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Akaçin İ, Ersoy Ş, Doluca O, Güngörmüşler M. Using custom-built primers and nanopore sequencing to evaluate CO-utilizer bacterial and archaeal populations linked to bioH 2 production. Sci Rep 2023; 13:17025. [PMID: 37813931 PMCID: PMC10562470 DOI: 10.1038/s41598-023-44357-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 10/06/2023] [Indexed: 10/11/2023] Open
Abstract
The microbial community composition of five distinct thermophilic hot springs was effectively described in this work, using broad-coverage nanopore sequencing (ONT MinION sequencer). By examining environmental samples from the same source, but from locations with different temperatures, bioinformatic analysis revealed dramatic changes in microbial diversity and archaeal abundance. More specifically, no archaeal presence was reported with universal bacterial primers, whereas a significant archaea presence and also a wider variety of bacterial species were reported. These results revealed the significance of primer preference for microbiomes in extreme environments. Bioinformatic analysis was performed by aligning the reads to 16S microbial databases for identification using three different alignment methods, Epi2Me (Fastq 16S workflow), Kraken, and an in-house BLAST tool, including comparison at the genus and species levels. As a result, this approach to data analysis had a significant impact on the genera identified, and thus, it is recommended that use of multiple analysis tools to support findings on taxonomic identification using the 16S region until more precise bioinformatics tools become available. This study presents the first compilation of the ONT-based inventory of the hydrogen producers in the designated hot springs in Türkiye.
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Affiliation(s)
- İlayda Akaçin
- Division of Bioengineering, Graduate School, Izmir University of Economics, Sakarya Caddesi No: 156, 35330, Balçova, Izmir, Türkiye
| | - Şeymanur Ersoy
- Division of Bioengineering, Graduate School, Izmir University of Economics, Sakarya Caddesi No: 156, 35330, Balçova, Izmir, Türkiye
| | - Osman Doluca
- Division of Bioengineering, Graduate School, Izmir University of Economics, Sakarya Caddesi No: 156, 35330, Balçova, Izmir, Türkiye
- Department of Biomedical Engineering, Faculty of Engineering, Izmir University of Economics, Sakarya Caddesi No: 156, 35330, Balçova, Izmir, Türkiye
| | - Mine Güngörmüşler
- Division of Bioengineering, Graduate School, Izmir University of Economics, Sakarya Caddesi No: 156, 35330, Balçova, Izmir, Türkiye.
- Department of Genetics and Bioengineering, Faculty of Engineering, Izmir University of Economics, Sakarya Caddesi No: 156, 35330, Balçova, Izmir, Türkiye.
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Slobodkina GB, Merkel AY, Kuchierskaya AA, Slobodkin AI. Moorella sulfitireducens sp. nov., a thermophilic anaerobic bacterium isolated from a terrestrial thermal spring. Extremophiles 2022; 26:33. [DOI: 10.1007/s00792-022-01285-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/25/2022] [Indexed: 11/10/2022]
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Judicial Opinions 112–122. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Opinion 112 denies the request to place
Seliberia
Aristovskaya and Parinkina 1963 (Approved Lists 1980) on the list of rejected names because the information provided is insufficient. For the same reason, Opinion 113 denies the request to reject
Shewanella irciniae
Lee et al. 2006 and Opinion 114 denies the request to reject the name
Enterobacter siamensis
Khunthongpan et al. 2014. Opinion 115 rejects the epithet of
Moorella thermoautotrophica
(Wiegel et al. 1981) Collins et al. 1994, which is regarded as a nomen confusum. To assess the consequences of Rule 8, Opinion 116 revisits names of taxa above the rank of genus which should comprise the stem of the name of a nomenclatural type and a category-specific ending but fail to do so. Such names should be orthographically corrected if the sole error is the inadvertent usage of an incorrect stem or be regarded as illegitimate if otherwise. The necessary corrections are made for a number of names. In Opinion 117, the request to designate
Methylothermus subterraneus
Hirayama et al. 2011 as the type species of the genus
Methylothermus
is denied because an equivalent action compatible with the Code was already conducted. In Opinion 118, the possible orthographical correction of the name
Flaviaesturariibacter
is treated, as are the analogous cases of
Fredinandcohnia
and
Hydrogeniiclostidium
. The genus names are corrected to Flaviaestuariibacter, Ferdinandcohnia and
Hydrogeniiclostridium
, respectively. Opinion 119 concludes that assigning
Actinomycetales
Buchanan 1917 (Approved Lists 1980) as nomenclatural type of the class
Actinobacteria
Stackebrandt et al. 1997 would not render that name legitimate if Rule 8 remained retroactive. The request is granted but
Actinomycetales
is also assigned as type of
Actinomycetes
Krassilnikov 1949 (Approved Lists 1980). In Opinion 120, the possible orthographical correction of the name
Amycolatopsis albidoflavus
is treated. It is grammatically corrected to Amycolatopsis albidoflava. Six names which could according to Rule 61 be grammatically corrected by anyone are also corrected. Opinion 121 denies the request to revise Opinion 69 and notes that Opinion 69 does not have the undesirable consequences emphasized in the request. In Opinion 122, the request to reject various taxon names of
Mollicutes
proposed in 2018 is denied because it is based on misinterpretations of the Code, which are clarified. Alternative ways to solve the perceived problems are outlined. These Opinions were ratified by the voting members of the International Committee on Systematics of Prokaryotes.
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Kochetkova TV, Podosokorskaya OA, Elcheninov AG, Kublanov IV. Diversity of Thermophilic Prokaryotes Inhabiting Russian Natural Hot Springs. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722010064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Tang Y, Li Y, Zhang M, Xiong P, Liu L, Bao Y, Zhao Z. Link between characteristics of Fe(III) oxides and critical role in enhancing anaerobic methanogenic degradation of complex organic compounds. ENVIRONMENTAL RESEARCH 2021; 194:110498. [PMID: 33220246 DOI: 10.1016/j.envres.2020.110498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/18/2020] [Accepted: 11/13/2020] [Indexed: 06/11/2023]
Abstract
Fe(III) oxides have been investigated to accelerate anaerobic methanogenic degradation of complex organic compounds. However, the critical role linked to the characteristics of different types of Fe(III) oxides is still unclear. Study presented here performed a side-by-side comparison of four types of Fe(III) oxides including Fe(III)-citrate, ferrihydrite, hematite and magnetite to evaluate their effectiveness in methanogenic degradation of phenol. Results showed that, amorphous Fe(III)-citrate group showed the fastest phenol degradation and Fe2+ release among all the groups, followed by poorly crystalline ferrihydrite. Although Fe(III)-citrate group also showed the fastest methane production rate, the efficiency of electron recovery in methane production was only 58-78%, which was evidently lower than that in both crystalline hematite (86-89%) and magnetite (93-97%) groups. Methane production rate with non-conductive ferrihydrite was nearly same as that with conductive magnetite, both of which were significantly higher than that with semi-conductive hematite. X-ray Diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) analysis showed that sludge collected from hematite and magnetite group still respectively presented a relatively intact characteristic spectra involved in hematite and magnetite. Differently, the characteristic spectra involved in ferrihydrite was not evident in sludge collected from ferrihydrite group, whereas the characteristic spectra involved in magnetite was detected. Microbial community analysis showed that, both Fe(III)-citrate and ferrihydrite specially enriched Fe(III)-reducing bacteria capable of degrading phenol into fatty acids (Trichococcus and Caloramator) via dissimilatory Fe(III) reduction. Fe(III)-citrate also stimulated the growth of Syntrophus capable of degrading phenol/benzoate into acetate and proceeding direct interspecies electron transfer (DIET). In magnetite and hematite group, the abundance of Enterococcus species evidently increased, and they might proceed DIET with Methanothrix species in syntrophic conversion of fatty acids into methane.
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Affiliation(s)
- Yapeng Tang
- School of Ocean Science and Technology, Dalian University of Technology, Panjin, 124221, China
| | - Yang Li
- School of Ocean Science and Technology, Dalian University of Technology, Panjin, 124221, China.
| | - Mingqian Zhang
- School of Ocean Science and Technology, Dalian University of Technology, Panjin, 124221, China
| | - Pu Xiong
- School of Ocean Science and Technology, Dalian University of Technology, Panjin, 124221, China
| | - Lifen Liu
- School of Ocean Science and Technology, Dalian University of Technology, Panjin, 124221, China
| | - Yongming Bao
- School of Ocean Science and Technology, Dalian University of Technology, Panjin, 124221, China
| | - Zhiqiang Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China.
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Soldatova E, Dong Y, Li J, Liu Y, Zan J, Boeckx P, Sun Z. Nitrogen transformation and pathways in the shallow groundwater-soil system within agricultural landscapes. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2021; 43:441-459. [PMID: 33000346 DOI: 10.1007/s10653-020-00733-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
The present study considers the behavior of nitrogen compounds in the shallow groundwater-soil system as necessary for the functioning of the nitrogen cycle within agricultural landscapes and one of the first steps of the formation of groundwater chemical composition. Data were collected in 2011-2018 within the Poyang Lake area (Jiangxi Province, China), where agricultural landscapes prevail. The soil and groundwater samples were taken in different periods of an agricultural season at the beginning of the agricultural season (spring) and after harvesting (autumn). The combined geochemical data on the chemical and microbiological composition of the soils and shallow groundwater and isotopic data on dissolved nitrate allowed researchers to resolve that nitrogen enters the system in the form of organic compounds, particularly, due to the soil fertilization at the beginning of the agricultural season. Organic nitrogen compounds transform into nitrate under the influence of nitrifiers in the soil before getting the shallow aquifer, where the occurrence of denitrification is suggested. Within the Ganjiang and Xiushui interfluve, reducing conditions, together with the formation of clay minerals from the aqueous solution, may serve a geochemical barrier for the accumulation of nitrogen compounds preventing the transformation of ammonium to nitrate and providing its sorption. It also should be noted that bacterial diversity in the shallow groundwater has a strong relation with the amount of nitrate in the system, whereas in the soil, it is connected with sampling depth.
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Affiliation(s)
- Evgeniya Soldatova
- Laboratory of Modeling Hydrogeochemical and Hydrothermal Processes, Vernadsky Institute of Geochemistry and Analytical Chemistry of Russian Academy of Sciences, 119991, Moscow, Russia.
| | - Yihui Dong
- State Key Laboratory of Nuclear Resources and Environment, East China University of Technology, Nanchang, 330013, China
- School of Water Resources and Environmental Engineering, East China University of Technology, Nanchang, 330013, China
| | - Jiale Li
- State Key Laboratory of Nuclear Resources and Environment, East China University of Technology, Nanchang, 330013, China
- School of Water Resources and Environmental Engineering, East China University of Technology, Nanchang, 330013, China
| | - Yajie Liu
- School of Water Resources and Environmental Engineering, East China University of Technology, Nanchang, 330013, China
| | - Jinjing Zan
- School of Water Resources and Environmental Engineering, East China University of Technology, Nanchang, 330013, China
| | - Pascal Boeckx
- Isotope Bioscience Laboratory (ISOFYS), Ghent University, 9000, Ghent, Belgium
| | - Zhanxue Sun
- State Key Laboratory of Nuclear Resources and Environment, East China University of Technology, Nanchang, 330013, China
- School of Water Resources and Environmental Engineering, East China University of Technology, Nanchang, 330013, China
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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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Mostafa A, Im S, Song YC, Kang S, Kim DH. Enhanced Anaerobic Digestion of Long Chain Fatty Acid by Adding Magnetite and Carbon Nanotubes. Microorganisms 2020; 8:E333. [PMID: 32120882 PMCID: PMC7143112 DOI: 10.3390/microorganisms8030333] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 02/18/2020] [Accepted: 02/25/2020] [Indexed: 12/30/2022] Open
Abstract
This study investigated the impact of stimulating direct interspecies electron transfer (DIET), by supplementing nano-sized magnetite (nFe3O4, 0.5 g Fe/g VSS) and carbon nanotubes (CNT, 1 g/L), in anaerobic digestion of oleic acid (OA) at various concentrations (0.10 - 4.00 g chemical oxygen demand(COD)/L). Both supplementations could enhance CH4 production, and its beneficial impact increased with increased OA concentration. The biggest improvements of 114% and 165% compared to the control were achieved by nFe3O4 and CNT, respectively, at OA of 4 g COD/L. The enhancement can be attributed to the increased sludge conductivity: 7.1 ± 0.5 (control), 12.5 ± 0.8 (nFe3O4-added), and 15.7 ± 1.1 µS/cm (CNT-supplemented). Dissolved iron concentration, released from nFe3O4, seemed to have a negligible role in improving CH4 production. The excretion of electron shuttles, i.e., humic-like substances and protein-like substances, were found to be stimulated by supplementing nFe3O4 and CNT. Microbial diversity was found to be simplified under DIET-stimulating conditions, whereby five genera accounted for 88% of the total sequences in the control, while more than 82% were represented by only two genera (Methanotrix concilli and Methanosarcina flavescens) by supplementing nFe3O4 and CNT. In addition, the abudance of electro-active bacteria such as Syntrophomonas zehnderi was significantly increased from 17% to around 45%.
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Affiliation(s)
- Alsayed Mostafa
- Department of Civil Engineering, Inha University, 100 Inha-ro, Nam-gu, Incheon 402-751, Korea; (A.M.); (S.I.)
| | - Seongwon Im
- Department of Civil Engineering, Inha University, 100 Inha-ro, Nam-gu, Incheon 402-751, Korea; (A.M.); (S.I.)
| | - Young-Chae Song
- Department of Environmental Engineering, Korea Maritime and Ocean University, Busan 49112, Korea;
| | - Seoktae Kang
- Department of Civil and Environmental Engineering, KAIST 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea;
| | - Dong-Hoon Kim
- Department of Civil Engineering, Inha University, 100 Inha-ro, Nam-gu, Incheon 402-751, Korea; (A.M.); (S.I.)
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Ungkulpasvich U, Baramee S, Uke A, Kosugi A. Capillibacterium thermochitinicola gen. nov., sp. nov., a novel anaerobic thermophilic chitinolytic bacterium from compost. Int J Syst Evol Microbiol 2019; 71:004693. [PMID: 33724176 PMCID: PMC8375423 DOI: 10.1099/ijsem.0.004693] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/22/2021] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-negative, spore forming, obligately anaerobic, thermophilic, chitin-degrading bacterium, designated UUS1-1T, was isolated from compost on Ishigaki Island, Japan by enrichment culturing using chitin powder as the carbon source. The strain has unique, long, hair-like rod morphological features and exhibits strong degradation activity toward crystalline chitin under thermophilic conditions. Growth of the novel strain was observed at 45-65 °C (optimum, 55 °C) and pH 6.5-7.5 (optimum, pH 7.0). In addition to chitin, the strain utilized several other carbon sources, including N-acetylglucosamine, glucose, galactose, mannose, maltose, cellobiose, fructose and sucrose. The end products of chitin degradation were acetate, lactate, H2 and CO2. Phylogenetic tree analysis based on 16S rRNA gene sequences revealed a clear affiliation of the proposed bacterium to the phylum Firmicutes; the most closely related species were Hydrogenispora ethanolica LX-BT and Desulfotomaculum thermobenzoicum DSM6193T with similarities of 90.4 and 87.8 %, respectively. The G+C content of the genomic DNA was 52.1 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between the genomes of UUS1-1T and H. ethanolica LX-BT were 65.5 and 21.0 %, respectively. The cellular fatty acid composition of the strain was C16 : 0, anteiso-C15 : 0, C14 : 0, C12 : 0 3-OH and dimethyl acetal-C13 : 0. Based on phenotypic, chemotaxonomic and genotypic analysis, strain UUS1-1T represents a novel genus and species, for which the name Capillibacterium thermochitinicola gen. nov., sp. nov. is proposed. The type strain is UUS1-1T (=JCM 33882T=DSM 111537T).
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Affiliation(s)
- Umbhorn Ungkulpasvich
- School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Sirilak Baramee
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
- Present address: Pilot Plant Development and Training Institute (PDTI), King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Ayaka Uke
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Akihiko Kosugi
- School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
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Zhao J, Wang L, Tang L, Ren R, You W, Farooq R, Wang Z, Zhang Y. Changes in bacterial community structure and humic acid composition in response to enhanced extracellular electron transfer process in coastal sediment. Arch Microbiol 2019; 201:897-906. [DOI: 10.1007/s00203-019-01659-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/25/2019] [Accepted: 04/10/2019] [Indexed: 12/24/2022]
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Sanchez-Garcia L, Fernandez-Martinez MA, García-Villadangos M, Blanco Y, Cady SL, Hinman N, Bowden ME, Pointing SB, Lee KC, Warren-Rhodes K, Lacap-Bugler D, Cabrol NA, Parro V, Carrizo D. Microbial Biomarker Transition in High-Altitude Sinter Mounds From El Tatio (Chile) Through Different Stages of Hydrothermal Activity. Front Microbiol 2019; 9:3350. [PMID: 30697206 PMCID: PMC6340942 DOI: 10.3389/fmicb.2018.03350] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/31/2018] [Indexed: 01/22/2023] Open
Abstract
Geothermal springs support microbial communities at elevated temperatures in an ecosystem with high preservation potential that makes them interesting analogs for early evolution of the biogeosphere. The El Tatio geysers field in the Atacama Desert has astrobiological relevance due to the unique occurrence of geothermal features with steep hydrothermal gradients in an otherwise high altitude, hyper-arid environment. We present here results of our multidisciplinary field and molecular study of biogeochemical evidence for habitability and preservation in silica sinter at El Tatio. We sampled three morphologically similar geyser mounds characterized by differences in water activity (i.e., episodic liquid water, steam, and inactive geyser lacking hydrothermal activity). Multiple approaches were employed to determine (past and present) biological signatures and dominant metabolism. Lipid biomarkers indicated relative abundance of thermophiles (dicarboxylic acids) and sulfate reducing bacteria (branched carboxylic acids) in the sinter collected from the liquid water mound; photosynthetic microorganisms such as cyanobacteria (alkanes and isoprenoids) in the steam sinter mound; and archaea (squalane and crocetane) as well as purple sulfur bacteria (cyclopropyl acids) in the dry sinter from the inactive geyser. The three sinter structures preserved biosignatures representative of primary (thermophilic) and secondary (including endoliths and environmental contaminants) microbial communities. Sequencing of environmental 16S rRNA genes and immuno-assays generally corroborated the lipid-based microbial identification. The multiplex immunoassays and the compound-specific isotopic analysis of carboxylic acids, alkanols, and alkanes indicated that the principal microbial pathway for carbon fixation in the three sinter mounds was through the Calvin cycle, with a relative larger contribution of the reductive acetyl-CoA pathway in the dry system. Other inferred metabolic traits varied from the liquid mound (iron and sulfur chemistry), to the steam mound (nitrogen cycle), to the dry mound (perchlorate reduction). The combined results revealed different stages of colonization that reflect differences in the lifetime of the mounds, where primary communities dominated the biosignatures preserved in sinters from the still active geysers (liquid and steam mounds), in contrast to the surviving metabolisms and microbial communities at the end of lifetime of the inactive geothermal mound.
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Affiliation(s)
| | | | | | | | - Sherry L Cady
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Nancy Hinman
- Department of Geosciences, University of Montana, Missoula, MT, United States
| | - Mark E Bowden
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Stephen B Pointing
- Yale-NUS College, National University of Singapore, Singapore, Singapore
| | - Kevin C Lee
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Kimberly Warren-Rhodes
- SETI Institute, Mountain View, CA, United States.,NASA Ames Research Center, Moffett Field, CA, United States
| | | | - Nathalie A Cabrol
- SETI Institute, Mountain View, CA, United States.,NASA Ames Research Center, Moffett Field, CA, United States
| | - Victor Parro
- Centro de Astrobiología (CSIC-INTA), Madrid, Spain
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Draft Genome Sequence of Moorella sp. Strain Hama-1, a Novel Acetogenic Bacterium Isolated from a Thermophilic Digestion Reactor. GENOME ANNOUNCEMENTS 2018; 6:6/24/e00517-18. [PMID: 29903821 PMCID: PMC6003730 DOI: 10.1128/genomea.00517-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Moorella sp. strain Hama-1 was isolated from a thermophilic anaerobic digestion reactor treating poly(l-lactic acid). The strain is a thermophilic acetogen capable of lactate oxidation under anaerobic conditions. Here, we report the draft genome sequence of strain Hama-1, comprising 3.27 Mb in 48 contigs, with a G+C content of 56.6%.
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13
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Stable Isotope Probing for Microbial Iron Reduction in Chocolate Pots Hot Spring, Yellowstone National Park. Appl Environ Microbiol 2018; 84:AEM.02894-17. [PMID: 29602784 DOI: 10.1128/aem.02894-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/26/2018] [Indexed: 11/20/2022] Open
Abstract
Chocolate Pots hot springs (CP) is a circumneutral-pH Fe-rich geothermal feature located in Yellowstone National Park. Previous Fe(III)-reducing enrichment culture studies with CP sediments identified close relatives of known dissimilatory Fe(III)-reducing bacterial (FeRB) taxa, including Geobacter and Melioribacter However, the abundances and activities of such organisms in the native microbial community are unknown. Here, we used stable isotope probing experiments combined with 16S rRNA gene amplicon and shotgun metagenomic sequencing to gain an understanding of the in situ Fe(III)-reducing microbial community at CP. Fe-Si oxide precipitates collected near the hot spring vent were incubated with unlabeled and 13C-labeled acetate to target active FeRB. We searched reconstructed genomes for homologs of genes involved in known extracellular electron transfer (EET) systems to identify the taxa involved in Fe redox transformations. Known FeRB taxa containing putative EET systems (Geobacter, Ignavibacteria) increased in abundance under acetate-amended conditions, whereas genomes related to Ignavibacterium and Thermodesulfovibrio that contained putative EET systems were recovered from incubations without electron donor. Our results suggest that FeRB play an active role in Fe redox cycling within Fe-Si oxide-rich deposits located at the hot spring vent.IMPORTANCE The identification of past near-surface hydrothermal environments on Mars emphasizes the importance of using modern Earth environments, such as CP, to gain insight into potential Fe-based microbial life on other rocky worlds, as well as ancient Fe-rich Earth ecosystems. By combining stable carbon isotope probing techniques and DNA sequencing technology, we gained insight into the pathways of microbial Fe redox cycling at CP. The results suggest that microbial Fe(III) oxide reduction is prominent in situ, with important implications for the generation of geochemical and stable Fe isotopic signatures of microbial Fe redox metabolism within Fe-rich circumneutral-pH thermal spring environments on Earth and Mars.
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14
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Draft Genome Sequence of the Thermophilic Acetogen Moorella humiferrea DSM 23265. GENOME ANNOUNCEMENTS 2018; 6:6/17/e00357-18. [PMID: 29700162 PMCID: PMC5920165 DOI: 10.1128/genomea.00357-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Moorella humiferrea is an endospore-forming, anaerobic, and thermophilic bacterium which was isolated from a terrestrial hydrothermal spring. M. humiferrea is able to use humic acid or 10-anthraquinone-2,6-disulfonate as an electron-shuttling compound for growth and Fe(III) reduction. The genome has a size of 2.629 Mb and contains 2,668 predicted protein-coding genes.
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15
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Dai K, Wen JL, Zhang F, Ma XW, Cui XY, Zhang Q, Zhao TJ, Zeng RJ. Electricity production and microbial characterization of thermophilic microbial fuel cells. BIORESOURCE TECHNOLOGY 2017; 243:512-519. [PMID: 28697453 DOI: 10.1016/j.biortech.2017.06.167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 06/23/2017] [Accepted: 06/29/2017] [Indexed: 06/07/2023]
Abstract
Thermophilic microbial fuel cell (TMFC) offers many benefits, but the investigations on the diversity of exoelectrogenic bacteria are scarce. In this study, a two-chamber TMFC was constructed using ethanol as an electron donor, and the microbial dynamics were analyzed by high-throughput sequencing and 16S rRNA clone-library sequencing. The open-circuit potential of TMFC was approximately 650mV, while the maximum voltage was around 550mV. The maximum power density was 437mW/m2, and the columbic efficiency in this work was 20.5±6.0%. The Firmicutes bacteria, related to the uncultured bacterium clone A55_D21_H_B_C01 with a similarity of 99%, accounted for 90.9% of all bacteria in the TMFC biofilm. This unknown bacterium has the potential to become a new thermophilic exoelectrogenic bacterium that is yet to be cultured. The development of TMFC-involved biotechnologies will be beneficial for the production of valuable chemicals and generation of energy in the future.
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Affiliation(s)
- Kun Dai
- Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao, Hebei 066004, People's Republic of China
| | - Jun-Li Wen
- Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao, Hebei 066004, People's Republic of China
| | - Fang Zhang
- Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao, Hebei 066004, People's Republic of China.
| | - Xi-Wen Ma
- Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao, Hebei 066004, People's Republic of China
| | - Xiang-Yu Cui
- Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao, Hebei 066004, People's Republic of China
| | - Qi Zhang
- Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao, Hebei 066004, People's Republic of China
| | - Ting-Jia Zhao
- Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao, Hebei 066004, People's Republic of China
| | - Raymond J Zeng
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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16
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Propionate metabolism and diversity of relevant functional genes by in silico analysis and detection in subsurface petroleum reservoirs. World J Microbiol Biotechnol 2017; 33:182. [PMID: 28942530 DOI: 10.1007/s11274-017-2350-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 09/21/2017] [Indexed: 10/18/2022]
Abstract
Propionate is a common metabolic intermediate occurring in environmental samples including petroleum reservoirs. Available microbial genomes were obtained from the NCBI database and analyzed in silico by hmmscan to check three metabolic pathways of propionate production in petroleum reservoir systems. The succinate pathway was the dominant one while the other two (lactate and 1,2-propanediol pathways) contributed less to the formation of propionate according to the Hidden Markov Model calculation. The mmdA gene encoding methylmalonyl-CoA decarboxylase was used as a biomarker gene to detect the diversity of microbes involved in the propionate formation in Jiangsu oil reservoirs. The mmdA gene clone library showed that microbes affiliated within the genus of Archaeoglobus, Thermococcus, Anaerobaculum, as well as more than ten other genera were the potential microorganisms involved in the production of propionate. Meanwhile, as the biomarker genes involved in the other two propionate-producing pathways, the functional genes of lcdA and pduP were tested with PCR amplification, but no positive results were observed in Jiangsu oil reservoirs.
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17
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Iron oxides alter methanogenic pathways of acetate in production water of high-temperature petroleum reservoir. Appl Microbiol Biotechnol 2017; 101:7053-7063. [PMID: 28730409 DOI: 10.1007/s00253-017-8422-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 07/03/2017] [Accepted: 07/04/2017] [Indexed: 12/21/2022]
Abstract
Acetate is a key intermediate in anaerobic crude oil biodegradation and also a precursor for methanogenesis in petroleum reservoirs. The impact of iron oxides, viz. β-FeOOH (akaganéite) and magnetite (Fe3O4), on the methanogenic acetate metabolism in production water of a high-temperature petroleum reservoir was investigated. Methane production was observed in all the treatments amended with acetate. In the microcosms amended with acetate solely about 30% of the acetate utilized was converted to methane, whereas methane production was stimulated in the presence of magnetite (Fe3O4) resulting in a 48.34% conversion to methane. Methane production in acetate-amended, β-FeOOH (akaganéite)-supplemented microcosms was much faster and acetate consumption was greatly improved compared to the other conditions in which the stoichiometric expected amounts of methane were not produced. Microbial community analysis showed that Thermacetogenium spp. (known syntrophic acetate oxidizers) and hydrogenotrophic methanogens closely related to Methanothermobacter spp. were enriched in acetate and acetate/magnetite (Fe3O4) microcosms suggesting that methanogenic acetate metabolism was through hydrogenotrophic methanogenesis fueled by syntrophic acetate oxidizers. The acetate/β-FeOOH (akaganéite) microcosms, however, differed by the dominance of archaea closely related to the acetoclastic Methanosaeta thermophila. These observations suggest that supplementation of β-FeOOH (akaganéite) accelerated the production of methane further, driven the alteration of the methanogenic community, and changed the pathway of acetate methanogenesis from hydrogenotrophic methanogenesis fueled by syntrophic acetate oxidizers to acetoclastic.
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18
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Liebensteiner MG, Pinkse MWH, Nijsse B, Verhaert PDEM, Tsesmetzis N, Stams AJM, Lomans BP. Perchlorate and chlorate reduction by the Crenarchaeon Aeropyrum pernix and two thermophilic Firmicutes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:936-945. [PMID: 26332065 DOI: 10.1111/1758-2229.12335] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 08/27/2015] [Indexed: 06/05/2023]
Abstract
This study reports the ability of one hyperthermophilic and two thermophilic microorganisms to grow anaerobically by the reduction of chlorate and perchlorate. Physiological, genomic and proteome analyses suggest that the Crenarchaeon Aeropyrum pernix reduces perchlorate with a periplasmic enzyme related to nitrate reductases, but that it lacks a functional chlorite-disproportionating enzyme (Cld) to complete the pathway. Aeropyrum pernix, previously described as a strictly aerobic microorganism, seems to rely on the chemical reactivity of reduced sulfur compounds with chlorite, a mechanism previously reported for perchlorate-reducing Archaeoglobus fulgidus. The chemical oxidation of thiosulfate (in excessive amounts present in the medium) and the reduction of chlorite result in the release of sulfate and chloride, which are the products of a biotic-abiotic perchlorate reduction pathway in Ae. pernix. The apparent absence of Cld in two other perchlorate-reducing microorganisms, Carboxydothermus hydrogenoformans and Moorella glycerini strain NMP, and their dependence on sulfide for perchlorate reduction is consistent with the observations made on Ar. fulgidus. Our findings suggest that microbial perchlorate reduction at high temperature differs notably from the physiology of perchlorate- and chlorate-reducing mesophiles and that it is characterized by the lack of a chlorite dismutase and is enabled by a combination of biotic and abiotic reactions.
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Affiliation(s)
- Martin G Liebensteiner
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
| | - Martijn W H Pinkse
- Analytical Biotechnology Section, Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
- Netherlands Proteomics Centre, Julianalaan 67, 2628 BC, Delft, The Netherlands
| | - Bart Nijsse
- Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
| | - Peter D E M Verhaert
- Analytical Biotechnology Section, Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
- Netherlands Proteomics Centre, Julianalaan 67, 2628 BC, Delft, The Netherlands
| | - Nicolas Tsesmetzis
- Shell International Exploration and Production Inc., 3333 Highway 6 South, Houston, TX, 77082, USA
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Bart P Lomans
- Shell Global Solutions International B.V., Kessler Park 1, 2288 GS, Rijswijk, The Netherlands
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19
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Liebensteiner MG, Oosterkamp MJ, Stams AJM. Microbial respiration with chlorine oxyanions: diversity and physiological and biochemical properties of chlorate- and perchlorate-reducing microorganisms. Ann N Y Acad Sci 2015; 1365:59-72. [PMID: 26104311 DOI: 10.1111/nyas.12806] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Chlorine oxyanions are valuable electron acceptors for microorganisms. Recent findings have shed light on the natural formation of chlorine oxyanions in the environment. These suggest a permanent introduction of respective compounds on Earth, long before their anthropogenic manufacture. Microorganisms that are able to grow by the reduction of chlorate and perchlorate are affiliated with phylogenetically diverse lineages, spanning from the Proteobacteria to the Firmicutes and archaeal microorganisms. Microbial reduction of chlorine oxyanions can be found in diverse environments and different environmental conditions (temperature, salinities, pH). It commonly involves the enzymes perchlorate reductase (Pcr) or chlorate reductase (Clr) and chlorite dismutase (Cld). Horizontal gene transfer seems to play an important role for the acquisition of functional genes. Novel and efficient Clds were isolated from microorganisms incapable of growing on chlorine oxyanions. Archaea seem to use a periplasmic Nar-type reductase (pNar) for perchlorate reduction and lack a functional Cld. Chlorite is possibly eliminated by alternative (abiotic) reactions. This was already demonstrated for Archaeoglobus fulgidus, which uses reduced sulfur compounds to detoxify chlorite. A broad biochemical diversity of the trait, its environmental dispersal, and the occurrence of relevant enzymes in diverse lineages may indicate early adaptations of life toward chlorine oxyanions on Earth.
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Affiliation(s)
| | - Margreet J Oosterkamp
- Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands.,Energy Biosciences Institute, University of Illinois, Urbana, Illinois
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands.,Department of Biological Engineering, University of Minho, Braga, Portugal
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20
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Zeng X, Zhang Z, Li X, Zhang X, Cao J, Jebbar M, Alain K, Shao Z. Anoxybacter fermentans gen. nov., sp. nov., a piezophilic, thermophilic, anaerobic, fermentative bacterium isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2014; 65:710-715. [PMID: 25505345 DOI: 10.1099/ijs.0.068221-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel piezophilic, thermophilic, anaerobic, fermentative bacterial strain, designated strain DY22613(T), was isolated from a deep-sea hydrothermal sulfide deposit at the East Pacific Rise (GPS position: 102.6° W 3.1° S). Cells of strain DY22613(T) were long, motile rods (10 to 20 µm in length and 0.5 µm in width) with peritrichous flagella and were Gram-stain-negative. Growth was recorded at 44-72 °C (optimum 60-62 °C) and at hydrostatic pressures of 0.1-55 MPa (optimum 20 MPa). The pH range for growth was from pH 5.0 to 9.0 with an optimum at pH 7.0. Growth was observed in the presence of 1 to 8 % (w/v) sea salts and 0.65 to 5.2 % (w/v) NaCl, with optimum salt concentrations at 3.5 % for sea salts and at 2.3 % for NaCl. Under optimal growth conditions, the shortest generation time observed was 27 min (60 °C, 20 MPa). Strain DY22613(T) was heterotrophic, able to utilize complex organic compounds, amino acids, sugars and organic acids including peptone, tryptone, beef extract, yeast extract, alanine, glutamine, methionine, phenylalanine, serine, threonine, fructose, fucose, galactose, gentiobiose, glucose, mannose, melibiose, palatinose, rhamnose, turanose, pyruvate, lactic acid, methyl ester, erythritol, galacturonic acid and glucosaminic acid. Strain DY22613(T) was able to reduce Fe(III) compounds, including Fe(III) oxyhydroxide (pH 7.0), amorphous iron(III) oxide (pH 9.0), goethite (α-FeOOH, pH 12.0), Fe(III) citrate and elementary sulfur. Products of fermentation were butyrate, acetate and hydrogen. Main cellular fatty acids were iso-C15 : 0, iso-C14 : 0 3-OH and C14 : 0. The genomic DNA G+C content of strain DY22613(T) was 36.7 mol%. Based on 16S rRNA gene sequence analysis, the strain forms a novel lineage within the class Clostridia and clusters with the order Haloanaerobiales (86.92 % 16S rRNA gene sequence similarity). The phylogenetic data suggest that the lineage represents at least a novel genus and species, for which the name Anoxybacter fermentans gen. nov., sp. nov. is proposed. The type strain is DY22613(T) ( = JCM 19466(T) = DSM 28033(T) = MCCC 1A06456(T)).
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Affiliation(s)
- Xiang Zeng
- Xiamen State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography SOA, Xiamen, Fujian 361005, PR China
| | - Zhao Zhang
- Xiamen State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography SOA, Xiamen, Fujian 361005, PR China
| | - Xi Li
- Xiamen State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography SOA, Xiamen, Fujian 361005, PR China
| | - Xiaobo Zhang
- Xiamen State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography SOA, Xiamen, Fujian 361005, PR China
| | - Junwei Cao
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Pointe du diable, F-29280 Plouzané, France.,Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography SOA, Xiamen, Fujian 361005, PR China.,Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France.,Xiamen State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, Fujian 361005, PR China.,CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, Fujian 361005, PR China
| | - Mohamed Jebbar
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Pointe du diable, F-29280 Plouzané, France.,CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France.,Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France
| | - Karine Alain
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Pointe du diable, F-29280 Plouzané, France.,CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France.,Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France
| | - Zongze Shao
- Xiamen State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography SOA, Xiamen, Fujian 361005, PR China
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21
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Brantner JS, Haake ZJ, Burwick JE, Menge CM, Hotchkiss ST, Senko JM. Depth-dependent geochemical and microbiological gradients in Fe(III) deposits resulting from coal mine-derived acid mine drainage. Front Microbiol 2014; 5:215. [PMID: 24860562 PMCID: PMC4030175 DOI: 10.3389/fmicb.2014.00215] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/23/2014] [Indexed: 02/01/2023] Open
Abstract
We evaluated the depth-dependent geochemistry and microbiology of sediments that have developed via the microbially-mediated oxidation of Fe(II) dissolved in acid mine drainage (AMD), giving rise to a 8–10 cm deep “iron mound” that is composed primarily of Fe(III) (hydr)oxide phases. Chemical analyses of iron mound sediments indicated a zone of maximal Fe(III) reducing bacterial activity at a depth of approximately 2.5 cm despite the availability of dissolved O2 at this depth. Subsequently, Fe(II) was depleted at depths within the iron mound sediments that did not contain abundant O2. Evaluations of microbial communities at 1 cm depth intervals within the iron mound sediments using “next generation” nucleic acid sequencing approaches revealed an abundance of phylotypes attributable to acidophilic Fe(II) oxidizing Betaproteobacteria and the chloroplasts of photosynthetic microeukaryotic organisms in the upper 4 cm of the iron mound sediments. While we observed a depth-dependent transition in microbial community structure within the iron mound sediments, phylotypes attributable to Gammaproteobacterial lineages capable of both Fe(II) oxidation and Fe(III) reduction were abundant in sequence libraries (comprising ≥20% of sequences) from all depths. Similarly, abundances of total cells and culturable Fe(II) oxidizing bacteria were uniform throughout the iron mound sediments. Our results indicate that O2 and Fe(III) reduction co-occur in AMD-induced iron mound sediments, but that Fe(II)-oxidizing activity may be sustained in regions of the sediments that are depleted in O2.
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Affiliation(s)
- Justin S Brantner
- Department of Biology, The University of Akron Akron, OH, USA ; Integrated Bioscience Program, The University of Akron Akron, OH, USA
| | - Zachary J Haake
- Department of Geosciences, The University of Akron Akron, OH, USA
| | - John E Burwick
- Department of Geosciences, The University of Akron Akron, OH, USA
| | | | | | - John M Senko
- Department of Biology, The University of Akron Akron, OH, USA ; Integrated Bioscience Program, The University of Akron Akron, OH, USA ; Department of Geosciences, The University of Akron Akron, OH, USA
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22
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Martinez CM, Alvarez LH, Celis LB, Cervantes FJ. Humus-reducing microorganisms and their valuable contribution in environmental processes. Appl Microbiol Biotechnol 2013; 97:10293-308. [PMID: 24220793 DOI: 10.1007/s00253-013-5350-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 10/17/2013] [Accepted: 10/19/2013] [Indexed: 02/08/2023]
Abstract
Humus constitutes a very abundant class of organic compounds that are chemically heterogeneous and widely distributed in terrestrial and aquatic environments. Evidence accumulated during the last decades indicating that humic substances play relevant roles on the transport, fate, and redox conversion of organic and inorganic compounds both in chemically and microbially driven reactions. The present review underlines the contribution of humus-reducing microorganisms in relevant environmental processes such as biodegradation of recalcitrant pollutants and mitigation of greenhouse gases emission in anoxic ecosystems, redox conversion of industrial contaminants in anaerobic wastewater treatment systems, and on the microbial production of nanocatalysts and alternative energy sources.
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Affiliation(s)
- Claudia M Martinez
- División de Ciencias Ambientales, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), Camino a la Presa San José 2055, Col. Lomas 4a Sección, San Luis Potosí, SLP, 78216, Mexico
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23
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Alves JI, van Gelder AH, Alves MM, Sousa DZ, Plugge CM. Moorella stamsii sp. nov., a new anaerobic thermophilic hydrogenogenic carboxydotroph isolated from digester sludge. Int J Syst Evol Microbiol 2013; 63:4072-4076. [DOI: 10.1099/ijs.0.050369-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel anaerobic, thermophilic, carbon monoxide-utilizing bacterium, strain E3-OT, was isolated from anaerobic sludge from a municipal solid waste digester. Cells were straight rods, 0.6–1 µm in diameter and 2–3 µm in length and grew as single cells or in pairs. Cells formed round terminal endospores. The temperature range for growth was 50–70 °C, with an optimum at 65 °C. The pH range for growth was 5.7–8.0, with an optimum at 7.5. Strain E3-OT had the ability to ferment various sugars, such as fructose, galactose, glucose, mannose, raffinose, ribose, sucrose and xylose, producing mainly H2 and acetate. In addition, the isolate was able to grow with CO as the sole carbon and energy source. CO oxidation was coupled to H2 and CO2 formation. The G+C content of the genomic DNA was 54.6 mol%. Based on 16S rRNA gene sequence analysis, this bacterium is most closely related to
Moorella glycerini
(97 % sequence identity). Based on the physiological features and phylogenetic analysis, it is proposed that strain E3-OT should be classified in the genus
Moorella
as a representative of a novel species, Moorella
stamsii. The type strain of Moorella stamsii is E3-OT ( = DSM 26271T = CGMCC 1.5181T).
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Affiliation(s)
- J. I. Alves
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
- Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - A. H. van Gelder
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - M. M. Alves
- Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - D. Z. Sousa
- Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - C. M. Plugge
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
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24
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Yoneda Y, Yoshida T, Yasuda H, Imada C, Sako Y. A thermophilic, hydrogenogenic and carboxydotrophic bacterium, Calderihabitans maritimus gen. nov., sp. nov., from a marine sediment core of an undersea caldera. Int J Syst Evol Microbiol 2013; 63:3602-3608. [PMID: 23606483 DOI: 10.1099/ijs.0.050468-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A hydrogenogenic, carboxydotrophic marine bacterium, strain KKC1(T), was isolated from a sediment core sample taken from a submerged marine caldera. Cells were non-motile, Gram-stain-negative, 1.0-3.0 µm straight rods, often observed with round endospores. Strain KKC1(T) grew at 55-68 °C, pH 5.2-9.2 and 0.8-14 % (w/v) salinity. Optimum growth occurred at 65 °C, pH 7.0-7.5 and 2.46 % salinity with a doubling time of 3.7 h. The isolate grew chemolithotrophically, producing H2 from carbon monoxide (CO) oxidation with reduction of various electron acceptors, e.g. sulfite, thiosulfate, fumarate, ferric iron and AQDS (9,10-anthraquinone 2,6-disulfonate). KKC1(T) grew heterotrophically on pyruvate, lactate, fumarate, glucose, fructose and mannose with thiosulfate as an electron acceptor. When grown mixotrophically on CO and pyruvate, C16 : 0 constituted almost half of the total cellular fatty acids. The DNA G+C content was 50.6 mol%. The 16S rRNA gene sequence of KKC1(T) was most closely related to those of members of the genus Moorella with similarity ranging from 91 to 89 %. Based on physiological and phylogenetic novelty, we propose the isolate as a representative of a new genus and novel species with the name Calderihabitans maritimus gen. nov., sp. nov.; the type strain of the type species is KKC1(T) ( = DSM 26464(T) = NBRC 109353(T)).
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Affiliation(s)
- Yasuko Yoneda
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Takashi Yoshida
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Hisato Yasuda
- Center for Advance Marine Core Research, Kochi University, Kochi 783-8502, Japan
| | - Chiaki Imada
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Yoshihiko Sako
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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