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Hwang IY, Kalyuzhnaya MG, Lee EY. Quantitative assessment of methane bioconversion based on kinetics and bioenergetics. BIORESOURCE TECHNOLOGY 2024; 410:131269. [PMID: 39163949 DOI: 10.1016/j.biortech.2024.131269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 08/06/2024] [Accepted: 08/11/2024] [Indexed: 08/22/2024]
Abstract
The biological conversion of methane under ambient conditions can be performed by methanotrophs that utilize methane as both a sole source of energy and a carbon source. However, compared to the established microbial chassis used for general fermentation with sugar as a feedstock, the productivity of methanotrophs is low. The fundamental knowledge of their metabolic or cellular bottlenecks is limited. In this review, the industrial-scale potential of methane bioconversion was evaluated. In particular, the enzyme kinetics associated with the oxidation and assimilation of methane were investigated to evaluate the potential of methane fermentation. The kinetics of enzymes involved in methane metabolism were compared with those used in the metabolic processes of traditional fermentation (glycolysis). Through this analysis, the current limitations of methane metabolism were identified. Methods for increasing the efficiency of methane bioconversion and directions for the industrial application of methane-based fermentation were discussed.
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Affiliation(s)
- In Yeub Hwang
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), College of Engineering, Kyung Hee University, Gyeonggi-do 17104, Republic of Korea
| | - M G Kalyuzhnaya
- Department of Biology, San Diego State University, San Diego CA92182, USA.
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), College of Engineering, Kyung Hee University, Gyeonggi-do 17104, Republic of Korea.
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2
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Rodero MDR, Carmona-Martínez AA, Martínez-Fraile C, Herrero-Lobo R, Rodríguez E, García-Encina PA, Peña M, Muñoz R. Ectoines production from biogas in pilot bubble column bioreactors and their subsequent extraction via bio-milking. WATER RESEARCH 2023; 245:120665. [PMID: 37801795 DOI: 10.1016/j.watres.2023.120665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 09/17/2023] [Accepted: 09/22/2023] [Indexed: 10/08/2023]
Abstract
Despite the potential of biogas from waste/wastewater treatment as a renewable energy source, the presence of pollutants and the rapid decrease in the levelized cost of solar and wind power constrain the use of biogas for energy generation. Biogas conversion into ectoine, one of the most valuable bioproducts (1000 €/kg), constitutes a new strategy to promote a competitive biogas market. The potential for a stand-alone 20 L bubble column bioreactor operating at 6% NaCl and two 10 L interconnected bioreactors (at 0 and 6% NaCl, respectively) for ectoine production from biogas was comparatively assessed. The stand-alone reactor supported the best process performance due to its highest robustness and efficiency for ectoine accumulation (20-52 mgectoine/gVSS) and CH4 degradation (up to 84%). The increase in N availability and internal gas recirculation did not enhance ectoine synthesis. However, a 2-fold increase in the internal gas recirculation resulted in an approximately 1.3-fold increase in CH4 removal efficiency. Finally, the recovery of ectoine through bacterial bio-milking resulted in efficiencies of >70% without any negative impact of methanotrophic cell recycling to the bioreactors on CH4 biodegradation or ectoine synthesis.
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Affiliation(s)
- María Del Rosario Rodero
- Institute of Sustainable Processes, University of Valladolid, Valladolid 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid 47011, Spain
| | - Alessandro A Carmona-Martínez
- Institute of Sustainable Processes, University of Valladolid, Valladolid 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid 47011, Spain
| | - Cristina Martínez-Fraile
- Institute of Sustainable Processes, University of Valladolid, Valladolid 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid 47011, Spain
| | - Raquel Herrero-Lobo
- Institute of Sustainable Processes, University of Valladolid, Valladolid 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid 47011, Spain
| | - Elisa Rodríguez
- Institute of Sustainable Processes, University of Valladolid, Valladolid 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid 47011, Spain
| | - Pedro A García-Encina
- Institute of Sustainable Processes, University of Valladolid, Valladolid 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid 47011, Spain
| | - Mar Peña
- Institute of Sustainable Processes, University of Valladolid, Valladolid 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid 47011, Spain
| | - Raúl Muñoz
- Institute of Sustainable Processes, University of Valladolid, Valladolid 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid 47011, Spain.
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Tikhonova EN, Suleimanov RZ, Oshkin IY, Konopkin AA, Fedoruk DV, Pimenov NV, Dedysh SN. Growing in Saltwater: Biotechnological Potential of Novel Methylotuvimicrobium- and Methylomarinum-like Methanotrophic Bacteria. Microorganisms 2023; 11:2257. [PMID: 37764101 PMCID: PMC10538026 DOI: 10.3390/microorganisms11092257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/02/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Methanotrophic bacteria that possess a unique ability of using methane as a sole source of carbon and energy have attracted considerable attention as potential producers of a single-cell protein. So far, this biotechnology implied using freshwater methanotrophs, although many regions of the world have limited freshwater resources. This study aimed at searching for novel methanotrophs capable of fast growth in saltwater comparable in composition with seawater. A methane-oxidizing microbial consortium containing Methylomarinum- and Methylotuvimicrobium-like methanotrophs was enriched from sediment from the river Chernavka (water pH 7.5, total salt content 30 g L-1), a tributary river of the hypersaline Lake Elton, southern Russia. This microbial consortium, designated Ch1, demonstrated stable growth on natural gas in a bioreactor in media with a total salt content of 23 to 35.9 g L-1 at a dilution rate of 0.19-0.21 h-1. The highest biomass yield of 5.8 g cell dry weight (CDW)/L with a protein content of 63% was obtained during continuous cultivation of the consortium Ch1 in a medium with a total salt content of 29 g L-1. Isolation attempts resulted in obtaining a pure culture of methanotrophic bacteria, strain Ch1-1. The 16S rRNA gene sequence of strain Ch1-1 displayed 97.09-97.24% similarity to the corresponding gene fragments of characterized representatives of Methylomarinum vadi, methanotrophs isolated from marine habitats. The genome of strain Ch1-1 was 4.8 Mb in size and encoded 3 rRNA operons, and about 4400 proteins. The genome contained the gene cluster coding for ectoine biosynthesis, which explains the ability of strain Ch1-1 to tolerate high salt concentration.
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Affiliation(s)
| | | | | | | | | | | | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (E.N.T.); (R.Z.S.); (I.Y.O.); (A.A.K.); (D.V.F.); (N.V.P.)
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4
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Insights into methanotroph carbon flux pave the way for methane biocatalysis. Trends Biotechnol 2023; 41:298-300. [PMID: 36710132 DOI: 10.1016/j.tibtech.2023.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/29/2023]
Abstract
Methanotrophic bacteria are used industrially as catalysts for the bioconversion of methane (CH4) to valuable products. A landmark study by Kalyuzhnaya et al. identified the primary metabolic route for CH4 flux to central metabolic intermediates and alternative fermentative products in an industrially promising methanotroph, leading to a systems-level understanding of methanotrophy.
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Yao X, Wang J, Hu B. How methanotrophs respond to pH: A review of ecophysiology. Front Microbiol 2023; 13:1034164. [PMID: 36687570 PMCID: PMC9853399 DOI: 10.3389/fmicb.2022.1034164] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/09/2022] [Indexed: 01/08/2023] Open
Abstract
Varying pH globally affects terrestrial microbial communities and biochemical cycles. Methanotrophs effectively mitigate methane fluxes in terrestrial habitats. Many methanotrophs grow optimally at neutral pH. However, recent discoveries show that methanotrophs grow in strongly acidic and alkaline environments. Here, we summarize the existing knowledge on the ecophysiology of methanotrophs under different pH conditions. The distribution pattern of diverse subgroups is described with respect to their relationship with pH. In addition, their responses to pH stress, consisting of structure-function traits and substrate affinity traits, are reviewed. Furthermore, we propose a putative energy trade-off model aiming at shedding light on the adaptation mechanisms of methanotrophs from a novel perspective. Finally, we take an outlook on methanotrophs' ecophysiology affected by pH, which would offer new insights into the methane cycle and global climate change.
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Affiliation(s)
- Xiangwu Yao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China,Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China,*Correspondence: Baolan Hu ✉
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Tanikawa D, Motokawa D, Itoiri Y, Kimura ZI, Ito M, Nagano A. Biogas purification and ammonia load reduction in sewage treatment by two-stage down-flow hanging sponge reactor. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158355. [PMID: 36041617 DOI: 10.1016/j.scitotenv.2022.158355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/13/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
In this study, a two-stage down-flow hanging sponge (TSDHS) reactor was used as biotrickling filter for biogas desulfurization by utilizing the anaerobic digester supernatant (ADS) of sewage sludge of an activated sludge process (ASP). The reactor comprises a closed-type first-stage down-flow hanging sponge (1st DHS) and an open-type second-stage down-flow hanging sponge (2nd DHS) reactors. In the 1st DHS, hydrogen sulfide in biogas was dissolved into the ADS, and then it was oxidized into elemental sulfur and sulfate by microbe using dissolved oxygen and nitrite in the ADS. More than 99.9 % of hydrogen sulfide was removed within 400 s of empty bed residence time, and >50 % of removed hydrogen sulfide was oxidized into elemental sulfur and accumulated at the surface of the sponge carrier in the 1st DHS. The 1st DHS effluent was fed into the 2nd DHS for nitrogen removal via nitrification and sulfur-based denitrification with the recirculation of the 2nd DHS effluent under nonaeration condition. In the 2nd DHS, 36.8 % of ammonia and 5.3 % of total inorganic nitrogen were removed. Sulfurimonas and Halothiobacillus were increased and contributed to the sulfur-based denitrification as well as the accumulation of elemental sulfur in the 1st DHS, respectively. In the 2nd DHS, Nitrosococcus, Nitrobacter, and Sulfuritalea were considered as the contributors of nitrogen removal via nitrification and sulfur-based denitrification. Further, this study shows that a TSDHS reactor can achieve not only desulfurization of biogas in the 1st DHS but also a 3.5 %-15 % reduction of the ammonia load in the 2nd DHS by effective utilization of the ADS during sewage treatment, assuming that the ADS is returned to the ASP.
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Affiliation(s)
- Daisuke Tanikawa
- Department of Civil and Environmental Engineering, National Institute of Technology (KOSEN), Kure College, P.C. 7378506 Kure, Japan.
| | - Daisuke Motokawa
- Advanced Course, Project Design Engineering, National Institute of Technology (KOSEN), Kure College, P.C. 7378506 Kure, Japan
| | - Yuya Itoiri
- Advanced Course, Project Design Engineering, National Institute of Technology (KOSEN), Kure College, P.C. 7378506 Kure, Japan
| | - Zen-Ichiro Kimura
- Department of Civil and Environmental Engineering, National Institute of Technology (KOSEN), Kure College, P.C. 7378506 Kure, Japan
| | - Masahiro Ito
- Technical Research & Development Center, Sanki Engineering Co., Ltd., P.C. 2420007 Yamato, Japan
| | - Akihiro Nagano
- Technical Research & Development Center, Sanki Engineering Co., Ltd., P.C. 2420007 Yamato, Japan
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Cantera S, Sousa DZ, Sánchez-Andrea I. Enhanced ectoines production by carbon dioxide capture: A step further towards circular economy. J CO2 UTIL 2022. [DOI: 10.1016/j.jcou.2022.102009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Carmona-Martínez AA, Marcos-Rodrigo E, Bordel S, Marín D, Herrero-Lobo R, García-Encina PA, Muñoz R. Elucidating the key environmental parameters during the production of ectoines from biogas by mixed methanotrophic consortia. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 298:113462. [PMID: 34365180 DOI: 10.1016/j.jenvman.2021.113462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 07/06/2021] [Accepted: 07/31/2021] [Indexed: 05/12/2023]
Abstract
Anaerobic digestion (AD) is a robust biotechnology for the valorisation of organic waste into biogas. However, the rapid decrease in renewable electricity prices requires alternative uses of biogas. In this context, the engineering of innovative platforms for the bio-production of chemicals from CH4 has recently emerged. The extremolyte and osmoprotectant ectoine, with a market price of ~1000€/Kg, is the industrial flagship of CH4-based bio-chemicals. This work aimed at optimizing the accumulation of ectoines using mixed microbial consortia enriched from saline environments (a salt lagoon and a salt river) and activated sludge, and biogas as feedstock. The influence of NaCl (0, 3, 6, 9 and 12 %) and Na2WO4 (0, 35 and 70 μg L-1) concentrations and incubation temperature (15, 25 and 35 °C) on the stoichiometry and kinetics of the methanotrophic consortia was investigated. Consortia enriched from activated sludge at 15 °C accumulated the highest yields of ectoine and hydroxyectoine at 6 % NaCl (105.0 ± 27.2 and 24.2 ± 5.4 mgextremolyte gbiomass-1, respectively). The consortia enriched from the salt lagoon accumulated the highest yield of ectoine and hydroxyectoine at 9 % NaCl (56.6 ± 2.5 and 51.0 ± 2.0 mgextremolyte gbiomass-1, respectively) at 25 °C. The supplementation of tungsten to the cultivation medium did not impact on the accumulation of ectoines in any of the consortia. A molecular characterization of the enrichments revealed a relative abundance of ectoine-accumulating methanotrophs of 7-16 %, with Methylomicrobium buryatense and Methylomicrobium japanense as the main players in the bioconversion of methane into ectoine.
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Affiliation(s)
- Alessandro A Carmona-Martínez
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain
| | - Eva Marcos-Rodrigo
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain
| | - Sergio Bordel
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain
| | - David Marín
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain
| | - Raquel Herrero-Lobo
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain
| | - Pedro A García-Encina
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain
| | - Raúl Muñoz
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain; Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina s/n., Valladolid, 47011, Spain.
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Rahalkar MC, Khatri K, Pandit P, Bahulikar RA, Mohite JA. Cultivation of Important Methanotrophs From Indian Rice Fields. Front Microbiol 2021; 12:669244. [PMID: 34539593 PMCID: PMC8447245 DOI: 10.3389/fmicb.2021.669244] [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: 02/18/2021] [Accepted: 08/09/2021] [Indexed: 11/15/2022] Open
Abstract
Methanotrophs are aerobic to micro-aerophilic bacteria, which oxidize and utilize methane, the second most important greenhouse gas. The community structure of the methanotrophs in rice fields worldwide has been studied mainly using culture-independent methods. Very few studies have focused on culturing methanotrophs from rice fields. We developed a unique method for the cultivation of methanotrophs from rice field samples. Here, we used a modified dilute nitrate mineral salts (dNMS) medium, with two cycles of dilution till extinction series cultivation with prolonged incubation time, and used agarose in the solid medium. The cultivation approach resulted in the isolation of methanotrophs from seven genera from the three major groups: Type Ia (Methylomonas, Methylomicrobium, and Methylocucumis), Type Ib (Methylocaldum and Methylomagnum), and Type II (Methylocystis and Methylosinus). Growth was obtained till 10–6–10–8 dilutions in the first dilution series, indicating the culturing of dominant methanotrophs. Our study was supported by 16S rRNA gene-based next-generation sequencing (NGS) of three of the rice samples. Our analyses and comparison with the global scenario suggested that the cultured members represented the major detected taxa. Strain RS1, representing a putative novel species of Methylomicrobium, was cultured; and the draft genome sequence was obtained. Genome analysis indicated that RS1 represented a new putative Methylomicrobium species. Methylomicrobium has been detected globally in rice fields as a dominant genus, although no Methylomicrobium strains have been isolated from rice fields worldwide. Ours is one of the first extensive studies on cultured methanotrophs from Indian rice fields focusing on the tropical region, and a unique method was developed. A total of 29 strains were obtained, which could be used as models for studying methane mitigation from rice fields and for environmental and biotechnological applications.
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Affiliation(s)
- Monali C Rahalkar
- C2, Bioenergy Group, MACS Agharkar Research Institute, Pune, India.,Department of Microbiology, Savitribai Phule Pune University, Pune, India
| | - Kumal Khatri
- C2, Bioenergy Group, MACS Agharkar Research Institute, Pune, India.,Department of Microbiology, Savitribai Phule Pune University, Pune, India
| | - Pranitha Pandit
- C2, Bioenergy Group, MACS Agharkar Research Institute, Pune, India.,Department of Microbiology, Savitribai Phule Pune University, Pune, India
| | - Rahul A Bahulikar
- Central Research Station, BAIF Development Research Foundation, Pune, India
| | - Jyoti A Mohite
- C2, Bioenergy Group, MACS Agharkar Research Institute, Pune, India.,Department of Microbiology, Savitribai Phule Pune University, Pune, India
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Cordova-Gonzalez A, Birgel D, Kappler A, Peckmann J. Variation of salinity and nitrogen concentration affects the pentacyclic triterpenoid inventory of the haloalkaliphilic aerobic methanotrophic bacterium Methylotuvimicrobium alcaliphilum. Extremophiles 2021; 25:285-299. [PMID: 33866428 PMCID: PMC8102298 DOI: 10.1007/s00792-021-01228-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 04/01/2021] [Indexed: 11/30/2022]
Abstract
The occurrence and activity of aerobic methanotrophs are influenced by environmental conditions, including pH, temperature, salinity, methane and oxygen concentrations, and nutrient availability. Aerobic methanotrophs synthesize a variety of lipids important for cell functions. However, culture-based experiments studying the influence of environmental parameters on lipid production by aerobic methanotrophs are scarce. Such information is crucial to interpret lipid patterns of methanotrophic bacteria in the environment. In this study, the alkaliphilic strain Methylotuvimicrobium alcaliphilum was cultivated under different salinities and different nitrate concentrations to assess the effect of changing conditions on the inventory of pentacyclic triterpenoids. The results indicate that hopanoid abundance is enhanced at lower salinity and higher nitrate concentration. The production of most pentacyclic triterpenoids was favored at low salinity, especially for aminotriol. Interestingly, 3-methyl-aminotetrol and tetrahymanol were favored at higher salinity. Bacteriohopanepolyols (BHPs), particularly aminotriol and 3-methyl-aminotriol, increased considerably at higher nitrate concentrations. Four novel N-containing BHPs—aminodiol, 3-methyl-aminodiol, and isomers of aminotriol and 3-methyl-aminotriol—were identified. This study highlights the significance of environmental factors for bacterial lipid production and documents the need for cultivation studies under variable conditions to utilize the full potential of the biomarker concept.
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Affiliation(s)
- Alexmar Cordova-Gonzalez
- Institut für Geologie, Centrum für Erdsystemforschung und Nachhaltigkeit, Universität Hamburg, Hamburg, Germany
| | - Daniel Birgel
- Institut für Geologie, Centrum für Erdsystemforschung und Nachhaltigkeit, Universität Hamburg, Hamburg, Germany.
| | - Andreas Kappler
- Geomikrobiologie, Zentrum für Angewandte Geowissenschaften, Universität Tübingen, Tübingen, Germany
| | - Jörn Peckmann
- Institut für Geologie, Centrum für Erdsystemforschung und Nachhaltigkeit, Universität Hamburg, Hamburg, Germany
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11
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Ruiz-Ruiz P, Gómez-Borraz TL, Revah S, Morales M. Methanotroph-microalgae co-culture for greenhouse gas mitigation: Effect of initial biomass ratio and methane concentration. CHEMOSPHERE 2020; 259:127418. [PMID: 32574848 DOI: 10.1016/j.chemosphere.2020.127418] [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: 12/04/2019] [Revised: 04/16/2020] [Accepted: 06/13/2020] [Indexed: 06/11/2023]
Abstract
This work evaluated the effect of different initial biomass ratios in a co-culture of an alkaliphilic methanotrophic bacteria consortium (AMB) and the green microalga Scenedesmus obtusiusculus (GM) on the maximum CH4 specific biodegradation rate and global carbon uptake. The highest maximum specific biodegradation rate was 589 ± 0.01 mgCH4 gbiomass-1 d-1 obtained for a proportion of 3:1 AMB-GM (w w-1) and 8% of initial CH4 in the headspace. The methane degradation rate was 1.5 times lower than the value obtained solely by the AMB consortium, and it was associated with pH increases due to the evolved CO2 consumption by the microalga. Increased activity of the AMB consortium along the experiments was due to progressive adaptation. Massive sequencing revealed the presence of methanotrophic/methylotrophic species such as Methylocystis sp., Methylomicrobium sp., Methylophaga sp., and Hyphomicrobium sp. Successful complete methane and carbon dioxide uptake was obtained with the 3:1, 4:1, and 5:1 AMB-GM biomass ratios, while for the rest of the ratios tested, more than 70% of the initial methane was transformed into biomass and inorganic carbon. This study showed that methanotrophic-microalgal co-cultures lead to a promising strategy for greenhouse gases mitigation in one step.
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Affiliation(s)
- Patricia Ruiz-Ruiz
- Doctorado en Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana-Cuajimalpa, Cd. de México, Mexico
| | - Tania L Gómez-Borraz
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Av. Vasco de Quiroga 4871, colonia Santa Fe Cuajimalpa, C.P. 05300, Cd. de México, Mexico
| | - Sergio Revah
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Av. Vasco de Quiroga 4871, colonia Santa Fe Cuajimalpa, C.P. 05300, Cd. de México, Mexico.
| | - Marcia Morales
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Av. Vasco de Quiroga 4871, colonia Santa Fe Cuajimalpa, C.P. 05300, Cd. de México, Mexico.
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12
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Houghton KM, Stewart LC. Temperature-gradient incubation isolates multiple competitive species from a single environmental sample. Access Microbiol 2020; 2:acmi000081. [PMID: 32974564 PMCID: PMC7470311 DOI: 10.1099/acmi.0.000081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 11/07/2019] [Indexed: 12/14/2022] Open
Abstract
High-throughput sequencing has allowed culture-independent investigation into a wide variety of microbiomes, but sequencing studies still require axenic culture experiments to determine ecological roles, confirm functional predictions and identify useful compounds and pathways. We have developed a new method for culturing and isolating multiple microbial species with overlapping ecological niches from a single environmental sample, using temperature-gradient incubation. This method was more effective than standard serial dilution-to-extinction at isolating methanotrophic bacteria. It also highlighted discrepancies between culture-dependent and -independent techniques; 16S rRNA gene amplicon sequencing of the same sample did not accurately reflect cultivatable strains using this method. We propose that temperature-gradient incubation could be used to separate out and study previously ‘unculturable’ strains, which co-exist in both natural and artificial environments.
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Affiliation(s)
- Karen M Houghton
- GNS Science, Wairakei Research Centre, 114 Karetoto Rd, Taupō 3384, New Zealand
| | - Lucy C Stewart
- GNS Science, 1 Fairway Drive, Avalon, Lower Hutt 5010, New Zealand
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But SY, Dedysh SN, Popov VO, Pimenov NV, Khmelenina VN. Construction of a Type-I Metanotroph with Reduced Capacity for Glycogen and Sucrose Accumulation. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820050063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Bordel S, Pérez R, Rodríguez E, Cantera S, Fernández-González N, Martínez MA, Muñoz R. Halotolerance mechanisms of the methanotroph Methylomicrobium alcaliphilum. Biotechnol Bioeng 2020; 117:3459-3474. [PMID: 32672837 DOI: 10.1002/bit.27506] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 06/18/2020] [Accepted: 07/15/2020] [Indexed: 11/12/2022]
Abstract
Methylomicrobium alcaliphilum is an alkaliphilic and halotolerant methanotroph. The physiological responses of M. alcaliphilum to high NaCl concentrations, were studied using RNA sequencing and metabolic modeling. This study revealed that M. alcaliphilum possesses an unusual respiratory chain, in which complex I is replaced by a Na+ extruding NQR complex (highly upregulated under high salinity conditions) and a Na+ driven adenosine triphosphate (ATP) synthase coexists with a conventional H+ driven ATP synthase. A thermodynamic and metabolic model showing the interplay between these different components is presented. Ectoine is the main osmoprotector used by the cells. Ectoine synthesis is activated by the transcription of an ect operon that contains five genes, including the ectoine hydroxylase coding ectD gene. Enzymatic tests revealed that the product of ectD does not have catalytic activity. A new Genome Scale Metabolic Model for M. alcaliphilum revealed a higher flux in the oxidative branch of the pentose phosphate pathway leading to NADPH production and contributing to resistance to oxidative stress.
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Affiliation(s)
- Sergio Bordel
- Department of Chemical Engineering and Environmental Technology, School of Insdustrial Engineering, University of Valladolid, Valladolid, Spain.,Institute of Sustainable Processes, Valladolid, Spain
| | - Rebeca Pérez
- Department of Chemical Engineering and Environmental Technology, School of Insdustrial Engineering, University of Valladolid, Valladolid, Spain.,Institute of Sustainable Processes, Valladolid, Spain
| | - Elisa Rodríguez
- Department of Chemical Engineering and Environmental Technology, School of Insdustrial Engineering, University of Valladolid, Valladolid, Spain.,Institute of Sustainable Processes, Valladolid, Spain
| | - Sara Cantera
- Laboratory of Microbiology, Wageningen University and Research Center, Wageningen, The Netherlands
| | - Nuria Fernández-González
- Department of Chemical Engineering and Environmental Technology, School of Insdustrial Engineering, University of Valladolid, Valladolid, Spain.,Institute of Sustainable Processes, Valladolid, Spain
| | - María A Martínez
- Institute of Sustainable Processes, Valladolid, Spain.,PROIMI Planta Piloto de Procesos Industriales Microbiológicos, CONICET, San Miguel de Tucumán, Argentina.,Facultad de Ciencias Exactas y Tecnología, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
| | - Raúl Muñoz
- Department of Chemical Engineering and Environmental Technology, School of Insdustrial Engineering, University of Valladolid, Valladolid, Spain.,Institute of Sustainable Processes, Valladolid, Spain
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15
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Nature and bioprospecting of haloalkaliphilics: a review. World J Microbiol Biotechnol 2020; 36:66. [DOI: 10.1007/s11274-020-02841-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 04/14/2020] [Indexed: 01/07/2023]
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16
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Saidi-Mehrabad A, Kits DK, Kim JJ, Tamas I, Schumann P, Khadka R, Strilets T, Smirnova AV, Rijpstra WIC, Sinninghe Damsté JS, Dunfield PF. Methylicorpusculum oleiharenae gen. nov., sp. nov., an aerobic methanotroph isolated from an oil sands tailings pond. Int J Syst Evol Microbiol 2020; 70:2499-2508. [DOI: 10.1099/ijsem.0.004064] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic methane oxidizing bacterium, designated XLMV4T, was isolated from the oxic surface layer of an oil sands tailings pond in Alberta, Canada. Strain XLMV4T is capable of growth on methane and methanol as energy sources. NH4Cl and sodium nitrate are nitrogen sources. Cells are Gram-negative, beige to yellow-pigmented, motile (via a single polar flagellum), short rods 2.0–3.3 µm in length and 1.0–1.6 µm in width. A thick capsule is produced. Surface glycoprotein or cup shape proteins typical of the genera Methylococcus, Methylothermus and
Methylomicrobium
were not observed. Major isoprenoid quinones are Q-8 and Q-7 at an approximate molar ratio of 71 : 22. Major polar lipids are phosphoglycerol and ornithine lipids. Major fatty acids are C16 : 1 ω8+C16 : 1 ω7 (34 %), C16 : 1 ω5 (16 %), and C18 : 1 ω7 (11 %). Optimum growth is observed at pH 8.0 and 25 °C. The DNA G+C content based on a draft genome sequence is 46.7 mol%. Phylogenetic analysis of 16S rRNA genes and a larger set of conserved genes place strain XLMV4T within the class
Gammaproteobacteria
and family
Methylococcaceae
, most closely related to members of the genera
Methylomicrobium
and
Methylobacter
(95.0–97.1 % 16S rRNA gene sequence identity). In silico genomic predictions of DNA–DNA hybridization values of strain XLMV4T to the nearest phylogenetic neighbours were all below 26 %. On the basis of the data presented, strain XLMV4T is considered to represent a new genus and species for which the name Methylicorpusculum oleiharenae is proposed. Strain XLMV4T (=DSMZ DSM 27269=ATCC TSD-186) is the type strain.
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Affiliation(s)
- Alireza Saidi-Mehrabad
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, Alberta, T6G 2E9, Canada
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta, T2N 1N4, Canada
| | - Dimitri K. Kits
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, Alberta, T6G 2E9, Canada
| | - Joong-Jae Kim
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta, T2N 1N4, Canada
| | - Ivica Tamas
- Departman Za Biologiju I Ekologiju, Prirodno-Matematicki Fakultet, Univerzitet u Novom Sadu, Trg Dositeja Obradovića 2, 21000 Novi Sad, Serbia
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta, T2N 1N4, Canada
| | - Peter Schumann
- Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures. Inhoffenstr. 7 B 38124 Braunschweig, Germany
| | - Roshan Khadka
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta, T2N 1N4, Canada
| | - Tania Strilets
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, Alberta, T6G 2E9, Canada
| | - Angela V. Smirnova
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta, T2N 1N4, Canada
| | - W. Irene C. Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
| | - Jaap S. Sinninghe Damsté
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA Utrecht, The Netherlands
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
| | - Peter F. Dunfield
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta, T2N 1N4, Canada
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17
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Jordan SFA, Treude T, Leifer I, Janßen R, Werner J, Schulz-Vogt H, Schmale O. Bubble-mediated transport of benthic microorganisms into the water column: Identification of methanotrophs and implication of seepage intensity on transport efficiency. Sci Rep 2020; 10:4682. [PMID: 32170164 PMCID: PMC7070025 DOI: 10.1038/s41598-020-61446-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/05/2020] [Indexed: 11/17/2022] Open
Abstract
Benthic microorganisms transported into the water column potentially influence biogeochemical cycles and the pelagic food web structure. In the present study six gas-releasing vent sites in the Coal Oil Point seep field (California) were investigated, and the dislocation of microorganisms from the sediment into the water column via gas bubbles released from the seabed was documented. It was found that the methanotrophs transport efficiency was dependent on the volumetric gas flow, with the highest transport rate of 22.7 × 103 cells mLgas−1 at a volumetric gas flow of 0.07 mLgas s−1, and the lowest rate of 0.2 × 103 cells mLgas−1 at a gas flow of 2.2 mLgas s−1. A simple budget approach showed that this bubble-mediated transport has the potential to maintain a relevant part of the water-column methanotrophs in the seep field. The bubble-mediated link between the benthic and pelagic environment was further supported by genetic analyses, indicating a transportation of methanotrophs of the family Methylomonaceae and oil degrading bacteria of the genus Cycloclasticus from the sediment into the water column. These findings demonstrate that the bubble-mediated transport of microorganisms influences the pelagic microbial abundance and community composition at gas-releasing seep sites.
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Affiliation(s)
| | - Tina Treude
- University of California, Los Angeles Department of Earth, Planetary, and Space Sciences, Los Angeles, California, USA
| | - Ira Leifer
- Bubbleology Research International, Solvang, California, USA
| | - René Janßen
- Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Johannes Werner
- Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Heide Schulz-Vogt
- Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Oliver Schmale
- Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany.
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18
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Cantera S, Phandanouvong-Lozano V, Pascual C, García-Encina PA, Lebrero R, Hay A, Muñoz R. A systematic comparison of ectoine production from upgraded biogas using Methylomicrobium alcaliphilum and a mixed haloalkaliphilic consortium. WASTE MANAGEMENT (NEW YORK, N.Y.) 2020; 102:773-781. [PMID: 31812092 DOI: 10.1016/j.wasman.2019.11.043] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 11/20/2019] [Accepted: 11/26/2019] [Indexed: 05/12/2023]
Abstract
Biogas is the byproduct of anaerobic digestion with the highest valorization potential, however its full exploitation is limited by the lack of tax incentives and the inherent presence of pollutants. The development of technologies for biogas conversion into added-value products is crucial in order to ensure the competitiveness of this bioresource. This study constitutes the first proof of concept of upgraded biogas bioconversion into the high profit margin product ectoine. Ectoine represents the most expensive product synthesized by microorganisms with a retail value of 1000 $ kg-1 and a yearly increasing demand that currently entails a total market opportunity of 15000 M€. First, the production of ectoine from upgraded biogas was assessed in batch bioreactors. The presence of H2S did not exert a negative effect on the growth of the haloalkaliphilic ectoine producers, and ectoine yields up to 49 mg g biomass-1 were obtained. A second experiment conducted in continuous bubble column bioreactors confirmed the feasibility of the process under continuous mode (with ectoine yields of 109 mg g biomass-1). Finally, this study revealed that the removal of toxic compounds (i.e. medium dilution rate of 0.5 day-1) and process operation with a consortium composed of methylotrophic/non-methylotrophic ectoine producers enhanced upgraded biogas bioconversion. This research discloses the basis for the application of this innovative technology and could boost the economic performance of anaerobic digestion.
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Affiliation(s)
- Sara Cantera
- Laboratory of Microbiology, Wageningen University and Research Center, The Netherlands
| | | | - Celia Pascual
- Department of Chemical Engineering and Environmental Technology, Universidad de Valladolid, Dr. Mergelina, s/n, Valladolid, Spain; Institute of Sustainable Processes, Universidad de Valladolid, Spain
| | - Pedro A García-Encina
- Department of Chemical Engineering and Environmental Technology, Universidad de Valladolid, Dr. Mergelina, s/n, Valladolid, Spain; Institute of Sustainable Processes, Universidad de Valladolid, Spain
| | - Raquel Lebrero
- Department of Chemical Engineering and Environmental Technology, Universidad de Valladolid, Dr. Mergelina, s/n, Valladolid, Spain; Institute of Sustainable Processes, Universidad de Valladolid, Spain
| | - Anthony Hay
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Raúl Muñoz
- Department of Chemical Engineering and Environmental Technology, Universidad de Valladolid, Dr. Mergelina, s/n, Valladolid, Spain; Institute of Sustainable Processes, Universidad de Valladolid, Spain.
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19
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Reddy KR, Rai RK, Green SJ, Chetri JK. Effect of temperature on methane oxidation and community composition in landfill cover soil. J Ind Microbiol Biotechnol 2019; 46:1283-1295. [PMID: 31317292 DOI: 10.1061/(asce)ee.1943-7870.0001712] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/11/2019] [Indexed: 05/26/2023]
Abstract
Municipal solid waste (MSW) landfills are the third largest anthropogenic source of methane (CH4) emissions in the United States. The majority of CH4 generated in landfills is converted to carbon dioxide (CO2) by CH4-oxidizing bacteria (MOB) present in the landfill cover soil, whose activity is controlled by various environmental factors including temperature. As landfill temperature can fluctuate substantially seasonally, rates of CH4 oxidation can also vary, and this could lead to incomplete oxidation. This study aims at analyzing the effect of temperature on CH4 oxidation potential and microbial community structure of methanotrophs in laboratory-based studies of landfill cover soil and cultivated consortia. Soil and enrichment cultures were incubated at temperatures ranging from 6 to 70 °C, and rates of CH4 oxidation were measured, and the microbial community structure was analyzed using 16S rRNA gene amplicon sequencing and shotgun metagenome sequencing. CH4 oxidation occurred at temperatures from 6 to 50 °C in soil microcosm tests, and 6-40 °C in enrichment culture batch tests; maximum rates of oxidation were obtained at 30 °C. A corresponding shift in the soil microbiota was observed, with a transition from putative psychrophilic to thermophilic methanotrophs with increasing incubation temperature. A strong shift in methanotrophic community structure was observed above 30 °C. At temperatures up to 30 °C, methanotrophs from the genus Methylobacter were dominant in soils and enrichment cultures; at a temperature of 40 °C, putative thermophilic methanotrophs from the genus Methylocaldum become dominant. Maximum rate measurements of nearly 195 μg CH4 g-1 day-1 were observed in soil incubations, while observed maximum rates in enrichments were significantly lower, likely as a result of diffusion limitations. This study demonstrates that temperature is a critical factor affecting rates of landfill soil CH4 oxidation in vitro and that changing rates of CH4 oxidation are in part driven by changes in methylotroph community structure.
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Affiliation(s)
- Krishna R Reddy
- Department of Civil and Materials Engineering, University of Illinois at Chicago, 842 West Taylor Street, Chicago, IL, 60607, USA.
| | - Raksha K Rai
- Department of Civil and Materials Engineering, University of Illinois at Chicago, 842 West Taylor Street, Chicago, IL, 60607, USA
| | - Stefan J Green
- Department of Biological Sciences, Sequencing Core, Resources Center, University of Illinois at Chicago, 835 S. Wolcott, Chicago, IL, 60612, USA
| | - Jyoti K Chetri
- Department of Civil and Materials Engineering, University of Illinois at Chicago, 842 West Taylor Street, Chicago, IL, 60607, USA
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20
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Whiddon KT, Gudneppanavar R, Hammer TJ, West DA, Konopka MC. Fluorescence-based analysis of the intracytoplasmic membranes of type I methanotrophs. Microb Biotechnol 2019; 12:1024-1033. [PMID: 31264365 PMCID: PMC6680624 DOI: 10.1111/1751-7915.13458] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/16/2019] [Indexed: 12/15/2022] Open
Abstract
Most methanotrophic bacteria maintain intracytoplasmic membranes which house the methane-oxidizing enzyme, particulate methane monooxygenase. Previous studies have primarily used transmission electron microscopy or cryo-electron microscopy to look at the structure of these membranes or lipid extraction methods to determine the per cent of cell dry weight composed of lipids. We show an alternative approach using lipophilic membrane probes and other fluorescent dyes to assess the extent of intracytoplasmic membrane formation in living cells. This fluorescence method is sensitive enough to show not only the characteristic shift in intracytoplasmic membrane formation that is present when methanotrophs are grown with or without copper, but also differences in intracytoplasmic membrane levels at intermediate copper concentrations. This technique can also be employed to monitor dynamic intracytoplasmic membrane changes in the same cell in real time under changing growth conditions. We anticipate that this approach will be of use to researchers wishing to visualize intracytoplasmic membranes who may not have access to electron microscopes. It will also have the capability to relate membrane changes in individual living cells to other measurements by fluorescence labelling or other single-cell analysis methods.
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Affiliation(s)
| | | | - Theodore J. Hammer
- Department of ChemistryThe University of AkronAkronOHUSA
- Department of Polymer ScienceThe University of AkronAkronOHUSA
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21
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The status of names whose nomenclatural types are based on strains deposited solely for patent purposes. Int J Syst Evol Microbiol 2019; 69:2616-2620. [DOI: 10.1099/ijsem.0.003527] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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22
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A Mutagenic Screen Identifies a TonB-Dependent Receptor Required for the Lanthanide Metal Switch in the Type I Methanotroph "Methylotuvimicrobium buryatense" 5GB1C. J Bacteriol 2019; 201:JB.00120-19. [PMID: 31085692 DOI: 10.1128/jb.00120-19] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/07/2019] [Indexed: 12/23/2022] Open
Abstract
Several of the metabolic enzymes in methanotrophic bacteria rely on metals for both their expression and their catalysis. The MxaFI methanol dehydrogenase enzyme complex uses calcium as a cofactor to oxidize methanol, while the alternative methanol dehydrogenase XoxF uses lanthanide metals such as lanthanum and cerium for the same function. Lanthanide metals, abundant in the earth's crust, strongly repress the transcription of mxaF yet activate the transcription of xoxF This regulatory program, called the "lanthanide switch," is central to methylotrophic metabolism, but only some of its components are known. To uncover additional components of the lanthanide switch, we developed a chemical mutagenesis system in the type I gammaproteobacterial methanotroph "Methylotuvimicrobium buryatense" 5GB1C and designed a selection system for mutants unable to repress the mxaF promoter in the presence of lanthanum. Whole-genome resequencing for multiple lanthanide switch mutants identified several unique point mutations in a single gene encoding a TonB-dependent receptor, which we have named LanA. The LanA TonB-dependent receptor is absolutely required for the lanthanide switch and controls the expression of a small set of genes. While mutation of the lanA gene does not affect the amount of cell-associated lanthanum, it is essential for growth in the absence of the MxaF methanol dehydrogenase, suggesting that LanA is involved in lanthanum uptake to supply the XoxF methanol dehydrogenase with its critical metal ion cofactor. The discovery of this novel component of the lanthanide regulatory system highlights the complexity of this circuit and suggests that further components are likely involved.IMPORTANCE Lanthanide metals, or rare earth elements, are abundant in nature and used heavily in technological devices. Biological interactions with lanthanides are just beginning to be unraveled. Until very recently, microbial mechanisms of lanthanide metal interaction and uptake were unknown. The TonB-dependent receptor LanA is the first lanthanum receptor identified in a methanotroph. Sequence homology searches with known metal transporters and regulators could not be used to identify LanA or other lanthanide metal switch components, and this method for mutagenesis and selection was required to identify the receptor. This work advances the knowledge of microbe-metal interactions in environmental niches that impact atmospheric methane levels and are thus relevant to climate change.
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23
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Bordel S, Rodríguez Y, Hakobyan A, Rodríguez E, Lebrero R, Muñoz R. Genome scale metabolic modeling reveals the metabolic potential of three Type II methanotrophs of the genus Methylocystis. Metab Eng 2019; 54:191-199. [DOI: 10.1016/j.ymben.2019.04.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/03/2019] [Accepted: 04/04/2019] [Indexed: 12/19/2022]
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24
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Nguyen LT, Lee EY. Biological conversion of methane to putrescine using genome-scale model-guided metabolic engineering of a methanotrophic bacterium Methylomicrobium alcaliphilum 20Z. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:147. [PMID: 31223337 PMCID: PMC6570963 DOI: 10.1186/s13068-019-1490-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/07/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Methane is the primary component of natural gas and biogas. The huge abundance of methane makes it a promising alternative carbon source for industrial biotechnology. Herein, we report diamine compound, putrescine, production from methane by an industrially promising methanotroph Methylomicrobium alcaliphilum 20Z. RESULTS We conducted adaptive evolution to improve putrescine tolerance of M. alcaliphilum 20Z because putrescine highly inhibits the cell growth. The evolved strain 20ZE was able to grow in the presence of 400 mM of putrescine dihydrochloride. The expression of linear pathway ornithine decarboxylase genes from Escherichia coli and Methylosinus trichosporium OB3b allowed the engineered strain to produce putrescine. A higher putrescine titer of 12.44 mg/L was obtained in the strain 20ZE-pACO with ornithine decarboxylase from M. trichosporium OB3b. For elimination of the putrescine utilization pathway, spermidine synthase (MEALZ_3408) was knocked out, resulting in no spermidine formation in the strain 20ZES1-pACO with a putrescine titer of 18.43 mg/L. Next, a genome-scale metabolic model was applied to identify gene knockout strategies. Acetate kinase (MEALZ_2853) and subsequently lactate dehydrogenase (MEALZ_0534) were selected as knockout targets, and the deletion of these genes resulted in an improvement of the putrescine titer to 26.69 mg/L. Furthermore, the putrescine titer was improved to 39.04 mg/L by overexpression of key genes in the ornithine biosynthesis pathway under control of the pTac promoter. Finally, suitable nitrogen sources for growth of M. alcaliphilum 20Z and putrescine production were optimized with the supplement of 2 mM ammonium chloride to nitrate mineral salt medium, and this led to the production of 98.08 mg/L putrescine, almost eightfold higher than that from the initial strain. Transcriptome analysis of the engineered strains showed upregulation of most genes involved in methane assimilation, citric acid cycle, and ammonia assimilation in ammonia nitrate mineral salt medium, compared to nitrate mineral salt medium. CONCLUSIONS The engineered M. alcaliphilum 20ZE4-pACO strain was able to produce putrescine up to 98.08 mg/L, almost eightfold higher than the initial strain. This study represents the bioconversion of methane to putrescine-a high value-added diamine compound.
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Affiliation(s)
- Linh Thanh Nguyen
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do 17104 Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do 17104 Republic of Korea
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25
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Biological conversion of propane to 2-propanol using group I and II methanotrophs as biocatalysts. ACTA ACUST UNITED AC 2019; 46:675-685. [DOI: 10.1007/s10295-019-02141-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 01/21/2019] [Indexed: 12/19/2022]
Abstract
Abstract
Propane is the main component of liquefied petroleum gas and is derived from crude oil processing. Methanotrophic bacteria can convert various alkanes using methane monooxygenase enzyme to primary alcohols. These are further oxidized to various aldehydes by alcohol dehydrogenases or methanol dehydrogenases. In this study, 2-propanol was produced from propane using the whole cells of Methylosinus trichosporium OB3b, Methylomicrobium alcaliphilum 20Z, and Methylomonas sp. DH-1 as the biocatalysts. The biocatalytic process of converting propane to 2-propanol was optimized by the use of several inhibitors and additives, such as EDTA, sodium phosphate, and sodium formate to prevent oxidation of 2-propanol to acetone and to enhance conversion of propane to propanol. The maximum titer of 2-propanol was 0.424 g/L, 0.311 g/L, and 0.610 g/L for Methylomonas sp. DH-1, M. alcaliphilum 20Z, and M. trichosporium OB3b whole cells, respectively. These results showed that type I and type II methanotrophs could be used as the potent biocatalyst for conversion of propane to propanol.
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26
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Cantera S, Sánchez-Andrea I, Sadornil LJ, García-Encina PA, Stams AJM, Muñoz R. Novel haloalkaliphilic methanotrophic bacteria: An attempt for enhancing methane bio-refinery. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 231:1091-1099. [PMID: 30602233 DOI: 10.1016/j.jenvman.2018.11.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 10/14/2018] [Accepted: 11/05/2018] [Indexed: 06/09/2023]
Abstract
Methane bioconversion into products with a high market value, such as ectoine or hydroxyectoine, can be optimized via isolation of more efficient novel methanotrophic bacteria. The research here presented focused on the enrichment of methanotrophic consortia able to co-produce different ectoines during CH4 metabolism. Four different enrichments (Cow3, Slu3, Cow6 and Slu6) were carried out in basal media supplemented with 3 and 6% NaCl, and using methane as the sole carbon and energy source. The highest ectoine accumulation (∼20 mg ectoine g biomass-1) was recorded in the two consortia enriched at 6% NaCl (Cow6 and Slu6). Moreover, hydroxyectoine was detected for the first time using methane as a feedstock in Cow6 and Slu6 (∼5 mg g biomass-1). The majority of the haloalkaliphilic bacteria identified by 16S rRNA community profiling in both consortia have not been previously described as methanotrophs. From these enrichments, two novel strains (representing novel species) capable of using methane as the sole carbon and energy source were isolated: Alishewanella sp. strain RM1 and Halomonas sp. strain PGE1. Halomonas sp. strain PGE1 showed higher ectoine yields (70-92 mg ectoine g biomass-1) than those previously described for other methanotrophs under continuous cultivation mode (∼37-70 mg ectoine g biomass-1). The results here obtained highlight the potential of isolating novel methanotrophs in order to boost the competitiveness of industrial CH4-based ectoine production.
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Affiliation(s)
- Sara Cantera
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, Valladolid University, Dr. Mergelina, s/n, Valladolid, Spain
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
| | - Lidia J Sadornil
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, Valladolid University, Dr. Mergelina, s/n, Valladolid, Spain
| | - Pedro A García-Encina
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, Valladolid University, Dr. Mergelina, s/n, Valladolid, Spain
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
| | - Raúl Muñoz
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, Valladolid University, Dr. Mergelina, s/n, Valladolid, Spain.
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27
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Bio-conversion of methane into high profit margin compounds: an innovative, environmentally friendly and cost-effective platform for methane abatement. World J Microbiol Biotechnol 2019; 35:16. [PMID: 30617555 DOI: 10.1007/s11274-018-2587-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 12/31/2018] [Indexed: 01/04/2023]
Abstract
Despite the environmental relevance of CH4 and forthcoming stricter regulations, the development of cost-efficient and environmentally friendly technologies for CH4 abatement is still limited. To date, one of the most promising solutions for the mitigation of this important GHG consists of the bioconversion of CH4 into bioproducts with a high profit margin. In this context, methanotrophs have been already proven as cell-factories of some of the most expensive products synthesized by microorganisms. In the case of ectoine (1000 $ kg-1), already described methanotrophic genera such as Methylomicrobium can accumulate up to 20% (ectoine wt-1) using methane as the only carbon source. Moreover, α-methanotrophs, such as Methylosynus and Methylocystis, are able to store bioplastic concentrations up to 50-60% of their total cell content. More than that, methanotrophs are one of the greatest potential producers of methanol and exopolysaccharides. Although this methanotrophic factory could be enhanced throughout metabolic engineering, the valorization of CH4 into valuable metabolites has been already consistently demonstrated under continuous and discontinuous mode, producing more than one compound in the same bioprocess, and using both, single strains and specific consortia. This review states the state-of-the-art of this innovative biotechnological platform by assessing its potential and current limitations.
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Orata FD, Meier-Kolthoff JP, Sauvageau D, Stein LY. Phylogenomic Analysis of the Gammaproteobacterial Methanotrophs (Order Methylococcales) Calls for the Reclassification of Members at the Genus and Species Levels. Front Microbiol 2018; 9:3162. [PMID: 30631317 PMCID: PMC6315193 DOI: 10.3389/fmicb.2018.03162] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/06/2018] [Indexed: 11/13/2022] Open
Abstract
The order Methylococcales constitutes the methanotrophs – bacteria that can metabolize methane, a potent greenhouse gas, as their sole source of energy. These bacteria are significant players in the global carbon cycle and can produce value-added products from methane, such as biopolymers, biofuels, and single-cell proteins for animal feed, among others. Previous studies using single-gene phylogenies have shown inconsistencies in the currently established taxonomic structure of this group. This study aimed to determine and resolve these issues by using whole-genome sequence analyses. Phylogenomic analysis and the use of similarity indexes for genomic comparisons – average amino acid identity, digital DNA–DNA hybridization (dDDH), and average nucleotide identity (ANI) – were performed on 91 Methylococcales genomes. Results suggest the reclassification of members at the genus and species levels. Firstly, to resolve polyphyly of the genus Methylomicrobium, Methylomicrobium alcaliphilum, “Methylomicrobium buryatense,” Methylomicrobium japanense, Methylomicrobium kenyense, and Methylomicrobium pelagicum are reclassified to a newly proposed genus, Methylotuvimicrobium gen. nov.; they are therefore renamed to Methylotuvimicrobium alcaliphilum comb. nov., “Methylotuvimicrobium buryatense” comb. nov., Methylotuvimicrobium japanense comb. nov., Methylotuvimicrobium kenyense comb. nov., and Methylotuvimicrobium pelagicum comb. nov., respectively. Secondly, due to the phylogenetic affinity and phenotypic similarities of Methylosarcina lacus with Methylomicrobium agile and Methylomicrobium album, the reclassification of the former species to Methylomicrobium lacus comb. nov. is proposed. Thirdly, using established same-species delineation thresholds (70% dDDH and 95% ANI), Methylobacter whittenburyi is proposed to be a later heterotypic synonym of Methylobacter marinus (89% dDDH and 99% ANI). Also, the effectively but not validly published “Methylomonas denitrificans” was identified as Methylomonas methanica (92% dDDH and 100% ANI), indicating that the former is a later heterotypic synonym of the latter. Lastly, strains MC09, R-45363, and R-45371, currently identified as M. methanica, each represent a putative novel species of the genus Methylomonas (21–35% dDDH and 74–88% ANI against M. methanica) and were reclassified as Methylomonas sp. strains. It is imperative to resolve taxonomic inconsistencies within this group, first and foremost, to avoid confusion with ecological and evolutionary interpretations in subsequent studies.
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Affiliation(s)
- Fabini D Orata
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Jan P Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Dominic Sauvageau
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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29
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Cantera S, Sánchez-Andrea I, Lebrero R, García-Encina PA, Stams AJM, Muñoz R. Multi-production of high added market value metabolites from diluted methane emissions via methanotrophic extremophiles. BIORESOURCE TECHNOLOGY 2018; 267:401-407. [PMID: 30031279 DOI: 10.1016/j.biortech.2018.07.057] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/09/2018] [Accepted: 07/11/2018] [Indexed: 05/12/2023]
Abstract
This study constitutes the first-proof-of-concept of a methane biorefinery based on the multi-production of high profit margin substances (ectoine, hydroxyectoine, polyhydroxyalkanoates (PHAs) and exopolysaccharides (EPS)) using methane as the sole carbon and energy source. Two bubble column bioreactors were operated under different magnesium concentrations (0.2, 0.02 and 0.002 g L-1) to validate and optimize this innovative strategy for valorization of CH4 emissions. High Mg2+ concentrations promoted the accumulation of ectoine (79.7-94.2 mg g biomass-1), together with high hydroxyectoine yields (up to 13 mg g biomass-1) and EPS concentrations (up to 2.6 g L culture broth-1). Unfortunately, PHA synthesis was almost negligible (14.3 mg L-1) and only found at the lowest Mg2+ concentration tested. Halomonas, Marinobacter, Methylophaga and Methylomicrobium, previously described as ectoine producers, were dominant in both bioreactors, Methylomicrobium being the only described methanotroph. This study encourages further research on CH4 biorefineries capable of creating value out of GHG mitigation.
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Affiliation(s)
- S Cantera
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, Valladolid University, Dr. Mergelina, s/n, Valladolid, Spain
| | - I Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - R Lebrero
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, Valladolid University, Dr. Mergelina, s/n, Valladolid, Spain
| | - P A García-Encina
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, Valladolid University, Dr. Mergelina, s/n, Valladolid, Spain
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - R Muñoz
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, Valladolid University, Dr. Mergelina, s/n, Valladolid, Spain.
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30
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Ro SY, Rosenzweig AC. Recent Advances in the Genetic Manipulation of Methylosinus trichosporium OB3b. Methods Enzymol 2018; 605:335-349. [PMID: 29909832 DOI: 10.1016/bs.mie.2018.02.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Methanotrophic bacteria utilize methane as their sole carbon and energy source. Studies of the model Type II methanotroph Methylosinus trichosporium OB3b have provided insight into multiple aspects of methanotrophy, including methane assimilation, copper accumulation, and metal-dependent gene expression. Development of genetic tools for chromosomal editing was crucial for advancing these studies. Recent interest in methanotroph metabolic engineering has led to new protocols for genetic manipulation of methanotrophs that are effective and simple to use. We have incorporated these newer molecular tools into existing protocols for Ms. trichosporium OB3b. The modifications include additional shuttle and replicative plasmids as well as improved gene delivery and genotyping. The methods described here render gene editing in Ms. trichosporium OB3b efficient and accessible.
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Affiliation(s)
- Soo Y Ro
- Northwestern University, Evanston, IL, United States
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31
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Methane utilization in Methylomicrobium alcaliphilum 20Z R: a systems approach. Sci Rep 2018; 8:2512. [PMID: 29410419 PMCID: PMC5802761 DOI: 10.1038/s41598-018-20574-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 01/22/2018] [Indexed: 12/20/2022] Open
Abstract
Biological methane utilization, one of the main sinks of the greenhouse gas in nature, represents an attractive platform for production of fuels and value-added chemicals. Despite the progress made in our understanding of the individual parts of methane utilization, our knowledge of how the whole-cell metabolic network is organized and coordinated is limited. Attractive growth and methane-conversion rates, a complete and expert-annotated genome sequence, as well as large enzymatic, 13C-labeling, and transcriptomic datasets make Methylomicrobium alcaliphilum 20ZR an exceptional model system for investigating methane utilization networks. Here we present a comprehensive metabolic framework of methane and methanol utilization in M. alcaliphilum 20ZR. A set of novel metabolic reactions governing carbon distribution across central pathways in methanotrophic bacteria was predicted by in-silico simulations and confirmed by global non-targeted metabolomics and enzymatic evidences. Our data highlight the importance of substitution of ATP-linked steps with PPi-dependent reactions and support the presence of a carbon shunt from acetyl-CoA to the pentose-phosphate pathway and highly branched TCA cycle. The diverged TCA reactions promote balance between anabolic reactions and redox demands. The computational framework of C1-metabolism in methanotrophic bacteria can represent an efficient tool for metabolic engineering or ecosystem modeling.
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32
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Deng Y, Liu Y, Dumont M, Conrad R. Salinity Affects the Composition of the Aerobic Methanotroph Community in Alkaline Lake Sediments from the Tibetan Plateau. MICROBIAL ECOLOGY 2017; 73:101-110. [PMID: 27878346 DOI: 10.1007/s00248-016-0879-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/12/2016] [Indexed: 06/06/2023]
Abstract
Lakes are widely distributed on the Tibetan Plateau, which plays an important role in natural methane emission. Aerobic methanotrophs in lake sediments reduce the amount of methane released into the atmosphere. However, no study to date has analyzed the methanotroph community composition and their driving factors in sediments of these high-altitude lakes (>4000 m). To provide new insights on this aspect, the abundance and composition in the sediments of six high-altitude alkaline lakes (including both freshwater and saline lakes) on the Tibetan Plateau were studied. The quantitative PCR, terminal restriction fragment length polymorphism, and 454-pyrosequencing methods were used to target the pmoA genes. The pmoA gene copies ranged 104-106 per gram fresh sediment. Type I methanotrophs predominated in Tibetan lake sediments, with Methylobacter and uncultivated type Ib methanotrophs being dominant in freshwater lakes and Methylomicrobium in saline lakes. Combining the pmoA-pyrosequencing data from Tibetan lakes with other published pmoA-sequencing data from lake sediments of other regions, a significant salinity and alkalinity effect (P = 0.001) was detected, especially salinity, which explained ∼25% of methanotroph community variability. The main effect was Methylomicrobium being dominant (up to 100%) in saline lakes only. In freshwater lakes, however, methanotroph composition was relatively diverse, including Methylobacter, Methylocystis, and uncultured type Ib clusters. This study provides the first methanotroph data for high-altitude lake sediments (>4000 m) and shows that salinity is a driving factor for the community composition of aerobic methanotrophs.
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Affiliation(s)
- Yongcui Deng
- College of Geographic Sciences, Nanjing Normal University, 1 Wenyuan Road, 210023, Nanjing, China
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043, Marburg, Germany
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, 1 Wenyuan Road, 210023, Nanjing, China
| | - Yongqin Liu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, 100085, Beijing, China.
| | - Marc Dumont
- Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043, Marburg, Germany
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33
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Rush D, Osborne KA, Birgel D, Kappler A, Hirayama H, Peckmann J, Poulton SW, Nickel JC, Mangelsdorf K, Kalyuzhnaya M, Sidgwick FR, Talbot HM. The Bacteriohopanepolyol Inventory of Novel Aerobic Methane Oxidising Bacteria Reveals New Biomarker Signatures of Aerobic Methanotrophy in Marine Systems. PLoS One 2016; 11:e0165635. [PMID: 27824887 PMCID: PMC5100885 DOI: 10.1371/journal.pone.0165635] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 10/15/2016] [Indexed: 12/24/2022] Open
Abstract
Aerobic methane oxidation (AMO) is one of the primary biologic pathways regulating the amount of methane (CH4) released into the environment. AMO acts as a sink of CH4, converting it into carbon dioxide before it reaches the atmosphere. It is of interest for (paleo)climate and carbon cycling studies to identify lipid biomarkers that can be used to trace AMO events, especially at times when the role of methane in the carbon cycle was more pronounced than today. AMO bacteria are known to synthesise bacteriohopanepolyol (BHP) lipids. Preliminary evidence pointed towards 35-aminobacteriohopane-30,31,32,33,34-pentol (aminopentol) being a characteristic biomarker for Type I methanotrophs. Here, the BHP compositions were examined for species of the recently described novel Type I methanotroph bacterial genera Methylomarinum and Methylomarinovum, as well as for a novel species of a Type I Methylomicrobium. Aminopentol was the most abundant BHP only in Methylomarinovum caldicuralii, while Methylomicrobium did not produce aminopentol at all. In addition to the expected regular aminotriol and aminotetrol BHPs, novel structures tentatively identified as methylcarbamate lipids related to C-35 amino-BHPs (MC-BHPs) were found to be synthesised in significant amounts by some AMO cultures. Subsequently, sediments and authigenic carbonates from methane-influenced marine environments were analysed. Most samples also did not contain significant amounts of aminopentol, indicating that aminopentol is not a useful biomarker for marine aerobic methanotophic bacteria. However, the BHP composition of the marine samples do point toward the novel MC-BHPs components being potential new biomarkers for AMO.
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Affiliation(s)
- Darci Rush
- School of Civil Engineering & Geosciences, Newcastle University, Drummond Building, Newcastle upon Tyne, NE1 7RU, Newcastle-upon-Tyne, United Kingdom
- * E-mail:
| | - Kate A. Osborne
- School of Civil Engineering & Geosciences, Newcastle University, Drummond Building, Newcastle upon Tyne, NE1 7RU, Newcastle-upon-Tyne, United Kingdom
| | - Daniel Birgel
- Institute of Geology, University of Hamburg, Hamburg, Germany
| | - Andreas Kappler
- Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
- Center for Geomicrobiology, Department of Bioscience, Ny Munkegade 116, 8000, Aarhus C, Denmark
| | - Hisako Hirayama
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Japan
| | - Jörn Peckmann
- Institute of Geology, University of Hamburg, Hamburg, Germany
- Department of Geodynamics and Sedimentology, University of Vienna, 1090, Vienna, Austria
| | - Simon W. Poulton
- School of Earth and Environment, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Julia C. Nickel
- GFZ German Research Centre for Geosciences, Telegrafenberg, D-14473, Potsdam, Germany
| | - Kai Mangelsdorf
- GFZ German Research Centre for Geosciences, Telegrafenberg, D-14473, Potsdam, Germany
| | - Marina Kalyuzhnaya
- Faculty of Biology, San Diego State University, 5500 Campanile Drive, San Diego, 92182, United States of America
| | - Frances R. Sidgwick
- School of Civil Engineering & Geosciences, Newcastle University, Drummond Building, Newcastle upon Tyne, NE1 7RU, Newcastle-upon-Tyne, United Kingdom
| | - Helen M. Talbot
- School of Civil Engineering & Geosciences, Newcastle University, Drummond Building, Newcastle upon Tyne, NE1 7RU, Newcastle-upon-Tyne, United Kingdom
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34
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Cantera S, Lebrero R, Sadornil L, García-Encina PA, Muñoz R. Valorization of CH4 emissions into high-added-value products: Assessing the production of ectoine coupled with CH4 abatement. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2016; 182:160-165. [PMID: 27472052 DOI: 10.1016/j.jenvman.2016.07.064] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 07/17/2016] [Accepted: 07/18/2016] [Indexed: 06/06/2023]
Abstract
This study assessed an innovative strategy for the valorization of dilute methane emissions based on the bio-conversion of CH4 (the second most important greenhouse gas (GHG)) into ectoine by the methanotrophic ectoine-producing strain Methylomicrobium alcaliphilum 20 Z. The influence of CH4 (2-20%), Cu(2+) (0.05-50 μM) and NaCl (0-9%) concentration as well as temperature (25-35 °C) on ectoine synthesis and specific CH4 biodegradation rate was evaluated for the first time. Concentrations of 20% CH4 (at 3% NaCl, 0.05 μM Cu(2+), 25 °C) and 6% NaCl (at 4% CH4, 0.05 μM Cu(2+), 25 °C) supported the maximum intra-cellular ectoine production yield (31.0 ±1.7 and 66.9 ±4.2 mg g biomass(-1), respectively). On the other hand, extra-cellular ectoine concentrations of up to 4.7 ± 0.1 mg L(-1) were detected at high Cu(2+)concentrations (50 μM), despite this methanotroph has not been previously classified as an ectoine-excreting strain. This research demonstrated the feasibility of the bio-conversion of dilute emissions of methane into high-added value products in an attempt to develop a sustainable GHG bioeconomy.
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Affiliation(s)
- Sara Cantera
- Department of Chemical Engineering and Environmental Technology, Valladolid University, Dr. Mergelina, s/n, Valladolid, Spain
| | - Raquel Lebrero
- Department of Chemical Engineering and Environmental Technology, Valladolid University, Dr. Mergelina, s/n, Valladolid, Spain
| | - Lidia Sadornil
- Department of Chemical Engineering and Environmental Technology, Valladolid University, Dr. Mergelina, s/n, Valladolid, Spain
| | - Pedro A García-Encina
- Department of Chemical Engineering and Environmental Technology, Valladolid University, Dr. Mergelina, s/n, Valladolid, Spain
| | - Raúl Muñoz
- Department of Chemical Engineering and Environmental Technology, Valladolid University, Dr. Mergelina, s/n, Valladolid, Spain.
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35
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Strong PJ, Kalyuzhnaya M, Silverman J, Clarke WP. A methanotroph-based biorefinery: Potential scenarios for generating multiple products from a single fermentation. BIORESOURCE TECHNOLOGY 2016; 215:314-323. [PMID: 27146469 DOI: 10.1016/j.biortech.2016.04.099] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/17/2016] [Accepted: 04/19/2016] [Indexed: 05/12/2023]
Abstract
Methane, a carbon source for methanotrophic bacteria, is the principal component of natural gas and is produced during anaerobic digestion of organic matter (biogas). Methanotrophs are a viable source of single cell protein (feed supplement) and can produce various products, since they accumulate osmolytes (e.g. ectoine, sucrose), phospholipids (potential biofuels) and biopolymers (polyhydroxybutyrate, glycogen), among others. Other cell components, such as surface layers, metal chelating proteins (methanobactin), enzymes (methane monooxygenase) or heterologous proteins hold promise as future products. Here, scenarios are presented where ectoine, polyhydroxybutyrate or protein G are synthesised as the primary product, in conjunction with a variety of ancillary products that could enhance process viability. Single or dual-stage processes and volumetric requirements for bioreactors are discussed, in terms of an annual biomass output of 1000 tonnesyear(-1). Product yields are discussed in relation to methane and oxygen consumption and organic waste generation.
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Affiliation(s)
- P J Strong
- Centre for Solid Waste Bioprocessing, School of Civil Engineering, School of Chemical Engineering, The University of Queensland, Brisbane 4072, Australia.
| | - M Kalyuzhnaya
- Biology Department, San Diego State University, San Diego, CA 92182-4614, United States
| | - J Silverman
- Calysta, 1140 O'Brien Drive, Menlo Park, CA 94025, United States
| | - W P Clarke
- Centre for Solid Waste Bioprocessing, School of Civil Engineering, School of Chemical Engineering, The University of Queensland, Brisbane 4072, Australia
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36
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Rodriguez-Mora MJ, Edgcomb VP, Taylor C, Scranton MI, Taylor GT, Chistoserdov AY. The Diversity of Sulfide Oxidation and Sulfate Reduction Genes Expressed by the Bacterial Communities of the Cariaco Basin, Venezuela. Open Microbiol J 2016; 10:140-9. [PMID: 27651847 PMCID: PMC5012083 DOI: 10.2174/1874285801610010140] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 12/15/2015] [Accepted: 01/29/2016] [Indexed: 11/22/2022] Open
Abstract
Qualitative expression of dissimilative sulfite reductase (dsrA), a key gene in sulfate reduction, and sulfide:quinone oxidoreductase (sqr), a key gene in sulfide oxidation was investigated. Neither of the two could be amplified from mRNA retrieved with Niskin bottles but were amplified from mRNA retrieved by the Deep SID. The sqr and sqr-like genes retrieved from the Cariaco Basin were related to the sqr genes from a Bradyrhizobium sp., Methylomicrobium alcaliphilum, Sulfurovum sp. NBC37-1, Sulfurimonas autotrophica, Thiorhodospira sibirica and Chlorobium tepidum. The dsrA gene sequences obtained from the redoxcline of the Cariaco Basin belonged to chemoorganotrophic and chemoautotrophic sulfate and sulfur reducers belonging to the class Deltaproteobacteria (phylum Proteobacteria) and the order Clostridiales (phylum Firmicutes).
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Affiliation(s)
- Maria J Rodriguez-Mora
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, 70504, USA
| | - Virginia P Edgcomb
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, 02543, USA
| | - Craig Taylor
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, 02543, USA
| | - Mary I Scranton
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, 11794, USA
| | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, 11794, USA
| | - Andrei Y Chistoserdov
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, 70504, USA
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37
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Wei JH, Yin X, Welander PV. Sterol Synthesis in Diverse Bacteria. Front Microbiol 2016; 7:990. [PMID: 27446030 PMCID: PMC4919349 DOI: 10.3389/fmicb.2016.00990] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/09/2016] [Indexed: 11/13/2022] Open
Abstract
Sterols are essential components of eukaryotic cells whose biosynthesis and function has been studied extensively. Sterols are also recognized as the diagenetic precursors of steranes preserved in sedimentary rocks where they can function as geological proxies for eukaryotic organisms and/or aerobic metabolisms and environments. However, production of these lipids is not restricted to the eukaryotic domain as a few bacterial species also synthesize sterols. Phylogenomic studies have identified genes encoding homologs of sterol biosynthesis proteins in the genomes of several additional species, indicating that sterol production may be more widespread in the bacterial domain than previously thought. Although the occurrence of sterol synthesis genes in a genome indicates the potential for sterol production, it provides neither conclusive evidence of sterol synthesis nor information about the composition and abundance of basic and modified sterols that are actually being produced. Here, we coupled bioinformatics with lipid analyses to investigate the scope of bacterial sterol production. We identified oxidosqualene cyclase (Osc), which catalyzes the initial cyclization of oxidosqualene to the basic sterol structure, in 34 bacterial genomes from five phyla (Bacteroidetes, Cyanobacteria, Planctomycetes, Proteobacteria, and Verrucomicrobia) and in 176 metagenomes. Our data indicate that bacterial sterol synthesis likely occurs in diverse organisms and environments and also provides evidence that there are as yet uncultured groups of bacterial sterol producers. Phylogenetic analysis of bacterial and eukaryotic Osc sequences confirmed a complex evolutionary history of sterol synthesis in this domain. Finally, we characterized the lipids produced by Osc-containing bacteria and found that we could generally predict the ability to synthesize sterols. However, predicting the final modified sterol based on our current knowledge of sterol synthesis was difficult. Some bacteria produced demethylated and saturated sterol products even though they lacked homologs of the eukaryotic proteins required for these modifications emphasizing that several aspects of bacterial sterol synthesis are still completely unknown.
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Affiliation(s)
| | | | - Paula V. Welander
- Department of Earth System Science, Stanford UniversityStanford, CA, USA
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38
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Laas P, Šatova E, Lips I, Lips U, Simm J, Kisand V, Metsis M. Near-Bottom Hypoxia Impacts Dynamics of Bacterioplankton Assemblage throughout Water Column of the Gulf of Finland (Baltic Sea). PLoS One 2016; 11:e0156147. [PMID: 27213812 PMCID: PMC4877108 DOI: 10.1371/journal.pone.0156147] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 05/10/2016] [Indexed: 11/19/2022] Open
Abstract
Over the past century the spread of hypoxia in the Baltic Sea has been drastic, reaching its ‘arm’ into the easternmost sub-basin, the Gulf of Finland. The hydrographic and climatological properties of the gulf offer a broad suite of discrete niches for microbial communities. The current study explores spatiotemporal dynamics of bacterioplankton community in the Gulf of Finland using massively parallel sequencing of 16S rRNA fragments obtained by amplifying community DNA from spring to autumn period. The presence of redoxcline and drastic seasonal changes make spatiotemporal dynamics of bacterioplankton community composition (BCC) and abundances in such estuary remarkably complex. To the best of our knowledge, this is the first study that analyses spatiotemporal dynamics of BCC in relation to phytoplankton bloom throughout the water column (and redoxcline), not only at the surface layer. We conclude that capability to survive (or benefit from) shifts between oxic and hypoxic conditions is vital adaptation for bacteria to thrive in such environments. Our results contribute to the understanding of emerging patterns in BCCs that occupy hydrographically similar estuaries dispersed all over the world, and we suggest the presence of a global redox- and salinity-driven metacommunity. These results have important implications for understanding long-term ecological and biogeochemical impacts of hypoxia expansion in the Baltic Sea (and similar ecosystems), as well as global biogeography of bacteria specialized inhabiting similar ecosystems.
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Affiliation(s)
- Peeter Laas
- Marine Systems Institute at Tallinn University of Technology, Akadeemia Rd. 15A, 12618, Tallinn, Estonia
- * E-mail:
| | - Elina Šatova
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Inga Lips
- Marine Systems Institute at Tallinn University of Technology, Akadeemia Rd. 15A, 12618, Tallinn, Estonia
| | - Urmas Lips
- Marine Systems Institute at Tallinn University of Technology, Akadeemia Rd. 15A, 12618, Tallinn, Estonia
| | - Jaak Simm
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Veljo Kisand
- Institute of Technology at University of Tartu, Nooruse 1, 50411, Tartu, Estonia
| | - Madis Metsis
- Institute of Mathematics and Natural Sciences, Tallinn University, Narva Rd. 25, 10120, Tallinn, Estonia
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39
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Singh JS, Strong PJ. Biologically derived fertilizer: A multifaceted bio-tool in methane mitigation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2016; 124:267-276. [PMID: 26547397 DOI: 10.1016/j.ecoenv.2015.10.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 10/14/2015] [Accepted: 10/15/2015] [Indexed: 06/05/2023]
Abstract
Methane emissions are affected by agricultural practices. Agriculture has increased in scale and intensity because of greater food, feed and energy demands. The application of chemical fertilizers in agriculture, particularly in paddy fields, has contributed to increased atmospheric methane emissions. Using organic fertilizers may improve crop yields and the methane sink potential within agricultural systems, which may be further improved when combined with beneficial microbes (i.e. biofertilizers) that improve the activity of methane oxidizing bacteria such as methanotrophs. Biofertilizers may be an effective tool for agriculture that is environmentally beneficial compared to conventional inorganic fertilizers. This review highlights and discusses the interplay between ammonia and methane oxidizing bacteria, the potential interactions of microbial communities with microbially-enriched organic amendments and the possible role of these biofertilizers in augmenting the methane sink potential of soils. It is suggested that biofertilizer applications should not only be investigated in terms of sustainable agriculture productivity and environmental management, but also in terms of their effects on methanogen and methanotroph populations.
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Affiliation(s)
- Jay Shankar Singh
- Department of Environmental Microbiology, BB Ambedkar (Central) University, Lucknow 226025, Uttar Pradesh, India.
| | - P J Strong
- Centre for Solid Waste Bioprocessing, School of Civil Engineering, School of Chemical Engineering, University of Queensland, St. Lucia, Queensland 4072, Australia.
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40
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Sherry A, Osborne KA, Sidgwick FR, Gray ND, Talbot HM. A temperate river estuary is a sink for methanotrophs adapted to extremes of pH, temperature and salinity. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:122-31. [PMID: 26617278 PMCID: PMC4959530 DOI: 10.1111/1758-2229.12359] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 11/19/2015] [Indexed: 05/08/2023]
Abstract
River Tyne (UK) estuarine sediments harbour a genetically and functionally diverse community of methane-oxidizing bacteria (methanotrophs), the composition and activity of which were directly influenced by imposed environmental conditions (pH, salinity, temperature) that extended far beyond those found in situ. In aerobic sediment slurries methane oxidation rates were monitored together with the diversity of a functional gene marker for methanotrophs (pmoA). Under near in situ conditions (4-30°C, pH 6-8, 1-15 g l(-1) NaCl), communities were enriched by sequences affiliated with Methylobacter and Methylomonas spp. and specifically a Methylobacter psychrophilus-related species at 4-21°C. More extreme conditions, namely high temperatures ≥ 40°C, high ≥ 9 and low ≤ 5 pH, and high salinities ≥ 35 g l(-1) selected for putative thermophiles (Methylocaldum), acidophiles (Methylosoma) and haloalkaliphiles (Methylomicrobium). The presence of these extreme methanotrophs (unlikely to be part of the active community in situ) indicates passive dispersal from surrounding environments into the estuary.
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Affiliation(s)
- Angela Sherry
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Kate A Osborne
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Frances R Sidgwick
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Neil D Gray
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Helen M Talbot
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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41
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Knief C. Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker. Front Microbiol 2015; 6:1346. [PMID: 26696968 PMCID: PMC4678205 DOI: 10.3389/fmicb.2015.01346] [Citation(s) in RCA: 278] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/16/2015] [Indexed: 01/06/2023] Open
Abstract
Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing "unknown methanotrophic bacteria." This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities.
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Affiliation(s)
- Claudia Knief
- Institute of Crop Science and Resource Conservation – Molecular Biology of the Rhizosphere, University of BonnBonn, Germany
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42
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Ling F, Hwang C, LeChevallier MW, Andersen GL, Liu WT. Core-satellite populations and seasonality of water meter biofilms in a metropolitan drinking water distribution system. ISME JOURNAL 2015; 10:582-95. [PMID: 26251872 DOI: 10.1038/ismej.2015.136] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 06/29/2015] [Accepted: 07/01/2015] [Indexed: 12/24/2022]
Abstract
Drinking water distribution systems (DWDSs) harbor the microorganisms in biofilms and suspended communities, yet the diversity and spatiotemporal distribution have been studied mainly in the suspended communities. This study examined the diversity of biofilms in an urban DWDS, its relationship with suspended communities and its dynamics. The studied DWDS in Urbana, Illinois received conventionally treated and disinfected water sourced from the groundwater. Over a 2-year span, biomass were sampled from household water meters (n=213) and tap water (n=20) to represent biofilm and suspended communities, respectively. A positive correlation between operational taxonomic unit (OTU) abundance and occupancy was observed. Examined under a 'core-satellite' model, the biofilm community comprised 31 core populations that encompassed 76.7% of total 16 S rRNA gene pyrosequences. The biofilm communities shared with the suspended community highly abundant and prevalent OTUs, which related to methano-/methylotrophs (i.e., Methylophilaceae and Methylococcaceae) and aerobic heterotrophs (Sphingomonadaceae and Comamonadaceae), yet differed by specific core populations and lower diversity and evenness. Multivariate tests indicated seasonality as the main contributor to community structure variation. This pattern was resilient to annual change and correlated to the cyclic fluctuations of core populations. The findings of a distinctive biofilm community assemblage and methano-/methyltrophic primary production provide critical insights for developing more targeted water quality monitoring programs and treatment strategies for groundwater-sourced drinking water systems.
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Affiliation(s)
- Fangqiong Ling
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chiachi Hwang
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Gary L Andersen
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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43
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Methylotrophs in natural habitats: current insights through metagenomics. Appl Microbiol Biotechnol 2015; 99:5763-79. [PMID: 26051673 DOI: 10.1007/s00253-015-6713-z] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/15/2015] [Accepted: 05/19/2015] [Indexed: 01/10/2023]
Abstract
The focus of this review is on the recent data from the omics approaches, measuring the presence of methylotrophs in natural environments. Both Bacteria and Archaea are considered. The data are discussed in the context of the current knowledge on the biochemistry of methylotrophy and the physiology of cultivated methylotrophs. One major issue discussed is the recent metagenomic data pointing toward the activity of "aerobic" methanotrophs, such as Methylobacter, in microoxic or hypoxic conditions. A related issue of the metabolic distinction between aerobic and "anaerobic" methylotrophy is addressed in the light of the genomic and metagenomic data for respective organisms. The role of communities, as opposed to single-organism activities in environmental cycling of single-carbon compounds, such as methane, is also discussed. In addition, the emerging issue of the role of non-traditional methylotrophs in global metabolism of single-carbon compounds and the role of methylotrophy pathways in non-methylotrophs is briefly mentioned.
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44
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Sorokin DY, Banciu HL, Muyzer G. Functional microbiology of soda lakes. Curr Opin Microbiol 2015; 25:88-96. [PMID: 26025021 DOI: 10.1016/j.mib.2015.05.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 04/30/2015] [Accepted: 05/01/2015] [Indexed: 10/23/2022]
Abstract
Soda lakes represent unique permanently haloalkaline system. Despite the harsh conditions, they are inhabited by abundant, mostly prokaryotic, microbial communities. This review summarizes results of studies of main functional groups of the soda lake prokaryotes responsible for carbon, nitrogen and sulfur cycling, including oxygenic and anoxygenic phototrophs, aerobic chemolithotrophs, fermenting and respiring anaerobes. The main conclusion from this work is that the soda lakes are very different from other high-salt systems in respect to microbial richness and activity. The reason for this difference is determined by the major physico-chemical features of two dominant salts - NaCl in neutral saline systems and sodium carbonates in soda lakes, that are influencing the amount of energy required for osmotic adaptation.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia; Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.
| | - Horia L Banciu
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Babeş-Bolyai University, Cluj-Napoca, Romania; Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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45
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Khmelenina VN, Rozova ON, But SY, Mustakhimov II, Reshetnikov AS, Beschastnyi AP, Trotsenko YA. Biosynthesis of secondary metabolites in methanotrophs: Biochemical and genetic aspects (Review). APPL BIOCHEM MICRO+ 2015. [DOI: 10.1134/s0003683815020088] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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46
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Chidambarampadmavathy K, Obulisamy P. K, Heimann K. Role of copper and iron in methane oxidation and bacterial biopolymer accumulation. Eng Life Sci 2015. [DOI: 10.1002/elsc.201400127] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Karthigeyan Chidambarampadmavathy
- Collegeof Marine and Environmental ScienceJames Cook University Townsville Queensland Australia
- Centre for Sustainable Fisheries and AquacultureJames Cook University Townsville Queensland Australia
| | - Karthikeyan Obulisamy P.
- Collegeof Marine and Environmental ScienceJames Cook University Townsville Queensland Australia
- Centre for Sustainable Fisheries and AquacultureJames Cook University Townsville Queensland Australia
| | - Kirsten Heimann
- Collegeof Marine and Environmental ScienceJames Cook University Townsville Queensland Australia
- Centre for Sustainable Fisheries and AquacultureJames Cook University Townsville Queensland Australia
- Centre for Biodiscovery and Molecular Development of TherapeuticsJames Cook University Townsville Queensland Australia
- Comparative Genomics CentreJames Cook University Townsville Queensland Australia
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47
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Stępniewska Z, Goraj W, Kuźniar A, Pytlak A, Ciepielski J, Frączek P. Biosynthesis of ectoine by the methanotrophic bacterial consortium isolated from Bogdanka coalmine (Poland). APPL BIOCHEM MICRO+ 2014. [DOI: 10.1134/s0003683814110039] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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48
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Tavormina PL, Hatzenpichler R, McGlynn S, Chadwick G, Dawson KS, Connon SA, Orphan VJ. Methyloprofundus sedimenti gen. nov., sp. nov., an obligate methanotroph from ocean sediment belonging to the 'deep sea-1' clade of marine methanotrophs. Int J Syst Evol Microbiol 2014; 65:251-259. [PMID: 25342114 DOI: 10.1099/ijs.0.062927-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
We report the isolation and growth characteristics of a gammaproteobacterial methane-oxidizing bacterium (Methylococcaceae strain WF1(T), 'whale fall 1') that shares 98 % 16S rRNA gene sequence identity with uncultivated free-living methanotrophs and the methanotrophic endosymbionts of deep-sea mussels, ≤94.6 % 16S rRNA gene sequence identity with species of the genus Methylobacter and ≤93.6 % 16S rRNA gene sequence identity with species of the genera Methylomonas and Methylosarcina. Strain WF1(T) represents the first cultivar from the 'deep sea-1' clade of marine methanotrophs, which includes members that participate in methane oxidation in sediments and the water column in addition to mussel endosymbionts. Cells of strain WF1(T) were elongated cocci, approximately 1.5 µm in diameter, and occurred singly, in pairs and in clumps. The cell wall was Gram-negative, and stacked intracytoplasmic membranes and storage granules were evident. The genomic DNA G+C content of WF1(T) was 40.5 mol%, significantly lower than that of currently described cultivars, and the major fatty acids were 16 : 0, 16 : 1ω9c, 16 : 1ω9t, 16 : 1ω8c and 16 : 2ω9,14. Growth occurred in liquid media at an optimal temperature of 23 °C, and was dependent on the presence of methane or methanol. Atmospheric nitrogen could serve as the sole nitrogen source for WF1(T), a capacity that had not been functionally demonstrated previously in members of Methylobacter. On the basis of its unique morphological, physiological and phylogenetic properties, this strain represents the type species within a new genus, and we propose the name Methyloprofundus sedimenti gen. nov., sp. nov. The type strain of Methyloprofundus sedimenti is WF1(T) ( = LMG 28393(T) = ATCC BAA-2619(T)).
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Affiliation(s)
- Patricia L Tavormina
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Roland Hatzenpichler
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Shawn McGlynn
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Grayson Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Katherine S Dawson
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Stephanie A Connon
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
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Takeuchi M, Kamagata Y, Oshima K, Hanada S, Tamaki H, Marumo K, Maeda H, Nedachi M, Hattori M, Iwasaki W, Sakata S. Methylocaldum marinum sp. nov., a thermotolerant, methane-oxidizing bacterium isolated from marine sediments, and emended description of the genus Methylocaldum. Int J Syst Evol Microbiol 2014; 64:3240-3246. [DOI: 10.1099/ijs.0.063503-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, methane-oxidizing bacterium (strain S8T) was isolated from marine sediments in Kagoshima Bay, Japan. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain is closely related to members of the genus
Methylocaldum
(97.6–97.9 % similarity) within the class
Gammaproteobacteria
. Strain S8T was a Gram-staining-negative, non-motile, coccoid or short rod-shaped organism. The temperature range for growth of strain S8T was 20–47 °C (optimum growth at 36 °C). It required NaCl (>0.5 %), tolerated up to 5 % NaCl and utilized methane and methanol. The major cellular fatty acid and major respiratory quinone were C16 : 0 and 18-methylene ubiquinone 8, respectively. The DNA G+C content was 59.7 mol%. Strain S8T possessed mmoX, which encodes soluble methane monooxygenase, as well as pmoA, which encodes the particulate methane monooxygenase. On the basis of this morphological, physiological, biochemical and genetic information, the first marine species in the genus
Methylocaldum
is proposed, with the name Methylocaldum marinum sp. nov. The type strain is S8T ( = NBRC 109686T = DSM 27392T). An emended description of the genus
Methylocaldum
is also provided.
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Affiliation(s)
- Mio Takeuchi
- Institute for Geo-resources and Environments, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Yoichi Kamagata
- Bioproduction Research Institute, AIST, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Kenshiro Oshima
- Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Chiba 277-8561, Japan
| | - Satoshi Hanada
- Bioproduction Research Institute, AIST, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, AIST, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Katsumi Marumo
- Institute of Geology and Geoinformation, AIST, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Hiroto Maeda
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-8580, Japan
| | - Munetomo Nedachi
- Department of Physics and Astronomy Graduate School of Science and Engineering/Faculty of Science, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-8580, Japan
| | - Masahira Hattori
- Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Chiba 277-8561, Japan
| | - Wataru Iwasaki
- Genetic Research Section, Atmosphere and Ocean Research Institute, the University of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Chiba 277-8564, Japan
- Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Chiba 277-8561, Japan
| | - Susumu Sakata
- Institute for Geo-resources and Environments, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
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50
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Sorokin DY, Berben T, Melton ED, Overmars L, Vavourakis CD, Muyzer G. Microbial diversity and biogeochemical cycling in soda lakes. Extremophiles 2014; 18:791-809. [PMID: 25156418 PMCID: PMC4158274 DOI: 10.1007/s00792-014-0670-9] [Citation(s) in RCA: 172] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 06/26/2014] [Indexed: 01/26/2023]
Abstract
Soda lakes contain high concentrations of sodium carbonates resulting in a stable elevated pH, which provide a unique habitat to a rich diversity of haloalkaliphilic bacteria and archaea. Both cultivation-dependent and -independent methods have aided the identification of key processes and genes in the microbially mediated carbon, nitrogen, and sulfur biogeochemical cycles in soda lakes. In order to survive in this extreme environment, haloalkaliphiles have developed various bioenergetic and structural adaptations to maintain pH homeostasis and intracellular osmotic pressure. The cultivation of a handful of strains has led to the isolation of a number of extremozymes, which allow the cell to perform enzymatic reactions at these extreme conditions. These enzymes potentially contribute to biotechnological applications. In addition, microbial species active in the sulfur cycle can be used for sulfur remediation purposes. Future research should combine both innovative culture methods and state-of-the-art 'meta-omic' techniques to gain a comprehensive understanding of the microbes that flourish in these extreme environments and the processes they mediate. Coupling the biogeochemical C, N, and S cycles and identifying where each process takes place on a spatial and temporal scale could unravel the interspecies relationships and thereby reveal more about the ecosystem dynamics of these enigmatic extreme environments.
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Affiliation(s)
- Dimitry Y. Sorokin
- Winogradsky Institute of Microbiology, RAS, Moscow, Russia
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Tom Berben
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Emily Denise Melton
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Lex Overmars
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Charlotte D. Vavourakis
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Gerard Muyzer
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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