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Yun JH, Lee H, Nam JW, Ko M, Park J, Lee DH, Lee SG, Kim HS. Unlocking synergies: Harnessing the potential of biological methane sequestration through metabolic coupling between Methylomicrobium alcaliphilum 20Z and Chlorella sp. HS2. BIORESOURCE TECHNOLOGY 2024; 399:130607. [PMID: 38499203 DOI: 10.1016/j.biortech.2024.130607] [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: 01/24/2024] [Revised: 03/09/2024] [Accepted: 03/15/2024] [Indexed: 03/20/2024]
Abstract
A halotolerant consortium between microalgae and methanotrophic bacteria could effectively remediate in situ CH4 and CO2, particularly using saline wastewater sources. Herein, Methylomicrobium alcaliphilum 20Z was demonstrated to form a mutualistic association with Chlorella sp. HS2 at a salinity level above 3.0%. Co-culture significantly enhanced the growth of both microbes, independent of initial inoculum ratios. Additionally, increased methane provision in enclosed serum bottles led to saturated methane removal. Subsequent analyses suggested nearly an order of magnitude increase in the amount of carbon sequestered in biomass in methane-fed co-cultures, conditions that also maintained a suitable cultural pH suitable for methanotrophic growth. Collectively, these results suggest a robust metabolic coupling between the two microbes and the influence of the factors other than gaseous exchange on the assembled consortium. Therefore, multi-faceted investigations are needed to harness the significant methane removal potential of the identified halotolerant consortium under conditions relevant to real-world operation scenarios.
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Affiliation(s)
- Jin-Ho Yun
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea.
| | - Hyewon Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea.
| | - Jang-Won Nam
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea.
| | - Minji Ko
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea.
| | - Jaehyun Park
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea.
| | - Dae-Hee Lee
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea; Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea; Graduate School of Engineering Biology, Korea Advanced Institute of Science & Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Seung-Goo Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea; Graduate School of Engineering Biology, Korea Advanced Institute of Science & Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Hee-Sik Kim
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Republic of Korea.
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Alvarez-Aponte ZI, Govindaraju AM, Hallberg ZF, Nicolas AM, Green MA, Mok KC, Fonseca-García C, Coleman-Derr D, Brodie EL, Carlson HK, Taga ME. Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates. THE ISME JOURNAL 2024; 18:wrae068. [PMID: 38648288 PMCID: PMC11287214 DOI: 10.1093/ismejo/wrae068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/15/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
Soil microbial communities impact carbon sequestration and release, biogeochemical cycling, and agricultural yields. These global effects rely on metabolic interactions that modulate community composition and function. However, the physicochemical and taxonomic complexity of soil and the scarcity of available isolates for phenotypic testing are significant barriers to studying soil microbial interactions. Corrinoids-the vitamin B12 family of cofactors-are critical for microbial metabolism, yet they are synthesized by only a subset of microbiome members. Here, we evaluated corrinoid production and dependence in soil bacteria as a model to investigate the ecological roles of microorganisms involved in metabolic interactions. We isolated and characterized a taxonomically diverse collection of 161 soil bacteria from a single study site. Most corrinoid-dependent bacteria in the collection prefer B12 over other corrinoids, while all tested producers synthesize B12, indicating metabolic compatibility between producers and dependents in the collection. Furthermore, a subset of producers release B12 at levels sufficient to support dependent isolates in laboratory culture at estimated ratios of up to 1000 dependents per producer. Within our isolate collection, we did not find strong phylogenetic patterns in corrinoid production or dependence. Upon investigating trends in the phylogenetic dispersion of corrinoid metabolism categories across sequenced bacteria from various environments, we found that these traits are conserved in 47 out of 85 genera. Together, these phenotypic and genomic results provide evidence for corrinoid-based metabolic interactions among bacteria and provide a framework for the study of nutrient-sharing ecological interactions in microbial communities.
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Affiliation(s)
- Zoila I Alvarez-Aponte
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Alekhya M Govindaraju
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Zachary F Hallberg
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Alexa M Nicolas
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Myka A Green
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Kenny C Mok
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Citlali Fonseca-García
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
- Plant Gene Expression Center, USDA-ARS, Albany, CA 94710, United States
| | - Devin Coleman-Derr
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
- Plant Gene Expression Center, USDA-ARS, Albany, CA 94710, United States
| | - Eoin L Brodie
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Hans K Carlson
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
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3
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Wang Y, Wu M, Lai CY, Lu X, Guo J. Methane Oxidation Coupled to Selenate Reduction in a Membrane Bioreactor under Oxygen-Limiting Conditions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21715-21726. [PMID: 38079577 DOI: 10.1021/acs.est.3c04958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Microbial methane oxidation coupled to a selenate reduction process has been proposed as a promising solution to treat contaminated water, yet the underlying microbial mechanisms are still unclear. In this study, a novel methane-based membrane bioreactor system integrating hollow fiber membranes for efficient gas delivery and ultrafiltration membranes for biomass retention was established to successfully enrich abundant suspended cultures able to perform methane-dependent selenate reduction under oxygen-limiting conditions. The microbial metabolic mechanisms were then systematically investigated through a combination of short-term batch tests, DNA-based stable isotope probing (SIP) microcosm incubation, and high-throughput sequencing analyses of 16S rRNA gene and functional genes (pmoA and narG). We confirmed that the methane-supported selenate reduction process was accomplished by a microbial consortia consisting of type-II aerobic methanotrophs and several heterotrophic selenate reducers. The mass balance and validation tests on possible intermediates suggested that methane was partially oxidized into acetate under oxygen-limiting conditions, which was consumed as a carbon source for selenate-reducing bacteria. High-throughput 16S rRNA gene sequencing, DNA-SIP incubation with 13CH4, and subsequent functional gene (pmoA and narG) sequencing results collectively proved that Methylocystis actively executed partial methane oxidation and Acidovorax and Denitratisoma were dominant selenate-reducing bacteria, thus forming a syntrophic partnership to drive selenate reduction. The findings not only advance our understanding of methane oxidation coupled to selenate reduction under oxygen-limiting conditions but also offer useful information on developing methane-based biotechnology for bioremediation of selenate-contaminated water.
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Affiliation(s)
- Yulu Wang
- Australian Centre for Water and Environmental Biotechnology (ACWEB, Formerly AWMC), The University of Queensland, St Lucia, Queensland 4072, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Acton, Canberra, Australian Capital Territory 2601, Australia
| | - Mengxiong Wu
- Australian Centre for Water and Environmental Biotechnology (ACWEB, Formerly AWMC), The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Chun-Yu Lai
- Australian Centre for Water and Environmental Biotechnology (ACWEB, Formerly AWMC), The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Xuanyu Lu
- Australian Centre for Water and Environmental Biotechnology (ACWEB, Formerly AWMC), The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (ACWEB, Formerly AWMC), The University of Queensland, St Lucia, Queensland 4072, Australia
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Barros-Rodríguez A, García-Gálvez C, Pacheco P, Kalyuzhnaya MG, Manzanera M. Isolation of Methane Enriched Bacterial Communities and Application as Wheat Biofertilizer under Drought Conditions: An Environmental Contribution. PLANTS (BASEL, SWITZERLAND) 2023; 12:2487. [PMID: 37447048 DOI: 10.3390/plants12132487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023]
Abstract
The search for methanotrophs as plant-growth-promoting rhizobacteria (PGPR) presents an important contribution to mitigating the impact of global warming by restoring the natural soil potential for consuming methane while benefiting plants during droughts. Our in silico simulations suggest that water, produced as a byproduct of methane oxidation, can satisfy the cell growth requirement. In addition to water, methanotrophs can produce metabolites that stimulate plant growth. Considering this, we proposed that applying methanotrophs as PGPR can alleviate the effect of droughts on crops, while stimulating atmospheric methane consumption. In this work, we isolated a series of methanotrophic communities from the rhizospheres of different crops, including Italian sweet pepper and zucchini, using an atmosphere enriched with pure methane gas, to determine their potential for alleviating drought stress in wheat plants. Subsequently, 23 strains of nonmethanotrophic bacteria present in the methanotrophic communities were isolated and characterized. We then analyzed the contribution of the methane-consuming consortia to the improvement of plant growth under drought conditions, showing that some communities contributed to increases in the wheat plants' lengths and weights, with statistically significant differences according to ANOVA models. Furthermore, we found that the presence of methane gas can further stimulate the plant-microbe interactions, resulting in larger plants and higher drought tolerance.
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Affiliation(s)
- Adoración Barros-Rodríguez
- Institute for Water Research and Department of Microbiology, University of Granada, 18071 Granada, Spain
- VitaNtech Biotechnology S.L., 18008 Granada, Spain
| | - Carlos García-Gálvez
- Institute for Water Research and Department of Microbiology, University of Granada, 18071 Granada, Spain
- VitaNtech Biotechnology S.L., 18008 Granada, Spain
| | - Pamela Pacheco
- Institute for Water Research and Department of Microbiology, University of Granada, 18071 Granada, Spain
| | | | - Maximino Manzanera
- Institute for Water Research and Department of Microbiology, University of Granada, 18071 Granada, Spain
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Berihu M, Somera TS, Malik A, Medina S, Piombo E, Tal O, Cohen M, Ginatt A, Ofek-Lalzar M, Doron-Faigenboim A, Mazzola M, Freilich S. A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data. MICROBIOME 2023; 11:8. [PMID: 36635724 PMCID: PMC9835355 DOI: 10.1186/s40168-022-01438-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The design of ecologically sustainable and plant-beneficial soil systems is a key goal in actively manipulating root-associated microbiomes. Community engineering efforts commonly seek to harness the potential of the indigenous microbiome through substrate-mediated recruitment of beneficial members. In most sustainable practices, microbial recruitment mechanisms rely on the application of complex organic mixtures where the resources/metabolites that act as direct stimulants of beneficial groups are not characterized. Outcomes of such indirect amendments are unpredictable regarding engineering the microbiome and achieving a plant-beneficial environment. RESULTS This study applied network analysis of metagenomics data to explore amendment-derived transformations in the soil microbiome, which lead to the suppression of pathogens affecting apple root systems. Shotgun metagenomic analysis was conducted with data from 'sick' vs 'healthy/recovered' rhizosphere soil microbiomes. The data was then converted into community-level metabolic networks. Simulations examined the functional contribution of treatment-associated taxonomic groups and linked them with specific amendment-induced metabolites. This analysis enabled the selection of specific metabolites that were predicted to amplify or diminish the abundance of targeted microbes functional in the healthy soil system. Many of these predictions were corroborated by experimental evidence from the literature. The potential of two of these metabolites (dopamine and vitamin B12) to either stimulate or suppress targeted microbial groups was evaluated in a follow-up set of soil microcosm experiments. The results corroborated the stimulant's potential (but not the suppressor) to act as a modulator of plant beneficial bacteria, paving the way for future development of knowledge-based (rather than trial and error) metabolic-defined amendments. Our pipeline for generating predictions for the selective targeting of microbial groups based on processing assembled and annotated metagenomics data is available at https://github.com/ot483/NetCom2 . CONCLUSIONS This research demonstrates how genomic-based algorithms can be used to formulate testable hypotheses for strategically engineering the rhizosphere microbiome by identifying specific compounds, which may act as selective modulators of microbial communities. Applying this framework to reduce unpredictable elements in amendment-based solutions promotes the development of ecologically-sound methods for re-establishing a functional microbiome in agro and other ecosystems. Video Abstract.
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Affiliation(s)
- Maria Berihu
- Agricultural Research Organization (ARO), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
| | - Tracey S. Somera
- United States Department of Agriculture-Agricultural Research Service Tree Fruit Research Lab, 1104 N. Western Ave, Wenatchee, WA 98801 USA
| | | | - Shlomit Medina
- Agricultural Research Organization (ARO), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
| | - Edoardo Piombo
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Grugliasco, Italy
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, P.O. Box 7026, 75007 Uppsala, Sweden
| | - Ofir Tal
- Agricultural Research Organization (ARO), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
- Kinneret Limnological Laboratory (KLL) Israel Oceanographic and Limnological Research (IOLR), P.O. Box 447, 49500 Migdal, Israel
| | - Matan Cohen
- Agricultural Research Organization (ARO), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
| | - Alon Ginatt
- Agricultural Research Organization (ARO), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
| | | | - Adi Doron-Faigenboim
- Agricultural Research Organization (ARO), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
| | - Mark Mazzola
- United States Department of Agriculture-Agricultural Research Service Tree Fruit Research Lab, 1104 N. Western Ave, Wenatchee, WA 98801 USA
- Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland, 7600 South Africa
| | - Shiri Freilich
- Agricultural Research Organization (ARO), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
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Transcriptome profiling of Paraburkholderia aromaticivorans AR20-38 during ferulic acid bioconversion. AMB Express 2022; 12:148. [DOI: 10.1186/s13568-022-01487-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/01/2022] [Indexed: 11/28/2022] Open
Abstract
AbstractThe importance and need of renewable-based, sustainable feedstocks increased in recent years. Lignin-derived monomers have high potential, energetic and economic value in the microbial bioconversion to valuable biomolecules. The bacterium Paraburkholderia aromaticivorans AR20-38 produces a remarkable yield of vanillic acid from ferulic acid at moderate and low temperatures and is therefore a good candidate for biotechnological applications. To understand this bioconversion process on a molecular level, a transcriptomic study during the bioconversion process was conducted to elucidate gene expression patterns. Differentially expressed genes, cellular transporters as well as transcriptional factors involved in the bioconversion process could be described. Additional enzymes known for xenobiotic degradation were differentially expressed and a potential membrane vesicle mechanism was detected. The bioconversion mechanism on a transcriptional level of P. aromaticivorans could be elucidated and results can be used for strain optimization. Additionally, the transcriptome study showed the high potential of the strain for other degradation applications.
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Rani V, Prasanna R, Kaushik R. Prospecting the significance of methane-utilizing bacteria in agriculture. World J Microbiol Biotechnol 2022; 38:176. [PMID: 35922575 DOI: 10.1007/s11274-022-03331-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/08/2022] [Indexed: 11/29/2022]
Abstract
Microorganisms act as both the source and sink of methane, a potent greenhouse gas, thus making a significant contribution to the environment as an important driver of climate change. The rhizosphere and phyllosphere of plants growing in natural (mangroves) and artificial wetlands (flooded agricultural ecosystems) harbor methane-utilizing bacteria that oxidize methane at the source and reduce its net flux. For several decades, microorganisms have been used as biofertilizers to promote plant growth. However, now their role in reducing net methane flux, especially from flooded agricultural ecosystems is gaining momentum globally. Research in this context has mainly focused on taxonomic aspects related to methanotrophy among diverse bacterial genera, and environmental factors that govern methane utilization in natural and artificial wetland ecosystems. In the last few decades, concerted efforts have been made to develop multifunctional microbial inoculants that can oxidize methane and alleviate greenhouse gas emissions, as well as promote plant growth. In this context, combinations of taxonomic groups commonly found in rice paddies and those used as biofertilizers are being explored. This review deals with methanotrophy among diverse bacterial domains, factors influencing methane-utilizing ability, and explores the potential of novel methane-utilizing microbial consortia with plant growth-promoting traits in flooded ecosystems.
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Affiliation(s)
- Vijaya Rani
- ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Radha Prasanna
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rajeev Kaushik
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
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Kaupper T, Mendes LW, Poehlein A, Frohloff D, Rohrbach S, Horn MA, Ho A. The methane-driven interaction network in terrestrial methane hotspots. ENVIRONMENTAL MICROBIOME 2022; 17:15. [PMID: 35382875 PMCID: PMC8981696 DOI: 10.1186/s40793-022-00409-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Biological interaction affects diverse facets of microbial life by modulating the activity, diversity, abundance, and composition of microbial communities. Aerobic methane oxidation is a community function, with emergent community traits arising from the interaction of the methane-oxidizers (methanotrophs) and non-methanotrophs. Yet little is known of the spatial and temporal organization of these interaction networks in naturally-occurring complex communities. We hypothesized that the assembled bacterial community of the interaction network in methane hotspots would converge, driven by high substrate availability that favors specific methanotrophs, and in turn influences the recruitment of non-methanotrophs. These environments would also share more co-occurring than site-specific taxa. RESULTS We applied stable isotope probing (SIP) using 13C-CH4 coupled to a co-occurrence network analysis to probe trophic interactions in widespread methane-emitting environments, and over time. Network analysis revealed predominantly unique co-occurring taxa from different environments, indicating distinctly co-evolved communities more strongly influenced by other parameters than high methane availability. Also, results showed a narrower network topology range over time than between environments. Co-occurrence pattern points to Chthoniobacter as a relevant yet-unrecognized interacting partner particularly of the gammaproteobacterial methanotrophs, deserving future attention. In almost all instances, the networks derived from the 13C-CH4 incubation exhibited a less connected and complex topology than the networks derived from the unlabelledC-CH4 incubations, likely attributable to the exclusion of the inactive microbial population and spurious connections; DNA-based networks (without SIP) may thus overestimate the methane-dependent network complexity. CONCLUSION We demonstrated that site-specific environmental parameters more strongly shaped the co-occurrence of bacterial taxa than substrate availability. Given that members of the interactome without the capacity to oxidize methane can exert interaction-induced effects on community function, understanding the co-occurrence pattern of the methane-driven interaction network is key to elucidating community function, which goes beyond relating activity to community composition, abundances, and diversity. More generally, we provide a methodological strategy that substantiates the ecological linkages between potentially interacting microorganisms with broad applications to elucidate the role of microbial interaction in community function.
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Affiliation(s)
- Thomas Kaupper
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Lucas W Mendes
- Center for Nuclear Energy in Agriculture, University of São Paulo CENA-USP, Piracicaba, SP, Brazil
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, George-August University Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Daria Frohloff
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Stephan Rohrbach
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Marcus A Horn
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany.
| | - Adrian Ho
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany.
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Proenca AM, Oliveira MM, Neves PFR, Giongo A, de Oliveira RR, Ott CT, Marconatto L, de Barros Neto HMC, Ketzer JMM, Medina-Silva R. Genomic, biochemical, and phylogenetic evaluation of bacteria isolated from deep-sea sediment harboring methane hydrates. Arch Microbiol 2022; 204:205. [PMID: 35266047 DOI: 10.1007/s00203-022-02814-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/04/2022] [Accepted: 02/18/2022] [Indexed: 11/25/2022]
Abstract
Over half of the organic carbon on Earth's surface is trapped in marine sediment as methane hydrates. Ocean warming causes hydrate dissociation and methane leakage to the water column, rendering the characterization of microbes from hydrate depositions a pressing matter. Through genomic, phylogenetic, and biochemical assays, we characterize the first microorganisms isolated from the Rio Grande Cone (Brazil), reservoir responsible for massive methane releases to the water column. From sediment harboring rich benthic communities, we obtained 43 strains of Brevibacillus sp., Paenibacillus sp. and groups of Bacillus sp. Methane-enriched samples yielded strains of the Pseudomonas fluorescens complex, exhibiting fluorescent siderophore production and broad multi-carbon catabolism. Genomic characterization of a novel Pseudomonas sp. strain indicated 32 genes not identified in the closest related type-species, including proteins involved with mercury resistance. Our results provide phylogenetic and genomic insights on the first bacterial isolates retrieved from a poorly explored region of the South Atlantic Ocean.
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Affiliation(s)
- Audrey Menegaz Proenca
- Geobiology Research Group, Institute of Petroleum and Natural Resources, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil.,Immunology and Microbiology Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil.,Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - Maiara Monteiro Oliveira
- Geobiology Research Group, Institute of Petroleum and Natural Resources, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil.,Immunology and Microbiology Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Paula Fernanda Ribas Neves
- Geobiology Research Group, Institute of Petroleum and Natural Resources, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil.,Immunology and Microbiology Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Adriana Giongo
- Geobiology Research Group, Institute of Petroleum and Natural Resources, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Rafael Rodrigues de Oliveira
- Geobiology Research Group, Institute of Petroleum and Natural Resources, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Carolina Telles Ott
- Immunology and Microbiology Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Letícia Marconatto
- Geobiology Research Group, Institute of Petroleum and Natural Resources, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | | | | | - Renata Medina-Silva
- Geobiology Research Group, Institute of Petroleum and Natural Resources, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil. .,Immunology and Microbiology Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil.
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10
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Praeg N, Schachner I, Schuster L, Illmer P. Carbon-dependent growth, community structure and methane oxidation performance of a soil-derived methanotrophic mixed culture. FEMS Microbiol Lett 2021; 368:6035239. [PMID: 33320954 DOI: 10.1093/femsle/fnaa212] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/11/2020] [Indexed: 11/13/2022] Open
Abstract
Soil-borne methane-oxidizing microorganisms act as a terrestrial methane (CH4) sink and are potentially useful in decreasing global CH4 emissions. Understanding the ecophysiology of methanotrophs is crucial for a thorough description of global carbon cycling. Here, we report the in situ balance of soils from abandoned landfills, meadows and wetlands, their capacities to produce and oxidize CH4 at laboratory-scale and the isolation of a soil-borne methanotrophic-heterotrophic mixed culture that was used for carbon (C1 and C2) feeding experiments. We showed that even with similar soil properties, the in situ CH4 balance depends on land-use. Different soils had different potentials to adapt to increased CH4 availability, leading to the highest CH4 oxidation capacities for landfill and wetland soils. The most efficient mixed culture isolated from the landfill was dominated by the methanotrophs Methylobacter sp. and Methylosinus sp., which were accompanied by Variovorax sp. and Pseudomonas sp. and remained active in oxidizing CH4 when supplied with additional C-sources. The ratios between type I and type II methanotrophs and between methanotrophic and heterotrophic bacteria changed when C-sources were altered. A significant effect of the application of the mixed culture on the CH4 oxidation of soils was established but the extent varied depending on soil type.
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Affiliation(s)
- Nadine Praeg
- Universität Innsbruck, Department of Microbiology, Technikerstrasse 25d, A-6020 Innsbruck, Austria
| | - Iris Schachner
- Universität Innsbruck, Department of Microbiology, Technikerstrasse 25d, A-6020 Innsbruck, Austria
| | - Lisa Schuster
- Universität Innsbruck, Department of Microbiology, Technikerstrasse 25d, A-6020 Innsbruck, Austria
| | - Paul Illmer
- Universität Innsbruck, Department of Microbiology, Technikerstrasse 25d, A-6020 Innsbruck, Austria
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11
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Ho A, Mendes LW, Lee HJ, Kaupper T, Mo Y, Poehlein A, Bodelier PLE, Jia Z, Horn MA. Response of a methane-driven interaction network to stressor intensification. FEMS Microbiol Ecol 2021; 96:5898668. [PMID: 32857837 DOI: 10.1093/femsec/fiaa180] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/25/2020] [Indexed: 01/04/2023] Open
Abstract
Microorganisms may reciprocally select for specific interacting partners, forming a network with interdependent relationships. The methanotrophic interaction network, comprising methanotrophs and non-methanotrophs, is thought to modulate methane oxidation and give rise to emergent properties beneficial for the methanotrophs. Therefore, microbial interaction may become relevant for community functioning under stress. However, empirical validation of the role and stressor-induced response of the interaction network remains scarce. Here, we determined the response of a complex methane-driven interaction network to a stepwise increase in NH4Cl-induced stress (0.5-4.75 g L-1, in 0.25-0.5 g L-1 increments) using enrichment of a naturally occurring complex community derived from a paddy soil in laboratory-scale incubations. Although ammonium and intermediates of ammonium oxidation are known to inhibit methane oxidation, methanotrophic activity was unexpectedly detected even in incubations with high ammonium levels, albeit rates were significantly reduced. Sequencing analysis of the 16S rRNA and pmoA genes consistently revealed divergent communities in the reference and stressed incubations. The 16S rRNA-based co-occurrence network analysis revealed that NH4Cl-induced stress intensification resulted in a less complex and modular network, likely driven by less stable interaction. Interestingly, the non-methanotrophs formed the key nodes, and appear to be relevant members of the community. Overall, stressor intensification unravels the interaction network, with adverse consequences for community functioning.
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Affiliation(s)
- Adrian Ho
- Institute of Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Lucas W Mendes
- Center of Nuclear Energy in Agriculture, University of São Paulo (CENA-USP), Avenida Centenario 303, 13416-000, Piracicaba-SP, Brazil
| | - Hyo Jung Lee
- Department of Biology, Kunsan National University, 558 Daehak-ro, Gunsan-si 54150, Republic of Korea
| | - Thomas Kaupper
- Institute of Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Yongliang Mo
- Institute of Soil Science, Chinese Academy of Sciences, No. 71 East Beijing Road, Xuan-Wu District, Nanjing 210008, China
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, the Netherlands
| | - Zhongjun Jia
- Institute of Soil Science, Chinese Academy of Sciences, No. 71 East Beijing Road, Xuan-Wu District, Nanjing 210008, China
| | - Marcus A Horn
- Institute of Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
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12
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Recovery in methanotrophic activity does not reflect on the methane-driven interaction network after peat mining. Appl Environ Microbiol 2021; 87:AEM.02355-20. [PMID: 33355115 PMCID: PMC8090869 DOI: 10.1128/aem.02355-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aerobic methanotrophs are crucial in ombrotrophic peatlands, driving the methane and nitrogen cycles. Peat mining adversely affects the methanotrophs, but activity and community composition/abundances may recover after restoration. Considering that the methanotrophic activity and growth are significantly stimulated in the presence of other microorganisms, the methane-driven interaction network, encompassing methanotrophs and non-methanotrophs (i.e., methanotrophic interactome), may also be relevant in conferring community resilience. Yet, little is known of the response and recovery of the methanotrophic interactome to disturbances. Here, we determined the recovery of the methanotrophic interactome as inferred by a co-occurrence network analysis, comparing a pristine and restored peatland. We coupled a DNA-based stable isotope probing (SIP) approach using 13C-CH4 to a co-occurrence network analysis derived from the 13C-enriched 16S rRNA gene sequences to relate the response in methanotrophic activity to the structuring of the interaction network. Methanotrophic activity and abundances recovered after peat restoration since 2000. 'Methylomonaceae' was the predominantly active methanotrophs in both peatlands, but differed in the relative abundance of Methylacidiphilaceae and Methylocystis However, bacterial community composition was distinct in both peatlands. Likewise, the methanotrophic interactome was profoundly altered in the restored peatland. Structuring of the interaction network after peat mining resulted in the loss of complexity and modularity, indicating a less connected and efficient network, which may have consequences in the event of recurring/future disturbances. Therefore, determining the response of the methane-driven interaction network, in addition to relating methanotrophic activity to community composition/abundances, provided a more comprehensive understanding of the resilience of the methanotrophs.Importance The resilience and recovery of microorganisms from disturbances are often determined with regard to their activity and community composition/abundances. Rarely has the response of the network of interacting microorganisms been considered, despite accumulating evidence showing that microbial interaction modulates community functioning. Comparing the methane-driven interaction network of a pristine and restored peatland, our findings revealed that the metabolically active microorganisms were less connected and formed less modular 'hubs' in the restored peatland, indicative of a less complex network which may have consequences with recurring disturbances and environmental changes. This also suggests that the resilience and full recovery in the methanotrophic activity and abundances do not reflect on the interaction network. Therefore, it is relevant to consider the interaction-induced response, in addition to documenting changes in activity and community composition/abundances, to provide a comprehensive understanding of the resilience of microorganisms to disturbances.
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Praeg N, Illmer P. Microbial community composition in the rhizosphere of Larix decidua under different light regimes with additional focus on methane cycling microorganisms. Sci Rep 2020; 10:22324. [PMID: 33339837 PMCID: PMC7749151 DOI: 10.1038/s41598-020-79143-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 12/01/2020] [Indexed: 02/05/2023] Open
Abstract
Microbial community and diversity in the rhizosphere is strongly influenced by biotic and/or abiotic factors, like root exudates, nutrient availability, edaphon and climate. Here we report on the microbial diversity within the rhizosphere of Larix decidua, a dominant tree species in the Alps, as compared with the microbiome within the surrounding soil. We describe how increased light intensity influenced the rhizobiome and put emphasize on methane cycling microorganisms. Microbial taxa were classified into 26 bacterial, 4 archaeal and 6 fungal phyla revealing significant differences between bulk and rhizosphere soils. The dominant prokaryotic phyla were Proteobacteria, Acidobacteria, Actinobacteria (both, rhizosphere and bulk soil) and Bacteroidetes (rhizosphere soil only) and dominant fungal phyla in both fractions included Ascomycota and Basidiomycota. The rhizosphere community was indicated by Suillus sp., plant growth-promoting bacteria and Candidatus Saccharibacteria. Predicted genes in membrane transport and carbohydrate metabolism were significantly more abundant in rhizosphere soils while genes connected with energy metabolisms and cell motility increased in bulk soils. Dominant methanotrophic microorganisms were Upland Soil Cluster (USC) α methanotrophs, Methylogaea spp. and Methylosinus spp., while most methanogens belonged to Methanomassiliicoccales. The overall abundance of methanotrophs distinctly increased in the rhizosphere but to a very different species-specific extent. The increased light intensity only led to minor changes in the rhizobiome, nevertheless a couple of indicator species (e.g. Pseudomonas sp.) for intensified light conditions were established.
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Affiliation(s)
- Nadine Praeg
- Department of Microbiology, Universität Innsbruck, Technikerstrasse 25d, 6020, Innsbruck, Austria.
| | - Paul Illmer
- Department of Microbiology, Universität Innsbruck, Technikerstrasse 25d, 6020, Innsbruck, Austria
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14
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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: 8] [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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Oshkin IY, Belova SE, Khokhlachev NS, Semenova VA, Chervyakova OP, Chernushkin DV, Tikhonova EN, Mardanov AV, Ravin NV, Popov VO, Pimenov NV, Dedysh SN. Molecular Analysis of the Microbial Community Developing in Continuous Culture of Methylococcus sp. Concept-8 on Natural Gas. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720050173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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16
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Finn DR, Ziv-El M, van Haren J, Park JG, Del Aguila-Pasquel J, Urquiza-Muñoz JD, Cadillo-Quiroz H. Methanogens and Methanotrophs Show Nutrient-Dependent Community Assemblage Patterns Across Tropical Peatlands of the Pastaza-Marañón Basin, Peruvian Amazonia. Front Microbiol 2020; 11:746. [PMID: 32390985 PMCID: PMC7193774 DOI: 10.3389/fmicb.2020.00746] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/30/2020] [Indexed: 11/17/2022] Open
Abstract
Tropical peatlands are globally important carbon reservoirs that play a crucial role in fluxes of atmospheric greenhouse gases. Amazon peatlands are expected to be large source of atmospheric methane (CH4) emissions, however little is understood about the rates of CH4 flux or the microorganisms that mediate it in these environments. Here we studied a mineral nutrient gradient across peatlands in the Pastaza-Marañón Basin, the largest tropical peatland in South America, to describe CH4 fluxes and environmental factors that regulate species assemblages of methanogenic and methanotrophic microorganisms. Peatlands were grouped as minerotrophic, mixed and ombrotrophic categories by their general water source leading to different mineral nutrient content (rich, mixed and poor) quantified by trace elements abundance. Microbial communities clustered dependent on nutrient content (ANOSIM p < 0.001). Higher CH4 flux was associated with minerotrophic communities compared to the other categories. The most dominant methanogens and methanotrophs were represented by Methanobacteriaceae, and Methylocystaceae, respectively. Weighted network analysis demonstrated tight clustering of most methanogen families with minerotrophic-associated microbial families. Populations of Methylocystaceae were present across all peatlands. Null model testing for species assemblage patterns and species rank distributions confirmed non-random aggregations of Methylococcacae methanotroph and methanogen families (p < 0.05). We conclude that in studied amazon peatlands increasing mineral nutrient content provides favorable habitats for Methanobacteriaceae, while Methylocystaceae populations seem to broadly distribute independent of nutrient content.
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Affiliation(s)
- Damien Robert Finn
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Michal Ziv-El
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Joost van Haren
- Biosphere 2, University of Arizona, Tucson, AZ, United States
| | - Jin Gyoon Park
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | | | - Jose David Urquiza-Muñoz
- Laboratorio de Suelos del Centro de Investigaciones de Recursos Naturales de la Amazonia Peruana, and Facultad de Ciencias Forestales, Universidad de la Amazonia Peruana, Iquitos, Peru
| | - Hinsby Cadillo-Quiroz
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ, United States
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17
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Singh R, Ryu J, Kim SW. Microbial consortia including methanotrophs: some benefits of living together. J Microbiol 2019; 57:939-952. [PMID: 31659683 DOI: 10.1007/s12275-019-9328-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/30/2019] [Accepted: 09/25/2019] [Indexed: 01/13/2023]
Abstract
With the progress of biotechnological research and improvements made in bioprocessing with pure cultures, microbial consortia have gained recognition for accomplishing biological processes with improved effectiveness. Microbes are indispensable tool in developing bioprocesses for the production of bioenergy and biochemicals while utilizing renewable resources due to technical, economic and environmental advantages. They communicate with specific cohorts in close proximity to promote metabolic cooperation. Use of positive microbial associations has been recognized widely, especially in food industries and bioremediation of toxic compounds and waste materials. Role of microbial associations in developing sustainable energy sources and substitutes for conventional fuels is highly promising with many commercial prospects. Detoxification of chemical contaminants sourced from domestic, agricultural and industrial wastes has also been achieved through microbial catalysis in pure and co-culture systems. Methanotrophs, the sole biological sink of greenhouse gas methane, catalyze the methane monooxygenasemediated oxidation of methane to methanol, a high energy density liquid and key platform chemical to produce commodity chemical compounds and their derivatives. Constructed microbial consortia have positive effects, such as improved biomass, biocatalytic potential, stability etc. In a methanotroph-heterotroph consortium, non-methanotrophs provide key nutrient factors and alleviate the toxicity from the culture. Non-methanotrophic organisms biologically stimulate the growth and activity of methanotrophs via production of growth stimulators. However, methanotrophs in association with co-cultured microorganisms are in need of further exploration and thorough investigation to study their interaction mode and application with improved effectiveness.
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Affiliation(s)
- Rajendra Singh
- Department of Environmental Engineering, Chosun University, Gwangju, 61452, Republic of Korea
| | - Jaewon Ryu
- Department of Energy Convergence, Chosun University, Gwangju, 61452, Republic of Korea
| | - Si Wouk Kim
- Department of Environmental Engineering, Chosun University, Gwangju, 61452, Republic of Korea. .,Department of Energy Convergence, Chosun University, Gwangju, 61452, Republic of Korea.
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18
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Community composition and methane oxidation activity of methanotrophs associated with duckweeds in a fresh water lake. J Biosci Bioeng 2019; 128:450-455. [DOI: 10.1016/j.jbiosc.2019.04.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 04/12/2019] [Accepted: 04/12/2019] [Indexed: 11/21/2022]
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Heděnec P, Angel R, Lin Q, Rui J, Li X. Increased methane concentration alters soil prokaryotic community structure along an artificial pH gradient. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-018-1421-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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20
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Bodelier PLE, Pérez G, Veraart AJ, Krause SMB. Methanotroph Ecology, Environmental Distribution and Functioning. METHANOTROPHS 2019. [DOI: 10.1007/978-3-030-23261-0_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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21
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Jeong SY, Kim TG. Development of a novel methanotrophic process with the helper micro-organism Hyphomicrobium sp. NM3. J Appl Microbiol 2018; 126:534-544. [PMID: 30365214 DOI: 10.1111/jam.14140] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/09/2018] [Accepted: 10/19/2018] [Indexed: 01/29/2023]
Abstract
AIMS Microbial consortia can be more efficient at biological processes than single isolates. The purposes of this study were to design and evaluate a synthetic microbial consortium containing the methanotroph Methylocystis sp. M6 and the helper Hyphomicrobium sp. NM3, and develop a novel methanotrophic process for this consortium utilizing a dialysis membrane. METHODS AND RESULTS Hyphomicrobium increased the methane-oxidation rate (MOR), biomass and stability at a dilution rate of 0·067 day-1 in fed-batch co-culture. qRT-PCR showed that Methylocystis population increased gradually with time, whereas Hyphomicrobium population remained stable despite cell washing, confirming synergistic population interaction. At 0·1 day-1 , spiking of Hyphomicrobium effectively increased the methanotrophic activity, after which Hyphomicrobium population decreased with time, indicating that the consortium is optimal at <0·1 day-1 . When Hyphomicrobium was grown in dialysis membrane within the bioreactor, MOR increased linearly up to 155·1 ± 1·0 mmol l-1 day-1 at 0·067, 0·1, 0·2 and 0·4 day-1 , which is the highest observed value for a methanotrophic reactor. CONCLUSIONS Hyphomicrobium sp. NM3 is a promising helper micro-organism for methanotrophs. Hyphomicrobium-methanotroph consortia used concurrently with existing methods can produce an efficient and stable methane oxidation system. SIGNIFICANCE AND IMPACT OF THE STUDY This novel methanotrophic process is superior to those previously reported in the literature, and can provide efficient and stable methane oxidation.
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Affiliation(s)
- S-Y Jeong
- Department of Microbiology, Pusan National University, Pusan, Korea
| | - T G Kim
- Department of Microbiology, Pusan National University, Pusan, Korea
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Yu WJ, Lee JW, Nguyen NL, Rhee SK, Park SJ. The characteristics and comparative analysis of methanotrophs reveal genomic insights into Methylomicrobium sp. enriched from marine sediments. Syst Appl Microbiol 2018; 41:415-426. [DOI: 10.1016/j.syapm.2018.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 05/04/2018] [Accepted: 05/04/2018] [Indexed: 10/16/2022]
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23
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Nguyen NL, Yu WJ, Gwak JH, Kim SJ, Park SJ, Herbold CW, Kim JG, Jung MY, Rhee SK. Genomic Insights Into the Acid Adaptation of Novel Methanotrophs Enriched From Acidic Forest Soils. Front Microbiol 2018; 9:1982. [PMID: 30210468 PMCID: PMC6119699 DOI: 10.3389/fmicb.2018.01982] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/06/2018] [Indexed: 01/08/2023] Open
Abstract
Soil acidification is accelerated by anthropogenic and agricultural activities, which could significantly affect global methane cycles. However, detailed knowledge of the genomic properties of methanotrophs adapted to acidic soils remains scarce. Using metagenomic approaches, we analyzed methane-utilizing communities enriched from acidic forest soils with pH 3 and 4, and recovered near-complete genomes of proteobacterial methanotrophs. Novel methanotroph genomes designated KS32 and KS41, belonging to two representative clades of methanotrophs (Methylocystis of Alphaproteobacteria and Methylobacter of Gammaproteobacteria), were dominant. Comparative genomic analysis revealed diverse systems of membrane transporters for ensuring pH homeostasis and defense against toxic chemicals. Various potassium transporter systems, sodium/proton antiporters, and two copies of proton-translocating F1F0-type ATP synthase genes were identified, which might participate in the key pH homeostasis mechanisms in KS32. In addition, the V-type ATP synthase and urea assimilation genes might be used for pH homeostasis in KS41. Genes involved in the modification of membranes by incorporation of cyclopropane fatty acids and hopanoid lipids might be used for reducing proton influx into cells. The two methanotroph genomes possess genes for elaborate heavy metal efflux pumping systems, possibly owing to increased heavy metal toxicity in acidic conditions. Phylogenies of key genes involved in acid adaptation, methane oxidation, and antiviral defense in KS41 were incongruent with that of 16S rRNA. Thus, the detailed analysis of the genome sequences provides new insights into the ecology of methanotrophs responding to soil acidification.
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Affiliation(s)
- Ngoc-Loi Nguyen
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
| | - Woon-Jong Yu
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
| | - Joo-Han Gwak
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
| | - So-Jeong Kim
- Geologic Environment Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, South Korea
| | - Soo-Je Park
- Department of Biology, Jeju National University, Jeju City, South Korea
| | - Craig W Herbold
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Jong-Geol Kim
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
| | - Man-Young Jung
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
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Abstract
Aerobic methanotrophs have long been known to play a critical role in the global carbon cycle, being capable of converting methane to biomass and carbon dioxide. Interestingly, these microbes exhibit great sensitivity to copper and rare-earth elements, with the expression of key genes involved in the central pathway of methane oxidation controlled by the availability of these metals. That is, these microbes have a "copper switch" that controls the expression of alternative methane monooxygenases and a "rare-earth element switch" that controls the expression of alternative methanol dehydrogenases. Further, it has been recently shown that some methanotrophs can detoxify inorganic mercury and demethylate methylmercury; this finding is remarkable, as the canonical organomercurial lyase does not exist in these methanotrophs, indicating that a novel mechanism is involved in methylmercury demethylation. Here, we review recent findings on methanotrophic interactions with metals, with a particular focus on these metal switches and the mechanisms used by methanotrophs to bind and sequester metals.
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25
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Living apart together-bacterial volatiles influence methanotrophic growth and activity. ISME JOURNAL 2018; 12:1163-1166. [PMID: 29382947 DOI: 10.1038/s41396-018-0055-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 10/31/2017] [Accepted: 12/21/2017] [Indexed: 11/08/2022]
Abstract
Volatile organic compounds play an important role in microbial interactions. However, little is known about how volatile-mediated interactions modulate biogeochemical processes. In this study, we show the effect of volatile-mediated interaction on growth and functioning of aerobic methane-oxidizing bacteria, grown in co-culture with five different heterotrophs. Both growth and methane oxidation of Methylobacter luteus were stimulated by interaction with specific heterotrophs. In Methylocystis parvus, we observed significant growth promotion, while methane oxidation was inhibited. Volatolomics of the interaction of each of the methanotrophs with Pseudomonas mandelii, revealed presence of a complex blend of volatiles, including dimethylsulfide, dimethyldisulfide, and bicyclic sesquiterpenes. Although the ecological role of the detected compounds remains to be elucidated, our results provide unprecedented insights into interspecific relations and associated volatiles for stimulating methanotroph functioning, which is of substantial environmental and biotechnological significance.
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Grodnitskaya ID, Trusova MY, Syrtsov SN, Koroban NV. Structure of microbial communities of peat soils in two bogs in Siberian tundra and forest zones. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718010083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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27
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Abstract
Vitamin B12 is synthesized only by certain bacteria and archaeon, but not by plants. The synthesized vitamin B12 is transferred and accumulates in animal tissues, which can occur in certain plant and mushroom species through microbial interaction. In particular, the meat and milk of herbivorous ruminant animals (e.g. cattle and sheep) are good sources of vitamin B12 for humans. Ruminants acquire vitamin B12, which is considered an essential nutrient, through a symbiotic relationship with the bacteria present in their stomachs. In aquatic environments, most phytoplankton acquire vitamin B12 through a symbiotic relationship with bacteria, and they become food for larval fish and bivalves. Edible plants and mushrooms rarely contain a considerable amount of vitamin B12, mainly due to concomitant bacteria in soil and/or their aerial surfaces. Thus, humans acquire vitamin B12 formed by microbial interaction via mainly ruminants and fish (or shellfish) as food sources. In this review, up-to-date information on vitamin B12 sources and bioavailability are also discussed. Impact statement To prevent vitamin B12 (B12) deficiency in high-risk populations such as vegetarians and elderly subjects, it is necessary to identify foods that contain high levels of B12. B12 is synthesized by only certain bacteria and archaeon, but not by plants or animals. The synthesized B12 is transferred and accumulated in animal tissues, even in certain plant tissues via microbial interaction. Meats and milks of herbivorous ruminant animals are good sources of B12 for humans. Ruminants acquire the essential B12 through a symbiotic relationship with bacteria inside the body. Thus, we also depend on B12-producing bacteria located in ruminant stomachs. While edible plants and mushrooms rarely contain a considerable amount of B12, mainly due to concomitant bacteria in soil and/or their aerial surfaces. In this mini-review, we described up-to-date information on B12 sources and bioavailability with reference to the interaction of microbes as B12-producers.
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Affiliation(s)
- Fumio Watanabe
- Department of Agricultural, Life and Environmental Sciences, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan
| | - Tomohiro Bito
- Department of Agricultural, Life and Environmental Sciences, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan
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28
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Yu Z, Beck DAC, Chistoserdova L. Natural Selection in Synthetic Communities Highlights the Roles of Methylococcaceae and Methylophilaceae and Suggests Differential Roles for Alternative Methanol Dehydrogenases in Methane Consumption. Front Microbiol 2017; 8:2392. [PMID: 29259591 PMCID: PMC5723320 DOI: 10.3389/fmicb.2017.02392] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 11/20/2017] [Indexed: 12/31/2022] Open
Abstract
We describe experiments that follow species dynamics and gene expression patterns in synthetic bacterial communities including species that compete for the single carbon substrate supplied, methane, and species unable to consume methane, which could only succeed through cooperative interactions. We demonstrate that these communities mostly select for two functional guilds, methanotrophs of the family Methylococcaceae and non-methanotrophic methylotrophs of the family Methylophilaceae, these taxonomic guilds outcompeting all other species included in the synthetic mix. The metatranscriptomics analysis uncovered that in both Methylococcaceae and Methylophilaceae, some of the most highly transcribed genes were the ones encoding methanol dehydrogenases (MDH). Remarkably, expression of alternative MDH genes (mxaFI versus xoxF), previously shown to be subjects to the rare Earth element switch, was found to depend on environmental conditions such as nitrogen source and methane and O2 partial pressures, and also to be species-specific. Along with the xoxF genes, genes encoding divergent cytochromes were highly expressed in both Methylophilaceae and Methylococcaceae, suggesting their function in methanol metabolism, likely encoding proteins serving as electron acceptors from XoxF enzymes. The research presented tested a synthetic community model that is much simplified compared to natural communities consuming methane, but more complex than the previously utilized two-species model. The performance of this model identifies prominent species for future synthetic ecology experiments and highlights both advantages of this approach and the challenges that it presents.
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Affiliation(s)
- Zheng Yu
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States
| | - David A C Beck
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States.,eScience Institute, University of Washington, Seattle, WA, United States
| | - Ludmila Chistoserdova
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States
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A novel methanotroph in the genus Methylomonas that contains a distinct clade of soluble methane monooxygenase. J Microbiol 2017; 55:775-782. [DOI: 10.1007/s12275-017-7317-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 08/25/2017] [Accepted: 08/31/2017] [Indexed: 10/18/2022]
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30
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Yu Z, Chistoserdova L. Communal metabolism of methane and the rare Earth element switch. J Bacteriol 2017; 199:e00328-17. [PMID: 28630125 PMCID: PMC5648859 DOI: 10.1128/jb.00328-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Metabolism of methane is an important part of biogeochemical cycling of carbon. Methane is also a major contributor to climate change. A specialized group of microbes that consume methane, the methanotrophs, represent a natural filter preventing an even faster accumulation of methane in the atmosphere. Methanotrophy can proceed via both anaerobic and aerobic modes. The anaerobic methanotrophs, represented by both archaea and bacteria, all appear to be engaged in syntrophic interdependencies with other species, to overcome the energetic barriers of methane metabolism in the absence of oxygen. In contrast, aerobic methanotrophy can be carried out by pure cultures of bacteria. Nevertheless, a concept of communal function in aerobic methane oxidation has been gaining momentum, based on data from natural cooccurrence of specific functional guilds, and based on results from laboratory manipulations. The mechanistic details are still sparse on how and why the methanotrophs share their carbon with other species, and whether and what they gain in return. In this minireview we highlight recent studies that led to this new concept of community function in aerobic methane oxidation. We first describe the stable isotope probing experiments employing heavy carbon-labeled methane, tracing methane carbon consumption. We then follow up with analysis of data from microcosm community dynamics. We further discuss the role of a synthetic community approach in unraveling the principles of carbon flow and species cooperation in methane consumption. Finally, we touch on the role of lanthanides, which are rare Earth elements, previously thought to be biologically inert, in bacterial metabolism of methane.
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Affiliation(s)
- Zheng Yu
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195
| | - Ludmila Chistoserdova
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195
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31
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Sheets JP, Lawson K, Ge X, Wang L, Yu Z, Li Y. Development and evaluation of a trickle bed bioreactor for enhanced mass transfer and methanol production from biogas. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.03.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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32
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Stępniewska Z, Goraj W, Kuźniar A, Łopacka N, Małysza M. Enrichment culture and identification of endophytic methanotrophs isolated from peatland plants. Folia Microbiol (Praha) 2017; 62:381-391. [PMID: 28275945 PMCID: PMC5579069 DOI: 10.1007/s12223-017-0508-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 02/16/2017] [Indexed: 11/24/2022]
Abstract
Aerobic methane-oxidizing bacteria (MOB) are an environmentally significant group of microorganisms due to their role in the global carbon cycle. Research conducted over the past few decades has increased the interest in discovering novel genera of methane-degrading bacteria, which efficiently utilize methane and decrease the global warming effect. Moreover, methanotrophs have more promising applications in environmental bioengineering, biotechnology, and pharmacy. The investigations were undertaken to recognize the variety of endophytic methanotrophic bacteria associated with Carex nigra, Vaccinium oxycoccus, and Eriophorum vaginatum originating from Moszne peatland (East Poland). Methanotrophic bacteria were isolated from plants by adding sterile fragments of different parts of plants (roots and stems) to agar mineral medium (nitrate mineral salts (NMS)) and incubated at different methane values (1–20% CH4). Single colonies were streaked on new NMS agar media and, after incubation, transferred to liquid NMS medium. Bacterial growth dynamics in the culture solution was studied by optical density—OD600 and methane consumption. Changes in the methane concentration during incubation were controlled by the gas chromatography technique. Characterization of methanotrophs was made by fluorescence in situ hybridization (FISH) with Mg705 and Mg84 for type I methanotrophs and Ma450 for type II methanotrophs. Identification of endophytes was performed after 16S ribosomal RNA (rRNA) and mmoX gene amplification. Our study confirmed the presence of both types of methanotrophic bacteria (types I and II) with the predominance of type I methanotrophs. Among cultivable methanotrophs, there were different strains of the genus Methylomonas and Methylosinus. Furthermore, we determined the potential of the examined bacteria for methane oxidation, which ranged from 0.463 ± 0.067 to 5.928 ± 0.169 μmol/L CH4/mL/day.
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Affiliation(s)
- Zofia Stępniewska
- Department of Biochemistry and Environmental Chemistry, Institute of Biotechnology, The John Paul II Catholic University of Lublin, Konstantynow 1I, 20-708, Lublin, Poland
| | - Weronika Goraj
- Department of Biochemistry and Environmental Chemistry, Institute of Biotechnology, The John Paul II Catholic University of Lublin, Konstantynow 1I, 20-708, Lublin, Poland.
| | - Agnieszka Kuźniar
- Department of Biochemistry and Environmental Chemistry, Institute of Biotechnology, The John Paul II Catholic University of Lublin, Konstantynow 1I, 20-708, Lublin, Poland
| | - Natalia Łopacka
- Department of Biochemistry and Environmental Chemistry, Institute of Biotechnology, The John Paul II Catholic University of Lublin, Konstantynow 1I, 20-708, Lublin, Poland
| | - Magdalena Małysza
- Department of Biochemistry and Environmental Chemistry, Institute of Biotechnology, The John Paul II Catholic University of Lublin, Konstantynow 1I, 20-708, Lublin, Poland
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33
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Vekeman B, Kerckhof FM, Cremers G, de Vos P, Vandamme P, Boon N, Op den Camp HJM, Heylen K. New Methyloceanibacter diversity from North Sea sediments includes methanotroph containing solely the soluble methane monooxygenase. Environ Microbiol 2016; 18:4523-4536. [PMID: 27501305 DOI: 10.1111/1462-2920.13485] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/04/2016] [Indexed: 12/14/2022]
Abstract
Marine methylotrophs play a key role in the global carbon cycle by metabolizing reduced one-carbon compounds that are found in high concentrations in marine environments. Genome, physiology and diversity studies have been greatly facilitated by the numerous model organisms brought into culture. However, the availability of marine representatives remains poor. Here, we report the isolation of four novel species from North Sea sediment enrichments closely related to the Alphaproteobacterium Methyloceanibacter caenitepidi. Each of the newly isolated Methyloceanibacter species exhibited a clear genome sequence divergence which was reflected in physiological differences. Notably one strain R-67174 was capable of oxidizing methane as sole source of carbon and energy using solely a soluble methane monooxygenase and represents the first marine Alphaproteobacterial methanotroph brought into culture. Differences in maximum cell density of >1.5 orders of magnitude were observed. Furthermore, three strains were capable of producing nitrous oxide from nitrate. Together, these findings highlight the metabolic and physiologic variability within closely related Methyloceanibacter species and provide a new understanding of the physiological basis of marine methylotrophy.
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Affiliation(s)
- Bram Vekeman
- Department of Biochemistry and Microbiology, Laboratory of Microbiology (LM-UGent), Ghent University, Karel Lodewijck Ledeganckstraat 35, Gent, 9000, Belgium
| | - Frederiek-Maarten Kerckhof
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, Gent, 9000, Belgium
| | - Geert Cremers
- Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, AJ Nijmegen, 6525, The Netherlands
| | - Paul de Vos
- Department of Biochemistry and Microbiology, Laboratory of Microbiology (LM-UGent), Ghent University, Karel Lodewijck Ledeganckstraat 35, Gent, 9000, Belgium
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Laboratory of Microbiology (LM-UGent), Ghent University, Karel Lodewijck Ledeganckstraat 35, Gent, 9000, Belgium.,BCCM/LMG Bacteria Collection, Ghent University, Karel Lodewijck Ledeganckstraat 35, Gent, 9000, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, Gent, 9000, Belgium
| | - Huub J M Op den Camp
- Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, AJ Nijmegen, 6525, The Netherlands
| | - Kim Heylen
- Department of Biochemistry and Microbiology, Laboratory of Microbiology (LM-UGent), Ghent University, Karel Lodewijck Ledeganckstraat 35, Gent, 9000, Belgium
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34
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Ho A, Angel R, Veraart AJ, Daebeler A, Jia Z, Kim SY, Kerckhof FM, Boon N, Bodelier PLE. Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System. Front Microbiol 2016; 7:1285. [PMID: 27602021 PMCID: PMC4993757 DOI: 10.3389/fmicb.2016.01285] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/04/2016] [Indexed: 11/13/2022] Open
Abstract
Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes.
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Affiliation(s)
- Adrian Ho
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Roey Angel
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna Vienna, Austria
| | - Annelies J Veraart
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Anne Daebeler
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna Vienna, Austria
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences Nanjing, China
| | - Sang Yoon Kim
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Frederiek-Maarten Kerckhof
- Center for Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University Ghent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University Ghent, Belgium
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
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35
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Minamisawa K, Imaizumi-Anraku H, Bao Z, Shinoda R, Okubo T, Ikeda S. Are Symbiotic Methanotrophs Key Microbes for N Acquisition in Paddy Rice Root? Microbes Environ 2016; 31:4-10. [PMID: 26960961 PMCID: PMC4791114 DOI: 10.1264/jsme2.me15180] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The relationships between biogeochemical processes and microbial functions in rice (Oryza sativa) paddies have been the focus of a large number of studies. A mechanistic understanding of methane–nitrogen (CH4–N) cycle interactions is a key unresolved issue in research on rice paddies. This minireview is an opinion paper for highlighting the mechanisms underlying the interactions between biogeochemical processes and plant-associated microbes based on recent metagenomic, metaproteomic, and isotope analyses. A rice symbiotic gene, relevant to rhizobial nodulation and mycorrhization in plants, likely accommodates diazotrophic methanotrophs or the associated bacterial community in root tissues under low-N fertilizer management, which may permit rice plants to acquire N via N2 fixation. The amount of N fixed in rice roots was previously estimated to be approximately 12% of plant N based on measurements of 15N natural abundance in a paddy field experiment. Community analyses also indicate that methanotroph populations in rice roots are susceptible to environmental conditions such as the microclimate of rice paddies. Therefore, CH4 oxidation by methanotrophs is a driving force in shaping bacterial communities in rice roots grown in CH4-rich environments. Based on these findings, we propose a hypothesis with unanswered questions to describe the interplay between rice plants, root microbiomes, and their biogeochemical functions (CH4 oxidation and N2 fixation).
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36
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Graham LE, Wilcox LW, Knack JJ. Why we need more algal metagenomes(1). JOURNAL OF PHYCOLOGY 2015; 51:1029-1036. [PMID: 26986998 DOI: 10.1111/jpy.12344] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 08/14/2015] [Indexed: 06/05/2023]
Abstract
A recent perspective article ably argued that fully sequencing more algal genomes would enable progress in diverse areas of fundamental and applied studies. More algal genomes would add resources needed to build well-supported phylogenies, improve our understanding of how horizontal gene transfer has influenced the evolution of algal genomes, provide useful ecological insights, and generate information essential to manipulating the genomes of industrially useful algae (J. Phycol. 51:1). We agree that more algal genomes would be quite beneficial, and also propose that more algal metagenomes would enable progress in both predictable and unforeseen directions.
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Affiliation(s)
- Linda E Graham
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Lee W Wilcox
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Jennifer J Knack
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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37
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Methanotrophic community abundance and composition in plateau soils with different plant species and plantation ways. Appl Microbiol Biotechnol 2015; 99:9237-44. [PMID: 26142389 DOI: 10.1007/s00253-015-6782-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 06/11/2015] [Accepted: 06/17/2015] [Indexed: 10/23/2022]
Abstract
Aerobic methane-oxidizing bacteria (MOB) play an important role in mitigating the methane emission in soil ecosystems to the atmosphere. However, the impact of plant species and plantation ways on the distribution of MOB remains unclear. The present study investigated MOB abundance and structure in plateau soils with different plant species and plantation ways (natural and managed). Soils were collected from unmanaged wild grassland and naturally forested sites, and managed farmland and afforested sites. A large variation in MOB abundance and structure was found in these studied soils. In addition, both type I MOB (Methylocaldum) and type II MOB (Methylocystis) were detected in these soils, while type II MOB usually outnumbered type I MOB. The distribution of soil MOB community was found to be collectively regulated by plantation way, plant species, the altitude of sampling site, and soil properties.
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38
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Baesman SM, Miller LG, Wei JH, Cho Y, Matys ED, Summons RE, Welander PV, Oremland RS. Methane Oxidation and Molecular Characterization of Methanotrophs from a Former Mercury Mine Impoundment. Microorganisms 2015; 3:290-309. [PMID: 27682090 PMCID: PMC5023233 DOI: 10.3390/microorganisms3020290] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 06/01/2015] [Accepted: 06/11/2015] [Indexed: 12/22/2022] Open
Abstract
The Herman Pit, once a mercury mine, is an impoundment located in an active geothermal area. Its acidic waters are permeated by hundreds of gas seeps. One seep was sampled and found to be composed of mostly CO2 with some CH4 present. The δ13CH4 value suggested a complex origin for the methane: i.e., a thermogenic component plus a biological methanogenic portion. The relatively 12C-enriched CO2 suggested a reworking of the ebullitive methane by methanotrophic bacteria. Therefore, we tested bottom sediments for their ability to consume methane by conducting aerobic incubations of slurried materials. Methane was removed from the headspace of live slurries, and subsequent additions of methane resulted in faster removal rates. This activity could be transferred to an artificial, acidic medium, indicating the presence of acidophilic or acid-tolerant methanotrophs, the latter reinforced by the observation of maximum activity at pH = 4.5 with incubated slurries. A successful extraction of sterol and hopanoid lipids characteristic of methanotrophs was achieved, and their abundances greatly increased with increased sediment methane consumption. DNA extracted from methane-oxidizing enrichment cultures was amplified and sequenced for pmoA genes that aligned with methanotrophic members of the Gammaproteobacteria. An enrichment culture was established that grew in an acidic (pH 4.5) medium via methane oxidation.
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Affiliation(s)
| | | | - Jeremy H Wei
- Department of Earth System Science, Stanford University, Stanford, CA 94305, USA.
| | - Yirang Cho
- Department of Earth System Science, Stanford University, Stanford, CA 94305, USA.
| | - Emily D Matys
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Roger E Summons
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Paula V Welander
- Department of Earth System Science, Stanford University, Stanford, CA 94305, USA.
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39
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Graham LE, Knack JJ, Graham ME, Graham JM, Zulkifly S. A metagenome for lacustrine Cladophora (Cladophorales) reveals remarkable diversity of eukaryotic epibionts and genes relevant to materials cycling. JOURNAL OF PHYCOLOGY 2015; 51:408-418. [PMID: 26986658 DOI: 10.1111/jpy.12296] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 02/11/2015] [Indexed: 06/05/2023]
Abstract
Periphyton dominated by the cellulose-rich filamentous green alga Cladophora forms conspicuous growths along rocky marine and freshwater shorelines worldwide, providing habitat for diverse epibionts. Bacterial epibionts have been inferred to display diverse functions of biogeochemical significance: N-fixation and other redox reactions, phosphorus accumulation, and organic degradation. Here, we report taxonomic diversity of eukaryotic and prokaryotic epibionts and diversity of genes associated with materials cycling in a Cladophora metagenome sampled from Lake Mendota, Dane Co., WI, USA, during the growing season of 2012. A total of 1,060 distinct 16S, 173 18S, and 351 28S rRNA operational taxonomic units, from which >220 genera or species of bacteria (~60), protists (~80), fungi (6), and microscopic metazoa (~80), were distinguished with the use of reference databases. We inferred the presence of several algal taxa generally associated with marine systems and detected Jaoa, a freshwater periphytic ulvophyte previously thought endemic to China. We identified six distinct nifH gene sequences marking nitrogen fixation, >25 bacterial and eukaryotic cellulases relevant to sedimentary C-cycling and technological applications, and genes encoding enzymes in aerobic and anaerobic pathways for vitamin B12 biosynthesis. These results emphasize the importance of Cladophora in providing habitat for microscopic metazoa, fungi, protists, and bacteria that are often inconspicuous, yet play important roles in ecosystem biogeochemistry.
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Affiliation(s)
- Linda E Graham
- Department of Botany, University of Wisconsin, Madison, Wisconsin, USA
| | - Jennifer J Knack
- Department of Botany, University of Wisconsin, Madison, Wisconsin, USA
| | - Melissa E Graham
- School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - James M Graham
- Department of Botany, University of Wisconsin, Madison, Wisconsin, USA
| | - Shahrizim Zulkifly
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
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40
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Iguchi H, Yurimoto H, Sakai Y. Interactions of Methylotrophs with Plants and Other Heterotrophic Bacteria. Microorganisms 2015; 3:137-51. [PMID: 27682083 PMCID: PMC5023238 DOI: 10.3390/microorganisms3020137] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 03/18/2015] [Accepted: 03/27/2015] [Indexed: 01/19/2023] Open
Abstract
Methylotrophs, which can utilize methane and/or methanol as sole carbon and energy sources, are key players in the carbon cycle between methane and CO2, the two most important greenhouse gases. This review describes the relationships between methylotrophs and plants, and between methanotrophs (methane-utilizers, a subset of methylotrophs) and heterotrophic bacteria. Some plants emit methane and methanol from their leaves, and provide methylotrophs with habitats. Methanol-utilizing methylotrophs in the genus Methylobacterium are abundant in the phyllosphere and have the ability to promote the growth of some plants. Methanotrophs also inhabit the phyllosphere, and methanotrophs with high methane oxidation activities have been found on aquatic plants. Both plant and environmental factors are involved in shaping the methylotroph community on plants. Methanotrophic activity can be enhanced by heterotrophic bacteria that provide growth factors (e.g., cobalamin). Information regarding the biological interaction of methylotrophs with other organisms will facilitate a better understanding of the carbon cycle that is driven by methylotrophs.
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Affiliation(s)
- Hiroyuki Iguchi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Hiroya Yurimoto
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Yasuyoshi Sakai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan.
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41
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Aerobic and nitrite-dependent methane-oxidizing microorganisms in sediments of freshwater lakes on the Yunnan Plateau. Appl Microbiol Biotechnol 2014; 99:2371-81. [PMID: 25698510 DOI: 10.1007/s00253-014-6141-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 09/24/2014] [Accepted: 10/06/2014] [Indexed: 10/24/2022]
Abstract
Both aerobic methane-oxidizing bacteria (MOB) and nitrite-dependent anaerobic methane oxidation (n-damo) bacteria can play an important role in mitigating the methane emission produced in anoxic sediment layers to the atmosphere. However, the environmental factors regulating the distribution of these methane-oxidizing microorganisms in lacustrine ecosystems remain essentially unclear. The present study investigated the distribution of aerobic MOB and n-damo bacteria in sediments of various freshwater lakes on the Yunnan Plateau (China). Quantitative PCR assay and clone library analysis illustrated the spatial variations in the abundances and structures of aerobic MOB and n-damo bacterial communities. Type I MOB (Methylosoma and Methylobacter) and type II MOB (Methylocystis) were detected, while type I MOB was more abundant than type II MOB. Lake sediments n-damo bacterial communities were composed of novel Methylomirabilis oxyfera-like pmoA genes. Lake sediments in the same geographic region could share a relatively similar aerobic MOB community structure. Moreover, Pearson's correlation analysis indicated that n-damo pmoA gene diversity showed a positive correlation with the ratio of organic matter to total nitrogen in lake sediment.
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42
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Jeong SY, Cho KS, Kim TG. Density-dependent enhancement of methane oxidation activity and growth of Methylocystis sp. by a non-methanotrophic bacterium Sphingopyxis sp. ACTA ACUST UNITED AC 2014. [PMID: 28626671 PMCID: PMC5466132 DOI: 10.1016/j.btre.2014.09.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Methanotrophs are a biological resource as they degrade the greenhouse gas methane and various organic contaminants. Several non-methanotrophic bacteria have shown potential to stimulate growth of methanotrophs when co-cultured, and however, the ecology is largely unknown. Effects of Sphingopyxis sp. NM1 on methanotrophic activity and growth of Methylocystis sp. M6 were investigated in this study. M6 and NM1 were mixed at mixing ratios of 9:1, 1:1, and 1:9 (v/v), using cell suspensions of 7.5 × 1011 cells L-1. Methane oxidation of M6 was monitored, and M6 population was estimated using fluorescence in situ hybridization (FISH). Real-time PCR was applied to quantify rRNA and expression of transcripts for three enzymes involved in the methane oxidation pathway. NM1 had a positive effect on M6 growth at a 1:9 ratio (p < 0.05), while no significant effects were observed at 9:1 and 1:1 ratios. NM1 enhanced the methane oxidation 1.34-fold at the 1:9 ratio. NM1 increased the population density and relative rRNA level of M6 by 2.4-fold and 5.4-fold at the 1:9 ratio, indicating that NM1 stimulated the population growth of M6. NM1 increased the relative transcriptional expression of all mRNA targets only at the 1:9 ratio. These results demonstrated that NM1 enhanced the methanotrophic activity and growth of M6, which was dependent on the proportion of NM1 present in the culture. This stimulation can be used as management and enhancement strategies for methanotrophic biotechnological processes.
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Affiliation(s)
- So-Yeon Jeong
- Global Top 5 Program, Department of Environmental Science and Engineering, Ewha Womans University, 52, Ewhayeodae-gil, Seodaemun-gu, Seoul 120-750, Republic of Korea
| | - Kyung-Suk Cho
- Global Top 5 Program, Department of Environmental Science and Engineering, Ewha Womans University, 52, Ewhayeodae-gil, Seodaemun-gu, Seoul 120-750, Republic of Korea
| | - Tae Gwan Kim
- Global Top 5 Program, Department of Environmental Science and Engineering, Ewha Womans University, 52, Ewhayeodae-gil, Seodaemun-gu, Seoul 120-750, Republic of Korea.,Department of Ecosystem Function, Bureau of Basic Ecological Research, National Institute of Ecology, 1210, Geumgang-ro, Maseo-myeon, Seocheon-gun, Chungcheongnam-do 325-813, Republic of Korea
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Ammonia- and methane-oxidizing microorganisms in high-altitude wetland sediments and adjacent agricultural soils. Appl Microbiol Biotechnol 2014; 98:10197-209. [PMID: 25030456 DOI: 10.1007/s00253-014-5942-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 07/02/2014] [Accepted: 07/06/2014] [Indexed: 10/25/2022]
Abstract
Ammonia oxidation is known to be carried out by ammonia-oxidizing bacteria (AOB) and archaea (AOA), while methanotrophs (methane-oxidizing bacteria (MOB)) play an important role in mitigating methane emissions from the environment. However, the difference of AOA, AOB, and MOB distribution in wetland sediment and adjacent upland soil remains unclear. The present study investigated the abundances and community structures of AOA, AOB, and MOB in sediments of a high-altitude freshwater wetland in Yunnan Province (China) and adjacent agricultural soils. Variations of AOA, AOB, and MOB community sizes and structures were found in water lily-vegetated and Acorus calamus-vegetated sediments and agricultural soils (unflooded rice soil, cabbage soil, and garlic soil and flooded rice soil). AOB community size was higher than AOA in agricultural soils and lily-vegetated sediment, but lower in A. calamus-vegetated sediment. MOB showed a much higher abundance than AOA and AOB. Flooded rice soil had the largest AOA, AOB, and MOB community sizes. Principal coordinate analyses and Jackknife Environment Clusters analyses suggested that unflooded and flooded rice soils had relatively similar AOA, AOB, and MOB structures. Cabbage soil and A. calamus-vegetated sediment had relatively similar AOA and AOB structures, but their MOB structures showed a large difference. Nitrososphaera-like microorganisms were the predominant AOA species in garlic soil but were present with a low abundance in unflooded rice soil and cabbage soil. Nitrosospira-like AOB were dominant in wetland sediments and agricultural soils. Type I MOB Methylocaldum and type II MOB Methylocystis were dominant in wetland sediments and agricultural soils. Moreover, Pearson's correlation analysis indicated that AOA Shannon diversity was positively correlated with the ratio of organic carbon to nitrogen (p < 0.05). This work could provide some new insights toward ammonia and methane oxidation in soil and wetland sediment ecosystems.
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Kerckhof FM, Courtens ENP, Geirnaert A, Hoefman S, Ho A, Vilchez-Vargas R, Pieper DH, Jauregui R, Vlaeminck SE, Van de Wiele T, Vandamme P, Heylen K, Boon N. Optimized cryopreservation of mixed microbial communities for conserved functionality and diversity. PLoS One 2014; 9:e99517. [PMID: 24937032 PMCID: PMC4061060 DOI: 10.1371/journal.pone.0099517] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 05/15/2014] [Indexed: 12/26/2022] Open
Abstract
The use of mixed microbial communities (microbiomes) for biotechnological applications has steadily increased over the past decades. However, these microbiomes are not readily available from public culture collections, hampering their potential for widespread use. The main reason for this lack of availability is the lack of an effective cryopreservation protocol. Due to this critical need, we evaluated the functionality as well as the community structure of three different types of microbiomes before and after cryopreservation with two cryoprotective agents (CPA). Microbiomes were selected based upon relevance towards applications: (1) a methanotrophic co-culture (MOB), with potential for mitigation of greenhouse gas emissions, environmental pollutants removal and bioplastics production; (2) an oxygen limited autotrophic nitrification/denitrification (OLAND) biofilm, with enhanced economic and ecological benefits for wastewater treatment, and (3) fecal material from a human donor, with potential applications for fecal transplants and pre/probiotics research. After three months of cryopreservation at −80°C, we found that metabolic activity, in terms of the specific activity recovery of MOB, aerobic ammonium oxidizing bacteria (AerAOB) and anaerobic AOB (AnAOB, anammox) in the OLAND mixed culture, resumes sooner when one of our selected CPA [dimethyl sulfoxide (DMSO) and DMSO plus trehalose and tryptic soy broth (DMSO+TT)] was added. However, the activity of the fecal community was not influenced by the CPA addition, although the preservation of the community structure (as determined by 16S rRNA gene sequencing) was enhanced by addition of CPA. In summary, we have evaluated a cryopreservation protocol that succeeded in preserving both community structure and functionality of value-added microbiomes. This will allow individual laboratories and culture collections to boost the use of microbiomes in biotechnological applications.
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Affiliation(s)
- Frederiek-Maarten Kerckhof
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Emilie N. P. Courtens
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Annelies Geirnaert
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Sven Hoefman
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, Gent, Belgium
| | - Adrian Ho
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Ramiro Vilchez-Vargas
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Dietmar H. Pieper
- Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ruy Jauregui
- Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Siegfried E. Vlaeminck
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Tom Van de Wiele
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, Gent, Belgium
| | - Kim Heylen
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, Gent, Belgium
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
- * E-mail:
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Hoefman S, van der Ha D, Iguchi H, Yurimoto H, Sakai Y, Boon N, Vandamme P, Heylen K, De Vos P. Methyloparacoccus murrellii gen. nov., sp. nov., a methanotroph isolated from pond water. Int J Syst Evol Microbiol 2014; 64:2100-2107. [DOI: 10.1099/ijs.0.057760-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel methanotrophic strains, R-49797T and OS501, were isolated from pond water in South Africa and Japan, respectively. Strains R-49797T and OS501 shared 99.7 % 16S rRNA gene sequence similarity. Cells were Gram-stain-negative, non-motile cocci with a diplococcoid tendency and contained type I methanotroph intracytoplasmic membranes. The pmoA gene encoding particulate methane monooxygenase was present. Soluble methane monoooxygenase (sMMO) activity, the mmoX gene encoding sMMO and the nifH gene encoding nitrogenase were not detected. Methane and methanol were utilized as sole carbon source. The strains grew optimally at 25–33 °C (range 20–37 °C) and at pH 6.3–6.8 (range 5.8–9.0). The strains did not support growth in media supplemented with 1 % (w/v) NaCl. For both strains, the two major fatty acids were C16 : 1ω7c and C16 : 0 and the DNA G+C content was 65.6 mol%. The isolates belong to the family
Methylococcaceae
of the class
Gammaproteobacteria
and cluster most closely among the genera
Methylocaldum
,
Methylococcus
and
Methylogaea
, with a 16S rRNA gene sequence similarity of 94.2 % between strain R-49797T and its closest related type strain (
Methylocaldum gracile
VKM 14LT). Based on the low 16S rRNA gene sequence similarities with its nearest phylogenetic neighbouring genera, the formation of a separate lineage based on 16S rRNA and pmoA gene phylogenetic analysis, and the unique combination of phenotypic characteristics of the two isolated strains compared with the genera
Methylocaldum
,
Methylococcus
and
Methylogaea
, we propose to classify these strains as representing a novel species of a new genus, Methyloparacoccus murrellii gen. nov., sp. nov., within the family
Methylococcaceae
. The type strain of Methyloparacoccus murrellii is R-49797T ( = LMG 27482T = JCM 19379T).
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Affiliation(s)
- Sven Hoefman
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - David van der Ha
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Hiroyuki Iguchi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hiroya Yurimoto
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yasuyoshi Sakai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Kim Heylen
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Paul De Vos
- BCCM/LMG Bacteria Collection, Gent, Belgium
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
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The more, the merrier: heterotroph richness stimulates methanotrophic activity. ISME JOURNAL 2014; 8:1945-8. [PMID: 24785289 DOI: 10.1038/ismej.2014.74] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 03/31/2014] [Accepted: 03/31/2014] [Indexed: 11/08/2022]
Abstract
Although microorganisms coexist in the same environment, it is still unclear how their interaction regulates ecosystem functioning. Using a methanotroph as a model microorganism, we determined how methane oxidation responds to heterotroph diversity. Artificial communities comprising of a methanotroph and increasing heterotroph richness, while holding equal starting cell numbers were assembled. We considered methane oxidation rate as a functional response variable. Our results showed a significant increase of methane oxidation with increasing heterotroph richness, suggesting a complex interaction in the cocultures leading to a stimulation of methanotrophic activity. Therefore, not only is the methanotroph diversity directly correlated to methanotrophic activity for some methanotroph groups as shown before, but also the richness of heterotroph interacting partners is relevant to enhance methane oxidation too. In this unprecedented study, we provide direct evidence showing how heterotroph richness exerts a response in methanotroph-heterotroph interaction, resulting in increased methanotrophic activity. Our study has broad implications in how methanotroph and heterotroph interact to regulate methane oxidation, and is particularly relevant in methane-driven ecosystems.
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Yoshida N, Iguchi H, Yurimoto H, Murakami A, Sakai Y. Aquatic plant surface as a niche for methanotrophs. Front Microbiol 2014; 5:30. [PMID: 24550901 PMCID: PMC3909826 DOI: 10.3389/fmicb.2014.00030] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 01/17/2014] [Indexed: 11/13/2022] Open
Abstract
This study investigated the potential local CH4 sink in various plant parts as a boundary environment of CH4 emission and consumption. By comparing CH4 consumption activities in cultures inoculated with parts from 39 plant species, we observed significantly higher consumption of CH4 associated with aquatic plants than other emergent plant parts such as woody plant leaves, macrophytic marine algae, and sea grass. In situ activity of CH4 consumption by methanotrophs associated with different species of aquatic plants was in the range of 3.7–37 μmol·h−1·g−1 dry weight, which was ca 5.7–370-fold higher than epiphytic CH4 consumption in submerged parts of emergent plants. The qPCR-estimated copy numbers of the particulate methane monooxygenase-encoding gene pmoA were variable among the aquatic plants and ranged in the order of 105–107 copies·g−1 dry weight, which correlated with the observed CH4 consumption activities. Phylogenetic identification of methanotrophs on aquatic plants based on the pmoA sequence analysis revealed a predominance of diverse gammaproteobacterial type-I methanotrophs, including a phylotype of a possible plant-associated methanotroph with the closest identity (86–89%) to Methylocaldum gracile.
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Affiliation(s)
- Naoko Yoshida
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University Kyoto, Japan ; Center for Fostering Young and Innovative Researchers, Nagoya Institute of Technology, Nagoya Aichi, Japan
| | - Hiroyuki Iguchi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University Kyoto, Japan
| | - Hiroya Yurimoto
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University Kyoto, Japan
| | - Akio Murakami
- Kobe University Research Center for Inland Seas Awaji, Hyogo, Japan ; Japan Science and Technology Agency, CREST Awaji, Hyogo, Japan
| | - Yasuyoshi Sakai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University Kyoto, Japan ; Advanced Low Carbon Technology Research and Development Program, Japan Science and Technology Agency Tokyo, Japan
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Exploration and prediction of interactions between methanotrophs and heterotrophs. Res Microbiol 2013; 164:1045-54. [DOI: 10.1016/j.resmic.2013.08.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 08/27/2013] [Indexed: 01/28/2023]
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49
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Selection of associated heterotrophs by methane-oxidizing bacteria at different copper concentrations. Antonie van Leeuwenhoek 2012; 103:527-37. [DOI: 10.1007/s10482-012-9835-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Accepted: 10/17/2012] [Indexed: 01/29/2023]
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50
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Effects of nonmethane volatile organic compounds on microbial community of methanotrophic biofilter. Appl Microbiol Biotechnol 2012; 97:6549-59. [DOI: 10.1007/s00253-012-4443-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 09/12/2012] [Accepted: 09/13/2012] [Indexed: 10/27/2022]
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