawater-treated bauxite residue, under moderate and extremely alkaline pH conditions (8.5 to 10.8) and coupled saline (EC ≈ 50 mS/cm) conditions. The haloalkaliphilic bacterial communities demonstrated strong adaptiveness to the increasing pH from 8.5 to 10.8. The dominant groups were Exiguobacterales and Bacillales at pH 8.5 and 10, but Lactobacillales and Bacillales at pH 10.8. The exposure to pH 10.8 initially delayed bacterial growth in the first 24 h, but which rapidly recovered to a peak rate at 48 h similar to that in the pH 10 treatment. Correspondingly, lactic acid concentration at pH 10.8 rapidly rose to as high as >2000 mg/L at 48 h. Bacterial growth and organic acid production were positively related to carbohydrate supply. Overall, these bacterial groups fermented glucose to produce mainly lactic acid (>80 %) and other acids (such as acetic acid, formic acid, and succinic acid), leading to 0.5-2.0 units of pH reduction, despite the strong buffering capacity in the culture solution. The bacteria could up-regulate their phosphatase activity to mineralise the organic P in the basal nutrient broth, but increasing soluble phosphate-P at a 1:10 of glucose-C was beneficial. The biofilm-sourced bacteria communities contained redundant fermentative haloalkaliphilic groups which were adaptive to strongly alkaline pH and saline conditions.
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Affiliation(s)
- Yuanying Ma
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Fang You
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - David Parry
- Rio Tinto, Brisbane, Queensland 4000, Australia
| | - Anja Urban
- Queensland Alumina Limited, Gladstone, Queensland 4680, Australia
| | - Longbin Huang
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
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Wang C, Wei W, Chen Z, Wang Y, Chen X, Ni BJ. Polystyrene microplastics and nanoplastics distinctively affect anaerobic sludge treatment for hydrogen and methane production. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:158085. [PMID: 35981580 DOI: 10.1016/j.scitotenv.2022.158085] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 06/15/2023]
Abstract
Microplastics and nanoplastics generally accumulated in waste activated sludge (WAS) after biological wastewater treatment. Currently, researches mainly focused on how plastics affected a particular sludge treatment method, without the comparison of different sludge systems. Herein, distinct responses of hydrogen-producing and methane-producing sludge systems were comprehensively evaluated with polystyrene microplastics (PS-MPs) and nanoplastics (PS-NPs) existence. Experimental results showed that PS particles would stimulate inhibition on anaerobic gas production except that PS-MPs were conducive to hydrogen accumulation, which was caused by the enhanced solubilization. Mechanistic investigation demonstrated that severe inhibition of PS-NPs to hydrogen production was derived from the excessively inhibitory hydrolysis despite of improving solubilization. Varying degrees of inhibition to acidification and methanation collectively contributed to reduced methane accumulation with exposure to PS-MPs and PS-NPs. Excessive oxidative stress would be generated in the presence of PS-MPs or PS-NPs, deteriorating microbial activities and richness of species responsible for hydrogen or methane production.
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Affiliation(s)
- Chen Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Wei Wei
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Zhijie Chen
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Yun Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Xueming Chen
- Fujian Provincial Engineering Research Center of Rural Waste Recycling Technology, College of Environment and Safety Engineering, Fuzhou University, Fujian 350116, China
| | - Bing-Jie Ni
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia.
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Xu J, Kumar Khanal S, Kang Y, Zhu J, Huang X, Zong Y, Pang W, Surendra KC, Xie L. Role of interspecies electron transfer stimulation in enhancing anaerobic digestion under ammonia stress: Mechanisms, advances, and perspectives. BIORESOURCE TECHNOLOGY 2022; 360:127558. [PMID: 35780934 DOI: 10.1016/j.biortech.2022.127558] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Ammonia stress is a commonly encountered issue in anaerobic digestion (AD) process when treating proteinaceous substrates. The enhanced relationship between syntrophic bacteria and methanogens triggered by interspecies electron transfer (IET) stimulation is one of the potential mechanisms for an improved methane yield from the AD plant under ammonia-stressed condition. There is, however, lack of synthesized information on the mechanistic understanding of IET facilitation in the ammonia-stressed AD processes. This review critically discusses recovery of AD system from ammonia-stressed condition, focusing on H2 transfer, redox compound-mediated IET, and conductive material-induced direct IET. The effects and the associated mechanisms of IET stimulation on mitigating ammonia stress and promoting methanogenesis were elucidated. Finally, prospects and challenges of IET stimulation were critically discussed. This review highlights, for the first time, the critical role of IET stimulation in enhancing AD process under ammonia-stressed condition.
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Affiliation(s)
- Jun Xu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China
| | - Samir Kumar Khanal
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i at Mānoa, 1955 East-West Road, Agricultural Science Building 218, Honolulu, HI 96822, USA
| | - Yurui Kang
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China
| | - Jiaxin Zhu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China
| | - Xia Huang
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China
| | - Yang Zong
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China
| | - Weihai Pang
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China
| | - K C Surendra
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i at Mānoa, 1955 East-West Road, Agricultural Science Building 218, Honolulu, HI 96822, USA; Global Institute for Interdisciplinary Studies, 44600 Kathmandu, Nepal
| | - Li Xie
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, 1239 Siping Road, Shanghai 200092, PR China.
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7
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Jia T, Zhang L, Zhao Q, Peng Y. The effect of biofilm growth on the sulfur oxidation pathway and the synergy of microorganisms in desulfurization reactors under different pH conditions. JOURNAL OF HAZARDOUS MATERIALS 2022; 432:128638. [PMID: 35306408 DOI: 10.1016/j.jhazmat.2022.128638] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/12/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
Biofilm growth affects the oxygen transfer in biofilm and thus the oxidation pathway of sulfur and the synergy of microorganisms. In this study, the effect of biofilm growth on the oxidation pathway of H2S and the synergy of microorganisms in desulfurization reactors under different pH conditions was first discussed to enhance the understanding of desulfurization process. A biotrickling filter (BTF) was operated for 168 days under acidic condition (pH<4.7) and 32 days under alkaline condition (7.0 <pH<10.2). In acidic period, the average growth mass (AGM) of biofilm was 0.04 g/L-BTF/d, and most of S-H2S was converted to S-SO42- (>89.0%). In alkaline period, the AGM raised to 0.97 g/L-BTF/d, and 77.0% of S-H2S was transferred to elemental sulfur (S0) and polysulfanes (R-Sx-R) accumulated in biofilm. The increase of biofilm and sulfur-oxidizing bacteria activity limited the oxygen transfer in alkaline biofilm, leading to the accumulation of S0 and the emergence of an obligate anaerobe- Acetoanaerobium (8.1%). The formation of R-Sx-R may be due to the reaction of S0 with thiols produced by a thiol-producing bacterium- Pseudomonas (6.7%). The uneven distribution of oxygen in biofilm caused by biofilm growth complicated the transfer pathway of sulfur and the synergy of microorganisms in desulfurization system.
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Affiliation(s)
- Tipei Jia
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, China
| | - Liang Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, China
| | - Qi Zhao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, China.
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Zhang J, Liu H, Zhang Y, Wu P, Li J, Ding P, Jiang Q, Cui MH. Heterotrophic precultivation is a better strategy than polarity reversal for the startup of acetate microbial electrosynthesis reactor. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2021.108319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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Duan Y, Zhou A, Yue X, Wang S, Gao Y, Luo Y, Zhang X, Zhang J. Initial-alkaline motivated fermentation of fine-sieving fractions and its effect on properties of cellulosic components. CHEMOSPHERE 2021; 284:131275. [PMID: 34323810 DOI: 10.1016/j.chemosphere.2021.131275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 05/26/2021] [Accepted: 06/15/2021] [Indexed: 06/13/2023]
Abstract
Exploration of value-added products from wastewater treatment plants (WWTPs) was promising for its sustainable development. This study simultaneously addressed the possibility of volatile fatty acids (VFAs) production boost and cellulosic components recovery from fine-sieving fractions (FSF) under initial alkaline conditions. The step utilization of FSF was relatively untapped in similar literatures. The effect of different initial pH values with 8.5, 9.5 and 10.5 (defined as F-8.5, F-9.5 and F-10.5) on fermentation performance were investigated. Then, the fermentation residues were collected to evaluate the changes in chemical structure and thermodynamic properties by fourier transform infrared spectroscopy (FTIR) and thermo-gravimetric (TG) analysis. Furthermore, analysis of the changes in microbial community structure and the interaction between functional genus and performance parameters were undertaken by high throughput sequencing and canonical correspondence analysis (CCA). Results showed that F-10.5 obtained the highest VFAs yields of 234 mg/g VSS, due to efficient polysaccharides release and inhibited methane production. However, high alkaline intensity caused proteins denaturation. Acidogenesis kinetics suggested that the fermentation rate was chemical-dominated. Although crystalline structure was more disordered with increasing alkalinity, the weight loss was lower than 2.5%, making it possible to recover cellulose from fermented residues. Interaction between functional genus and performance parameters revealed the microbial mechanism during the alkaline fermentation. Consequently, the initial-alkaline motivated fermentation was proved to be a promising technology in value-added products recovery to be cost economic, energy positive and environmental friendly.
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Affiliation(s)
- Yanqing Duan
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, PR China
| | - Aijuan Zhou
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, PR China; Shanxi Engineer Research Institute of Sludge Disposition and Resources, Taiyuan University of Technology, Taiyuan, 030024, PR China.
| | - Xiuping Yue
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, PR China; Shanxi Engineer Research Institute of Sludge Disposition and Resources, Taiyuan University of Technology, Taiyuan, 030024, PR China
| | - Sufang Wang
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, PR China
| | - Yanjuan Gao
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, PR China
| | - Yanhong Luo
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, PR China; North University of China, Taiyuan, 030051, PR China
| | - Xiao Zhang
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, PR China
| | - Jiaguang Zhang
- College of Civil Engineering, Taiyuan University of Technology, Taiyuan, 030024, PR China
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Procaryotic Diversity and Hydrogenotrophic Methanogenesis in an Alkaline Spring (La Crouen, New Caledonia). Microorganisms 2021; 9:microorganisms9071360. [PMID: 34201651 PMCID: PMC8307142 DOI: 10.3390/microorganisms9071360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/17/2021] [Accepted: 06/19/2021] [Indexed: 01/01/2023] Open
Abstract
(1) Background: The geothermal spring of La Crouen (New Caledonia) discharges warm (42 °C) alkaline water (pH~9) enriched in dissolved nitrogen with traces of methane, but its microbial diversity has not yet been studied. (2) Methods: Cultivation-dependent and -independent methods (e.g., Illumina sequencing and quantitative PCR based on 16S rRNA gene) were used to describe the prokaryotic diversity of this spring. (3) Results: Prokaryotes were mainly represented by Proteobacteria (57% on average), followed by Cyanobacteria, Chlorofexi, and Candidatus Gracilibacteria (GN02/BD1-5) (each > 5%). Both potential aerobes and anaerobes, as well as mesophilic and thermophilic microorganisms, were identified. Some of them had previously been detected in continental hyperalkaline springs found in serpentinizing environments (The Cedars, Samail, Voltri, and Zambales ophiolites). Gammaproteobacteria, Ca. Gracilibacteria and Thermotogae were significantly more abundant in spring water than in sediments. Potential chemolithotrophs mainly included beta- and gammaproteobacterial genera of sulfate-reducers (Ca. Desulfobacillus), methylotrophs (Methyloversatilis), sulfur-oxidizers (Thiofaba, Thiovirga), or hydrogen-oxidizers (Hydrogenophaga). Methanogens (Methanobacteriales and Methanosarcinales) were the dominant Archaea, as found in serpentinization-driven and deep subsurface ecosystems. A novel alkaliphilic hydrogenotrophic methanogen (strain CAN) belonging to the genus Methanobacterium was isolated, suggesting that hydrogenotrophic methanogenesis occurs at La Crouen.
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Analysis of bacterial flora of indigo fermentation fluids utilizing composted indigo leaves (sukumo) and indigo extracted from plants (Ryukyu-ai and Indian indigo). J Biosci Bioeng 2021; 132:279-286. [PMID: 34127379 DOI: 10.1016/j.jbiosc.2021.05.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 01/21/2023]
Abstract
Indigo is a fabric dye that requires reduction by microbial activity or chemical reagents to render it soluble in water. Sources of indigo for fermentation are primarily divided into composted indigo-containing plants and indigo extracted from plants. To elucidate the factors responsible for bacterial diversity, and for sustaining reduced state of indigo in different preparations, this study assessed fermentation-derived fluids using composted plant leaves, sukumo, and extracted indigo (Ryukyu-ai paste, and Indian indigo cake) prepared using different procedures. Regardless of the indigo source, obligate anaerobic bacteria, including the families Proteinivoraceae and Tissierellaceae, predominate (16.9-46.1%), suggesting their high affinity for this fermentation ecosystem (hyperalkaline and low redox potential). Moreover, bacterial communities in sukumo fermentations are more diverse than those from indigo extracts with the diversity tending to increase based on the fermentation period. Our results further suggest that the microbiota composition in sukumo fermentation is associated with the various bacterial nutrients derived from sukumo, including seed microorganisms. In addition, the debris derived from sukumo can reduce the pH stress experienced by the microorganisms. Further, regardless of 5.4 years difference in the fermentation age, the bacterial flora in two Ryukyu-ai batches exhibit similar features with low microbial diversities. The uniformity of the nutrient, along with the simple, yet strong, bacterial network in Ryukyu-ai fluids may be responsible for the stable bacterial flora composition. Taken together, these results indicate that the microbiota in indigo fermentation is highly influenced by the seed culture, the nutrient derived from raw materials, and the fermentation conditions.
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Quéméneur M, Erauso G, Bartoli M, Vandecasteele C, Wils L, Gil L, Monnin C, Pelletier B, Postec A. Alkalicella caledoniensis gen. nov., sp. nov., a novel alkaliphilic anaerobic bacterium isolated from 'La Crouen' alkaline thermal spring, New Caledonia. Int J Syst Evol Microbiol 2021; 71. [PMID: 34003738 DOI: 10.1099/ijsem.0.004810] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel anaerobic, alkaliphilic, mesophilic, Gram-stain-positive, endospore-forming bacterium was isolated from an alkaline thermal spring (42 °C, pH 9.0) in New Caledonia. This bacterium, designated strain LB2T, grew at 25-50 °C (optimum, 37 °C) and pH 8.2-10.8 (optimum, pH 9.5). Added NaCl was not required for growth (optimum, 0-1 %) but was tolerated up to 7 %. Strain LB2T utilized a limited range of substrates, such as peptone, pyruvate, yeast extract and xylose. End products detected from pyruvate fermentation were acetate and formate. Both ferric citrate and thiosulfate were used as electron acceptors. Elemental sulphur, nitrate, nitrite, fumarate, sulphate, sulfite and DMSO were not used as terminal electron acceptors. The two major cellular fatty acids were iso-C15 : 0 and C16 : 0. The genome consists of a circular chromosome (3.7 Mb) containing 3626 predicted protein-encoding genes with a G+C content of 36.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the isolate is a member of the family Proteinivoraceae, order Clostridiales within the phylum Firmicutes. Strain LB2T was most closely related to the thermophilic Anaerobranca gottschalkii LBS3T (93.2 % 16S rRNA gene sequence identity). Genome-based analysis of average nucleotide identity and digital DNA-DNA hybridization of strain LB2T with A. gottschalkii LBS3T showed respective values of 70.8 and 13.4 %. Based on phylogenetic, genomic, chemotaxonomic and physiological properties, strain LB2T is proposed to represent the first species of a novel genus, for which the name Alkalicella caledoniensis gen. nov., sp. nov. is proposed (type strain LB2T=DSM 100588T=JCM 30958T).
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Affiliation(s)
- Marianne Quéméneur
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Gaël Erauso
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Manon Bartoli
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | | | - Laura Wils
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Lisa Gil
- INRAe, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Christophe Monnin
- GET UMR5563 (CNRS/UPS/IRD/CNES), Géosciences Environnement Toulouse, 14 Avenue Edouard Belin, 31400 Toulouse, France
| | - Bernard Pelletier
- Centre IRD de Nouméa, 101 Promenade Roger Laroque, BP A5 - 98848 Nouméa cedex, Nouvelle-Calédonie
| | - Anne Postec
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
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Zhu K, Zhang L, Wang X, Mu L, Li C, Li A. Inhibition of norfloxacin on anaerobic digestion: Focusing on the recoverability and shifted microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 752:141733. [PMID: 32896787 DOI: 10.1016/j.scitotenv.2020.141733] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 05/23/2023]
Abstract
Antibacterial properties of norfloxacin (NOR) could cause adverse impact on engineered biological process. In this study, the objective was to investigate the inhibitory effects of NOR on anaerobic digestion focusing on the recoverability and microbial community changes. The effects of different concentrations of NOR on anaerobic digestion were studied with three continuous feed cycles. Results showed that NOR seriously inhibited the methane production with an 50% inhibitory concentration (IC50) of 0.41 mM. In addition, with extending of exposure time, inhibitory effect increasingly strengthened and the IC50 values decreased to 0.16 mM and 0.07 mM in the second and third feeding cycle, respectively. However, when the inhibitor in supernatant was removed, the performance recovered and the relative methane yield increased by 9 times from 25.38 mL/g VS to 257.05 mL/g VS. The transformation of NOR showed that the degradation of NOR in the anaerobic digestion was difficult and the recovery was due to the removal of NOR. The microbial analysis revealed that the inhibition of NOR on bacteria of Candidatus_Cloacimonas, Petrimonas, Ercella, Sphaerochaeta and hydrogenotrophic methanogens of Methanoculleus and Methanobacterium was recoverable when NOR was removed. However, it was irreversible for acetoclastic methanogen of Methanosaeta. These findings provided comprehensive understanding on the characteristics of NOR inhibition and also provided feasible strategy to recover the NOR inhibited anaerobic digestion.
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Affiliation(s)
- Kongyun Zhu
- Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, PR China
| | - Lei Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, PR China.
| | - Xuexue Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, PR China
| | - Lan Mu
- Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, PR China
| | - Changjing Li
- Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, PR China
| | - Aimin Li
- Key Laboratory of Industrial Ecology and Environmental Engineering, School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, PR China
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Postec A, Quéméneur M, Lecoeuvre A, Chabert N, Joseph M, Erauso G. Alkaliphilus serpentinus sp. nov. and Alkaliphilus pronyensis sp. nov., two novel anaerobic alkaliphilic species isolated from the serpentinite-hosted Prony Bay Hydrothermal Field (New Caledonia). Syst Appl Microbiol 2020; 44:126175. [PMID: 33422701 DOI: 10.1016/j.syapm.2020.126175] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 11/26/2022]
Abstract
Two novel anaerobic alkaliphilic strains, designated as LacTT and LacVT, were isolated from the Prony Bay Hydrothermal Field (PBHF, New Caledonia). Cells were motile, Gram-positive, terminal endospore-forming rods, displaying a straight to curved morphology during the exponential phase. Strains LacTT and LacVT were mesophilic (optimum 30°C), moderately alkaliphilic (optimum pH 8.2 and 8.7, respectively) and halotolerant (optimum 2% and 2.5% NaCl, respectively). Both strains were able to ferment yeast extract, peptone and casamino acids, but only strain LacTT could use sugars (glucose, maltose and sucrose). Both strains disproportionated crotonate into acetate and butyrate. Phylogenetic analysis revealed that strains LacTT and LacVT shared 96.4% 16S rRNA gene sequence identity and were most closely related to A. peptidifermentans Z-7036, A. namsaraevii X-07-2 and A. hydrothermalis FatMR1 (95.7%-96.3%). Their genome size was of 3.29Mb for strain LacTT and 3.06Mb for strain LacVT with a G+C content of 36.0 and 33.9mol%, respectively. The ANI value between both strains was 73.2 %. Finally, strains LacTT (=DSM 100337=JCM 30643) and LacVT (=DSM 100017=JCM 30644) are proposed as two novel species of the genus Alkaliphilus, order Clostridiales, phylum Firmicutes, Alkaliphilus serpentinus sp. nov. and Alkaliphilus pronyensis sp. nov., respectively. The genomes of the three Alkaliphilus species isolated from PBHF were consistently detected in the PBHF chimney metagenomes, although at very low abundance, but not significantly in the metagenomes of other serpentinizing systems (marine or terrestrial) worldwide, suggesting they represent indigenous members of the PBHF microbial ecosystem.
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Affiliation(s)
- Anne Postec
- AixMarseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France.
| | - Marianne Quéméneur
- AixMarseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Aurélien Lecoeuvre
- Université de Paris, Institut de Physique du Globe de Paris, CNRS UMR 7154, Paris, France
| | - Nicolas Chabert
- AixMarseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Manon Joseph
- AixMarseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Gaël Erauso
- AixMarseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
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Lang SQ, Brazelton WJ. Habitability of the marine serpentinite subsurface: a case study of the Lost City hydrothermal field. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020; 378:20180429. [PMID: 31902336 PMCID: PMC7015304 DOI: 10.1098/rsta.2018.0429] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
The Lost City hydrothermal field is a dramatic example of the biological potential of serpentinization. Microbial life is prevalent throughout the Lost City chimneys, powered by the hydrogen gas and organic molecules produced by serpentinization and its associated geochemical reactions. Microbial life in the serpentinite subsurface below the Lost City chimneys, however, is unlikely to be as dense or active. The marine serpentinite subsurface poses serious challenges for microbial activity, including low porosities, the combination of stressors of elevated temperature, high pH and a lack of bioavailable ∑CO2. A better understanding of the biological opportunities and challenges in serpentinizing systems would provide important insights into the total habitable volume of Earth's crust and for the potential of the origin and persistence of life in Earth's subsurface environments. Furthermore, the limitations to life in serpentinizing subsurface environments on Earth have significant implications for the habitability of subsurface environments on ocean worlds such as Europa and Enceladus. Here, we review the requirements and limitations of life in serpentinizing systems, informed by our research at the Lost City and the underwater mountain on which it resides, the Atlantis Massif. This article is part of a discussion meeting issue 'Serpentinite in the Earth System'.
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Affiliation(s)
- Susan Q. Lang
- School of the Earth, Ocean, and Environment, University of South Carolina, Columbia, SC 29208, USA
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16
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Zhang L, Long B, Wu J, Cheng Y, Zhang B, Zeng Y, Huang S, Zeng M. Evolution of microbial community during dry storage and recovery of aerobic granular sludge. Heliyon 2019; 5:e03023. [PMID: 31890963 PMCID: PMC6926229 DOI: 10.1016/j.heliyon.2019.e03023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/18/2019] [Accepted: 12/06/2019] [Indexed: 12/15/2022] Open
Abstract
Aerobic granular sludge (AGS) was imbedded in agar and stored at 4 °C for 30 days, and then the stored granules were recovered in a sequencing batch reactor fed real wastewater within 11 days. Variations in microbial community compositions were investigated during dry storage and recovery of AGS, aiming to elucidate the mechanism of granular stability loss and recovery. The storage and recovery of AGS involved microbial community evolution. The dominant bacterial genera of the mature AGS were Zoogloea (relative abundance of 22.39%), Thauera (16.03%) and Clostridium_sensu_stricto (11.17%), and those of the stored granules were Acidovorax (26.79%), Macellibacteroides (12.83%) and Pseudoxanthomonas (5.69%), respectively. However, the dominant genera were Streptococcus (43.64%), Clostridium_sensu_stricto (12.3.6%) and Lactococcus (11.47%) in the recovered AGS. Methanogens were always the dominant archaeal species in mature AGS (93.01%), stored granules (99.99%) and the recovered AGS (94.84%). Facultative anaerobes and anaerobes proliferated and dominated in the stored granules, and their metabolic activities gradually led to granular structure destruction and property deterioration. However, the stored granules served as carriers for the microbes originated from the real septic tank wastewater during recovery. They proliferated rapidly and secreted a large number of extracellular polymeric substances which helped to recover the granular structure in 11 days.
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Affiliation(s)
- Linan Zhang
- School of Architectural and Surveying & Mapping Engineering, Jiangxi University of Science and Technology, Hongqi Ave. 86, Ganzhou, 341000, Jiangxi, China
| | - Bei Long
- School of Architectural and Surveying & Mapping Engineering, Jiangxi University of Science and Technology, Hongqi Ave. 86, Ganzhou, 341000, Jiangxi, China
| | - Junfeng Wu
- Henan Province Key Laboratory of Water Pollution Control and Rehabilitation Technology, Mingyue Road, Pingdingshan, 467036, Henan, China
| | - Yuanyuan Cheng
- School of Architectural and Surveying & Mapping Engineering, Jiangxi University of Science and Technology, Hongqi Ave. 86, Ganzhou, 341000, Jiangxi, China
| | - Binchao Zhang
- School of Architectural and Surveying & Mapping Engineering, Jiangxi University of Science and Technology, Hongqi Ave. 86, Ganzhou, 341000, Jiangxi, China
| | - Yu Zeng
- School of Architectural and Surveying & Mapping Engineering, Jiangxi University of Science and Technology, Hongqi Ave. 86, Ganzhou, 341000, Jiangxi, China
| | - Sinong Huang
- School of Architectural and Surveying & Mapping Engineering, Jiangxi University of Science and Technology, Hongqi Ave. 86, Ganzhou, 341000, Jiangxi, China
| | - Mingjing Zeng
- School of Architectural and Surveying & Mapping Engineering, Jiangxi University of Science and Technology, Hongqi Ave. 86, Ganzhou, 341000, Jiangxi, China
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17
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Wang JB, Li X, Zhou ZW, Fan XY. Bacterial communities, metabolic functions and resistance genes to antibiotics and metals in two saline seafood wastewater treatment systems. BIORESOURCE TECHNOLOGY 2019; 287:121460. [PMID: 31121446 DOI: 10.1016/j.biortech.2019.121460] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/08/2019] [Accepted: 05/11/2019] [Indexed: 06/09/2023]
Abstract
This study investigated the bacterial communities, metabolic functions, antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) in two alternating anaerobic/aerobic biological filters (A/O-BFs) treating saline seafood wastewater (SSW). Firmicutes was the most abundant phylum in both systems, and halophilic and alkaliphilic bacteria were largely enriched. 15 potential pathogens were obtained. Metabolism was the predominant bacterial function. 49 ARGs and 7 MRGs were detected, and the total abundance of ARGs increased while that of MRGs decreased. Clear shifts in bacterial structure and function, ARGs and MRGs were observed in both systems and at different heights. Co-occurrence of ARGs and MRGs and their hosts were identified. ARGs and MRGs mainly negatively correlated with bacterial functions, which were also the important contributors to shifts in bacterial communities and functions. This study highlights the importance of investigating ARGs and MRGs in SSW treatment systems and their complex interactions with bacterial communities and functions.
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Affiliation(s)
- Jia-Bin Wang
- College of Architecture and Civil Engineering, Beijing University of Technology, Beijing 100124, China; School of Civil Engineering and Architecture, University of Jinan, Jinan 250022, China
| | - Xing Li
- College of Architecture and Civil Engineering, Beijing University of Technology, Beijing 100124, China
| | - Zhi-Wei Zhou
- College of Architecture and Civil Engineering, Beijing University of Technology, Beijing 100124, China
| | - Xiao-Yan Fan
- College of Architecture and Civil Engineering, Beijing University of Technology, Beijing 100124, China.
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18
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Quéméneur M, Erauso G, Frouin E, Zeghal E, Vandecasteele C, Ollivier B, Tamburini C, Garel M, Ménez B, Postec A. Hydrostatic Pressure Helps to Cultivate an Original Anaerobic Bacterium From the Atlantis Massif Subseafloor (IODP Expedition 357): Petrocella atlantisensis gen. nov. sp. nov. Front Microbiol 2019; 10:1497. [PMID: 31379757 PMCID: PMC6647913 DOI: 10.3389/fmicb.2019.01497] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/14/2019] [Indexed: 01/03/2023] Open
Abstract
Rock-hosted subseafloor habitats are very challenging for life, and current knowledge about microorganisms inhabiting such lithic environments is still limited. This study explored the cultivable microbial diversity in anaerobic enrichment cultures from cores recovered during the International Ocean Discovery Program (IODP) Expedition 357 from the Atlantis Massif (Mid-Atlantic Ridge, 30°N). 16S rRNA gene survey of enrichment cultures grown at 10–25°C and pH 8.5 showed that Firmicutes and Proteobacteria were generally dominant. However, cultivable microbial diversity significantly differed depending on incubation at atmospheric pressure (0.1 MPa), or hydrostatic pressures (HP) mimicking the in situ pressure conditions (8.2 or 14.0 MPa). An original, strictly anaerobic bacterium designated 70B-AT was isolated from core M0070C-3R1 (1150 meter below sea level; 3.5 m below seafloor) only from cultures performed at 14.0 MPa. This strain named Petrocella atlantisensis is a novel species of a new genus within the newly described family Vallitaleaceae (order Clostridiales, phylum Firmicutes). It is a mesophilic, moderately halotolerant and piezophilic chemoorganotroph, able to grow by fermentation of carbohydrates and proteinaceous compounds. Its 3.5 Mb genome contains numerous genes for ABC transporters of sugars and amino acids, and pathways for fermentation of mono- and di-saccharides and amino acids were identified. Genes encoding multimeric [FeFe] hydrogenases and a Rnf complex form the basis to explain hydrogen and energy production in strain 70B-AT. This study outlines the importance of using hydrostatic pressure in culture experiments for isolation and characterization of autochthonous piezophilic microorganisms from subseafloor rocks.
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Affiliation(s)
- Marianne Quéméneur
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France
| | - Gaël Erauso
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France
| | - Eléonore Frouin
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France
| | - Emna Zeghal
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France
| | | | - Bernard Ollivier
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France
| | - Christian Tamburini
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France
| | - Marc Garel
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France
| | - Bénédicte Ménez
- Université de Paris, Institut de Physique du Globe de Paris, CNRS UMR 7154, Paris, France
| | - Anne Postec
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, Marseille, France
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Kevbrin VV. Isolation and Cultivation of Alkaliphiles. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 172:53-84. [DOI: 10.1007/10_2018_84] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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20
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Wan R, Wang L, Chen Y, Zheng X, Su Y, Tao X. Insight into a direct carbon dioxide effect on denitrification and denitrifying bacterial communities in estuarine sediment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 643:1074-1083. [PMID: 30189524 DOI: 10.1016/j.scitotenv.2018.06.279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 06/22/2018] [Accepted: 06/22/2018] [Indexed: 06/08/2023]
Abstract
With the elevation of atmospheric CO2 content, the potential effects of CO2 on organisms and various environmental processes have gained increasing concern. Most previous studies on denitrification have been conducted on ecosystems comprising plants, soils and microbes, but they have ignored the direct effect of CO2 on denitrification and denitrifying bacterial communities. Here, by excluding the effects of plants, we found that both short- and long-term exposure to CO2 directly inhibited the denitrification process, and caused the total nitrogen removal efficiency to decrease by up to 37%. Compared with the control, long-term exposure to CO2 (30,000 ppm) also caused >276-fold increase in N2O emissions, and significantly inhibited the decomposition process. Enzymatic and qPCR assays showed that CO2 decreased the denitrifying enzymes activity (DEA) and the copy numbers of denitrifying genes, which directly resulted in the inhibitory effect of CO2 on denitrification process. Further study indicated that adverse effect of CO2 on DEA and denitrifying genes were caused by reducing the relative abundance of denitrifying bacteria. Moreover, the relative abundance of fermenting bacteria also decreased as CO2 concentration increased, which might result in insufficient liable carbon for the activity of denitrifying bacteria, and ultimately exacerbate the negative denitrification performance. Overall, this study suggests that, in the absence of plants, CO2 could directly affect the denitrifying and fermenting bacterial community, and inhibit denitrification and decomposition processes, which is detrimental to sediment nitrogen and carbon cycles.
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Affiliation(s)
- Rui Wan
- Anhui provincial engineering laboratory of water and soil pollution control and remediation, College of Environmental Science and Engineering, Anhui Normal University, 189 South of Jiuhua Road, Wuhu, Anhui 241002, China; State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Lei Wang
- Anhui provincial engineering laboratory of water and soil pollution control and remediation, College of Environmental Science and Engineering, Anhui Normal University, 189 South of Jiuhua Road, Wuhu, Anhui 241002, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China.
| | - Xiong Zheng
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yinglong Su
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xiucheng Tao
- Anhui provincial engineering laboratory of water and soil pollution control and remediation, College of Environmental Science and Engineering, Anhui Normal University, 189 South of Jiuhua Road, Wuhu, Anhui 241002, China
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Schouw A, Vulcano F, Roalkvam I, Hocking WP, Reeves E, Stokke R, Bødtker G, Steen IH. Genome Analysis of Vallitalea guaymasensis Strain L81 Isolated from a Deep-Sea Hydrothermal Vent System. Microorganisms 2018; 6:E63. [PMID: 29973550 PMCID: PMC6163223 DOI: 10.3390/microorganisms6030063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 06/28/2018] [Accepted: 06/29/2018] [Indexed: 12/21/2022] Open
Abstract
Abyssivirga alkaniphila strain L81T, recently isolated from a black smoker biofilm at the Loki’s Castle hydrothermal vent field, was previously described as a mesophilic, obligately anaerobic heterotroph able to ferment carbohydrates, peptides, and aliphatic hydrocarbons. The strain was classified as a new genus within the family Lachnospiraceae. Herein, its genome is analyzed and A. alkaniphila is reassigned to the genus Vallitalea as a new strain of V. guaymasensis, designated V. guaymasensis strain L81. The 6.4 Mbp genome contained 5651 protein encoding genes, whereof 4043 were given a functional prediction. Pathways for fermentation of mono-saccharides, di-saccharides, peptides, and amino acids were identified whereas a complete pathway for the fermentation of n-alkanes was not found. Growth on carbohydrates and proteinous compounds supported methane production in co-cultures with Methanoplanus limicola. Multiple confurcating hydrogen-producing hydrogenases, a putative bifurcating electron-transferring flavoprotein—butyryl-CoA dehydrogenase complex, and a Rnf-complex form a basis for the observed hydrogen-production and a putative reverse electron-transport in V. guaymasensis strain L81. Combined with the observation that n-alkanes did not support growth in co-cultures with M. limicola, it seemed more plausible that the previously observed degradation patterns of crude-oil in strain L81 are explained by unspecific activation and may represent a detoxification mechanism, representing an interesting ecological function. Genes encoding a capacity for polyketide synthesis, prophages, and resistance to antibiotics shows interactions with the co-occurring microorganisms. This study enlightens the function of the fermentative microorganisms from hydrothermal vents systems and adds valuable information on the bioprospecting potential emerging in deep-sea hydrothermal systems.
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Affiliation(s)
- Anders Schouw
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Francesca Vulcano
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Irene Roalkvam
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - William Peter Hocking
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Eoghan Reeves
- Department of Earth Science and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Runar Stokke
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Gunhild Bødtker
- Centre for Integrated Petroleum Research (CIPR), Uni Research AS, Nygårdsgaten 112, N-5008 Bergen, Norway.
| | - Ida Helene Steen
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
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Leandro T, Rodriguez N, Rojas P, Sanz JL, da Costa MS, Amils R. Study of methanogenic enrichment cultures of rock cores from the deep subsurface of the Iberian Pyritic Belt. Heliyon 2018; 4:e00605. [PMID: 29862366 PMCID: PMC5968172 DOI: 10.1016/j.heliyon.2018.e00605] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 02/15/2018] [Accepted: 04/10/2018] [Indexed: 11/26/2022] Open
Abstract
Two deep boreholes were drilled at 320 and 620 meters below surface in the Iberian Pyritic Belt (IPB) at Peña de Hierro (Huelva, Southwestern Spain). Cores were sampled and used for the establishment of enrichment cultures with methanogenic activity. The cultivable diversity of these enrichments was accessed using different cultivation techniques and several isolates were recovered in pure culture from various depths in both boreholes. Although no archaeal isolates were obtained in pure culture, strict anaerobes and facultative anaerobic bacteria belonging to the phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes were isolated and identified using the 16S rRNA gene sequence. Analysis of three selected enrichment cultures by amplification of both bacterial and archaeal 16S rRNA gene followed by pyrosequencing revealed further information on the populations enriched. The archaeal sequences obtained from the methanogenic enrichment cultures belonged to the orders Methanosarcinales and Methanocellales. To best of our knowledge this is the first report of enrichment in members of the Methanocellales in a deep terrestrial subsurface ecosystem. Several bacterial populations, predominantly consisting of Firmicutes and Proteobacteria, were also enriched. The prevalent microbial populations enriched as detected by pyrosequencing analysis, as well as the bacterial isolates cultivated were affiliated with known fermentative, sulfate reducing and acetogenic bacteria or methanogenic archaea. Our results show a great diversity in the microbial communities of the IPB deep subsurface.
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Affiliation(s)
- Tânia Leandro
- Centro de Biología Molecular Severo Ochoa (CBMSO, CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
- Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
| | - Nuria Rodriguez
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Spain
| | - Patricia Rojas
- Department of Molecular Biology, Universidad Autónoma de Madrid, Spain
| | - Jose L. Sanz
- Department of Molecular Biology, Universidad Autónoma de Madrid, Spain
| | - Milton S. da Costa
- Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
| | - Ricardo Amils
- Centro de Biología Molecular Severo Ochoa (CBMSO, CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Spain
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23
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Frouin E, Bes M, Ollivier B, Quéméneur M, Postec A, Debroas D, Armougom F, Erauso G. Diversity of Rare and Abundant Prokaryotic Phylotypes in the Prony Hydrothermal Field and Comparison with Other Serpentinite-Hosted Ecosystems. Front Microbiol 2018; 9:102. [PMID: 29467733 PMCID: PMC5808123 DOI: 10.3389/fmicb.2018.00102] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/17/2018] [Indexed: 01/21/2023] Open
Abstract
The Bay of Prony, South of New Caledonia, represents a unique serpentinite-hosted hydrothermal field due to its coastal situation. It harbors both submarine and intertidal active sites, discharging hydrogen- and methane-rich alkaline fluids of low salinity and mild temperature through porous carbonate edifices. In this study, we have extensively investigated the bacterial and archaeal communities inhabiting the hydrothermal chimneys from one intertidal and three submarine sites by 16S rRNA gene amplicon sequencing. We show that the bacterial community of the intertidal site is clearly distinct from that of the submarine sites with species distribution patterns driven by only a few abundant populations, affiliated to the Chloroflexi and Proteobacteria phyla. In contrast, the distribution of archaeal taxa seems less site-dependent, as exemplified by the co-occurrence, in both submarine and intertidal sites, of two dominant phylotypes of Methanosarcinales previously thought to be restricted to serpentinizing systems, either marine (Lost City Hydrothermal Field) or terrestrial (The Cedars ultrabasic springs). Over 70% of the phylotypes were rare and included, among others, all those affiliated to candidate divisions. We finally compared the distribution of bacterial and archaeal phylotypes of Prony Hydrothermal Field with those of five previously studied serpentinizing systems of geographically distant sites. Although sensu stricto no core microbial community was identified, a few uncultivated lineages, notably within the archaeal order Methanosarcinales and the bacterial class Dehalococcoidia (the candidate division MSBL5) were exclusively found in a few serpentinizing systems while other operational taxonomic units belonging to the orders Clostridiales, Thermoanaerobacterales, or the genus Hydrogenophaga, were abundantly distributed in several sites. These lineages may represent taxonomic signatures of serpentinizing ecosystems. These findings extend our current knowledge of the microbial diversity inhabiting serpentinizing systems and their biogeography.
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Affiliation(s)
- Eléonore Frouin
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Méline Bes
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Bernard Ollivier
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Marianne Quéméneur
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Anne Postec
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Didier Debroas
- CNRS UMR 6023, Laboratoire "Microorganismes - Génome et Environnement", Université Clermont Auvergne, Clermont-Ferrand, France
| | - Fabrice Armougom
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Gaël Erauso
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
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24
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Rowe AR, Yoshimura M, LaRowe DE, Bird LJ, Amend JP, Hashimoto K, Nealson KH, Okamoto A. In situ
electrochemical enrichment and isolation of a magnetite-reducing bacterium from a high pH serpentinizing spring. Environ Microbiol 2017; 19:2272-2285. [DOI: 10.1111/1462-2920.13723] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 03/05/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Annette R. Rowe
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Miho Yoshimura
- Department of Applied and Chemical Engineering; University of Tokyo; Tokyo Japan
| | - Doug E. LaRowe
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Lina J. Bird
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Jan P. Amend
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
- Department of Biological Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Kazuhito Hashimoto
- Center for Green Research on Energy and Environmental Materials; National Institute for Material Sciences; Tsukuba Ibaraki 305-0047 Japan
| | - Kenneth H. Nealson
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Akihiro Okamoto
- Center for Green Research on Energy and Environmental Materials; National Institute for Material Sciences; Tsukuba Ibaraki 305-0047 Japan
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25
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Pisapia C, Gérard E, Gérard M, Lecourt L, Lang SQ, Pelletier B, Payri CE, Monnin C, Guentas L, Postec A, Quéméneur M, Erauso G, Ménez B. Mineralizing Filamentous Bacteria from the Prony Bay Hydrothermal Field Give New Insights into the Functioning of Serpentinization-Based Subseafloor Ecosystems. Front Microbiol 2017; 8:57. [PMID: 28197130 PMCID: PMC5281578 DOI: 10.3389/fmicb.2017.00057] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 01/09/2017] [Indexed: 11/13/2022] Open
Abstract
Despite their potential importance as analogs of primitive microbial metabolisms, the knowledge of the structure and functioning of the deep ecosystems associated with serpentinizing environments is hampered by the lack of accessibility to relevant systems. These hyperalkaline environments are depleted in dissolved inorganic carbon (DIC), making the carbon sources and assimilation pathways in the associated ecosystems highly enigmatic. The Prony Bay Hydrothermal Field (PHF) is an active serpentinization site where, similar to Lost City (Mid-Atlantic Ridge), high-pH fluids rich in H2 and CH4 are discharged from carbonate chimneys at the seafloor, but in a shallower lagoonal environment. This study aimed to characterize the subsurface microbial ecology of this environment by focusing on the earliest stages of chimney construction, dominated by the discharge of hydrothermal fluids of subseafloor origin. By jointly examining the mineralogy and the microbial diversity of the conduits of juvenile edifices at the micrometric scale, we find a central role of uncultivated bacteria belonging to the Firmicutes in the ecology of the PHF. These bacteria, along with members of the phyla Acetothermia and Omnitrophica, are identified as the first chimneys inhabitants before archaeal Methanosarcinales. They are involved in the construction and early consolidation of the carbonate structures via organomineralization processes. Their predominance in the most juvenile and nascent hydrothermal chimneys, and their affiliation with environmental subsurface microorganisms, indicate that they are likely discharged with hydrothermal fluids from the subseafloor. They may thus be representative of endolithic serpentinization-based ecosystems, in an environment where DIC is limited. In contrast, heterotrophic and fermentative microorganisms may consume organic compounds from the abiotic by-products of serpentinization processes and/or from life in the deeper subsurface. We thus propose that the Firmicutes identified at PHF may have a versatile metabolism with the capability to use diverse organic compounds from biological or abiotic origin. From that perspective, this study sheds new light on the structure of deep microbial communities living at the energetic edge in serpentinites and may provide an alternative model of the earliest metabolisms.
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Affiliation(s)
- Céline Pisapia
- Geomicrobiology Group, Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche ScientifiqueParis, France
- DISCO beamline, Synchrotron SOLEILSaint Aubin, France
| | - Emmanuelle Gérard
- Geomicrobiology Group, Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche ScientifiqueParis, France
| | - Martine Gérard
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Institut de Recherche pour le Développement, Université Pierre et Marie CurieParis, France
| | - Léna Lecourt
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Institut de Recherche pour le Développement, Université Pierre et Marie CurieParis, France
| | - Susan Q. Lang
- Department of Earth and Ocean Sciences, School of the Earth, Ocean and Environment, University of South Carolina, ColumbiaSC, USA
| | - Bernard Pelletier
- GIS Grand Observatoire de l’environnement et de la biodiversité terrestre et marine dans le Pacifique Sud, Centre IRD de NouméaNouméa, New Caledonia
| | | | - Christophe Monnin
- Géosciences Environnement Toulouse, Université Paul Sabatier, Centre National de la Recherche Scientifique, Institut de Recherche pour le DéveloppementToulouse, France
| | - Linda Guentas
- UR227 COREUS, Centre IRD de NouméaNouméa, New Caledonia
- Laboratoire Matériaux Polymères Interfaces Environnement Marin EA 4323, Université de ToulonLa Garde, France
- Mediterranean Institute of Oceanography, Centre IRD de NouméaNouméa, New Caledonia
- Laboratoire Insulaire du Vivant et de l’Environnement, Université de la Nouvelle-CalédonieNouméa, New Caledonia
| | - Anne Postec
- Aix Marseille Université, Centre National de la Recherche Scientifique – Institut National des Sciences de L’Univers, Université de Toulon, Institut de Recherche pour le Développement, Mediterranean Institute of OceanographyMarseille, France
| | - Marianne Quéméneur
- Aix Marseille Université, Centre National de la Recherche Scientifique – Institut National des Sciences de L’Univers, Université de Toulon, Institut de Recherche pour le Développement, Mediterranean Institute of OceanographyMarseille, France
| | - Gaël Erauso
- Aix Marseille Université, Centre National de la Recherche Scientifique – Institut National des Sciences de L’Univers, Université de Toulon, Institut de Recherche pour le Développement, Mediterranean Institute of OceanographyMarseille, France
| | - Bénédicte Ménez
- Geomicrobiology Group, Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche ScientifiqueParis, France
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26
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Serpentinicella alkaliphila gen. nov., sp. nov., a novel alkaliphilic anaerobic bacterium isolated from the serpentinite-hosted Prony hydrothermal field, New Caledonia. Int J Syst Evol Microbiol 2016; 66:4464-4470. [DOI: 10.1099/ijsem.0.001375] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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27
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Galperin MY, Brover V, Tolstoy I, Yutin N. Phylogenomic analysis of the family Peptostreptococcaceae (Clostridium cluster XI) and proposal for reclassification of Clostridium litorale (Fendrich et al. 1991) and Eubacterium acidaminophilum (Zindel et al. 1989) as Peptoclostridium litorale gen. nov. comb. nov. and Peptoclostridium acidaminophilum comb. nov. Int J Syst Evol Microbiol 2016; 66:5506-5513. [PMID: 27902180 PMCID: PMC5244501 DOI: 10.1099/ijsem.0.001548] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In 1994, analyses of clostridial 16S rRNA gene sequences led to the assignment of 18
species to Clostridium cluster XI, separating them
from Clostridium sensu stricto
(Clostridium cluster I). Subsequently,
most cluster XI species have been assigned to the family Peptostreptococcaceae with some species
being reassigned to new genera. However, several misclassified Clostridium species remained, creating
a taxonomic conundrum and confusion regarding their status. Here, we have re-examined
the phylogeny of cluster XI species by comparing the 16S rRNA gene-based trees with
protein- and genome-based trees, where available. The resulting phylogeny of the
Peptostreptococcaceae was consistent
with the recent proposals on creating seven new genera within this family. This
analysis also revealed a tight clustering of Clostridium litorale and
Eubacterium acidaminophilum. Based on
these data, we propose reassigning these two organisms to the new genus
Peptoclostridium as
Peptoclostridium litorale gen. nov.
comb. nov. (the type species of the genus) and Peptoclostridium acidaminophilum comb.
nov., respectively. As correctly noted in the original publications, the genera
Acetoanaerobium and
Proteocatella also fall within cluster
XI, and can be assigned to the Peptostreptococcaceae.
Clostridium sticklandii, which falls
within radiation of genus Acetoanaerobium, is
proposed to be reclassified as Acetoanaerobium sticklandii comb. nov.
The remaining misnamed members of the Peptostreptococcaceae,
[Clostridium]
hiranonis, [Clostridium]
paradoxum and [Clostridium]
thermoalcaliphilum, still remain to be properly classified.
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Affiliation(s)
- Michael Y. Galperin
- National Center for Biotechnology Information, National
Library of Medicine, National Institutes of Health, Bethesda,
Maryland 20894, USA
- Correspondence Michael Y. Galperin
| | - Vyacheslav Brover
- National Center for Biotechnology Information, National
Library of Medicine, National Institutes of Health, Bethesda,
Maryland 20894, USA
| | - Igor Tolstoy
- National Center for Biotechnology Information, National
Library of Medicine, National Institutes of Health, Bethesda,
Maryland 20894, USA
| | - Natalya Yutin
- National Center for Biotechnology Information, National
Library of Medicine, National Institutes of Health, Bethesda,
Maryland 20894, USA
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28
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Mei N, Postec A, Monnin C, Pelletier B, Payri CE, Ménez B, Frouin E, Ollivier B, Erauso G, Quéméneur M. Metagenomic and PCR-Based Diversity Surveys of [FeFe]-Hydrogenases Combined with Isolation of Alkaliphilic Hydrogen-Producing Bacteria from the Serpentinite-Hosted Prony Hydrothermal Field, New Caledonia. Front Microbiol 2016; 7:1301. [PMID: 27625634 PMCID: PMC5003875 DOI: 10.3389/fmicb.2016.01301] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 08/08/2016] [Indexed: 12/01/2022] Open
Abstract
High amounts of hydrogen are emitted in the serpentinite-hosted hydrothermal field of the Prony Bay (PHF, New Caledonia), where high-pH (~11), low-temperature (< 40°C), and low-salinity fluids are discharged in both intertidal and shallow submarine environments. In this study, we investigated the diversity and distribution of potentially hydrogen-producing bacteria in Prony hyperalkaline springs by using metagenomic analyses and different PCR-amplified DNA sequencing methods. The retrieved sequences of hydA genes, encoding the catalytic subunit of [FeFe]-hydrogenases and, used as a molecular marker of hydrogen-producing bacteria, were mainly related to those of Firmicutes and clustered into two distinct groups depending on sampling locations. Intertidal samples were dominated by new hydA sequences related to uncultured Firmicutes retrieved from paddy soils, while submarine samples were dominated by diverse hydA sequences affiliated with anaerobic and/or thermophilic submarine Firmicutes pertaining to the orders Thermoanaerobacterales or Clostridiales. The novelty and diversity of these [FeFe]-hydrogenases may reflect the unique environmental conditions prevailing in the PHF (i.e., high-pH, low-salt, mesothermic fluids). In addition, novel alkaliphilic hydrogen-producing Firmicutes (Clostridiales and Bacillales) were successfully isolated from both intertidal and submarine PHF chimney samples. Both molecular and cultivation-based data demonstrated the ability of Firmicutes originating from serpentinite-hosted environments to produce hydrogen by fermentation, potentially contributing to the molecular hydrogen balance in situ.
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Affiliation(s)
- Nan Mei
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIOMarseille, France
| | - Anne Postec
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIOMarseille, France
| | - Christophe Monnin
- GET UMR5563 (Centre National de la Recherche Scientifique/UPS/IRD/CNES), Géosciences Environnement ToulouseToulouse, France
| | - Bernard Pelletier
- Institut pour la Recherche et le Développement (IRD) Centre de Nouméa, MIO UM 110Nouméa, Nouvelle-Calédonie
| | - Claude E. Payri
- Institut pour la Recherche et le Développement (IRD) Centre de Nouméa, MIO UM 110Nouméa, Nouvelle-Calédonie
| | - Bénédicte Ménez
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Univ Paris Diderot, Centre National de la Recherche ScientifiqueParis, France
| | - Eléonore Frouin
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIOMarseille, France
| | - Bernard Ollivier
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIOMarseille, France
| | - Gaël Erauso
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIOMarseille, France
| | - Marianne Quéméneur
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIOMarseille, France
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