1
|
Abdul Halim MF, Fonseca DR, Niehaus TD, Costa KC. Functionally redundant formate dehydrogenases enable formate-dependent growth in Methanococcus maripaludis. J Biol Chem 2024; 300:105550. [PMID: 38072055 PMCID: PMC10805699 DOI: 10.1016/j.jbc.2023.105550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 01/02/2024] Open
Abstract
Methanogens are essential for the complete remineralization of organic matter in anoxic environments. Most cultured methanogens are hydrogenotrophic, using H2 as an electron donor to reduce CO2 to CH4, but in the absence of H2 many can also use formate. Formate dehydrogenase (Fdh) is essential for formate oxidation, where it transfers electrons for the reduction of coenzyme F420 or to a flavin-based electron bifurcating reaction catalyzed by heterodisulfide reductase (Hdr), the terminal reaction of methanogenesis. Furthermore, methanogens that use formate encode at least two isoforms of Fdh in their genomes, but how these different isoforms participate in methanogenesis is unknown. Using Methanococcus maripaludis, we undertook a biochemical characterization of both Fdh isoforms involved in methanogenesis. Both Fdh1 and Fdh2 interacted with Hdr to catalyze the flavin-based electron bifurcating reaction, and both reduced F420 at similar rates. F420 reduction preceded flavin-based electron bifurcation activity for both enzymes. In a Δfdh1 mutant background, a suppressor mutation was required for Fdh2 activity. Genome sequencing revealed that this mutation resulted in the loss of a specific molybdopterin transferase (moeA), allowing for Fdh2-dependent growth, and the metal content of the proteins suggested that isoforms are dependent on either molybdenum or tungsten for activity. These data suggest that both isoforms of Fdh are functionally redundant, but their activities in vivo may be limited by gene regulation or metal availability under different growth conditions. Together these results expand our understanding of formate oxidation and the role of Fdh in methanogenesis.
Collapse
Affiliation(s)
- Mohd Farid Abdul Halim
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, St. Paul, Minnesota, USA
| | - Dallas R Fonseca
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, St. Paul, Minnesota, USA
| | - Thomas D Niehaus
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, St. Paul, Minnesota, USA
| | - Kyle C Costa
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, St. Paul, Minnesota, USA.
| |
Collapse
|
2
|
Conrad R. Complexity of temperature dependence in methanogenic microbial environments. Front Microbiol 2023; 14:1232946. [PMID: 37485527 PMCID: PMC10359720 DOI: 10.3389/fmicb.2023.1232946] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
There is virtually no environmental process that is not dependent on temperature. This includes the microbial processes that result in the production of CH4, an important greenhouse gas. Microbial CH4 production is the result of a combination of many different microorganisms and microbial processes, which together achieve the mineralization of organic matter to CO2 and CH4. Temperature dependence applies to each individual step and each individual microbe. This review will discuss the different aspects of temperature dependence including temperature affecting the kinetics and thermodynamics of the various microbial processes, affecting the pathways of organic matter degradation and CH4 production, and affecting the composition of the microbial communities involved. For example, it was found that increasing temperature results in a change of the methanogenic pathway with increasing contribution from mainly acetate to mainly H2/CO2 as immediate CH4 precursor, and with replacement of aceticlastic methanogenic archaea by thermophilic syntrophic acetate-oxidizing bacteria plus thermophilic hydrogenotrophic methanogenic archaea. This shift is consistent with reaction energetics, but it is not obligatory, since high temperature environments exist in which acetate is consumed by thermophilic aceticlastic archaea. Many studies have shown that CH4 production rates increase with temperature displaying a temperature optimum and a characteristic apparent activation energy (Ea). Interestingly, CH4 release from defined microbial cultures, from environmental samples and from wetland field sites all show similar Ea values around 100 kJ mol-1 indicating that CH4 production rates are limited by the methanogenic archaea rather than by hydrolysis of organic matter. Hence, the final rather than the initial step controls the methanogenic degradation of organic matter, which apparently is rarely in steady state.
Collapse
|
3
|
Song T, Liu Y, Kolton M, Wilson RM, Keller JK, Rolando JL, Chanton JP, Kostka JE. Porewater constituents inhibit microbially mediated greenhouse gas production (GHG) and regulate the response of soil organic matter decomposition to warming in anoxic peat from a Sphagnum-dominated bog. FEMS Microbiol Ecol 2023; 99:fiad060. [PMID: 37280172 DOI: 10.1093/femsec/fiad060] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 05/16/2023] [Accepted: 06/05/2023] [Indexed: 06/08/2023] Open
Abstract
Northern peatlands store approximately one-third of terrestrial soil carbon. Climate warming is expected to stimulate the microbially mediated degradation of peat soil organic matter (SOM), leading to increasing greenhouse gas (GHG; carbon dioxide, CO2; methane, CH4) production and emission. Porewater dissolved organic matter (DOM) plays a key role in SOM decomposition; however, the mechanisms controlling SOM decomposition and its response to warming remain unclear. The temperature dependence of GHG production and microbial community dynamics were investigated in anoxic peat from a Sphagnum-dominated peatland. In this study, peat decomposition, which was quantified by GHG production and carbon substrate utilization is limited by terminal electron acceptors (TEA) and DOM, and these controls of microbially mediated SOM degradation are temperature-dependent. Elevated temperature led to a slight decrease in microbial diversity, and stimulated the growth of specific methanotrophic and syntrophic taxa. These results confirm that DOM is a major driver of decomposition in peatland soils contains inhibitory compounds, but the inhibitory effect is alleviated by warming.
Collapse
Affiliation(s)
- Tianze Song
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Yutong Liu
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
- Department of Civil & Environmental Engineering, Pennsylvania State University, University Park, University Park, PA 16802, United States
| | - Max Kolton
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
- French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion, University of the Negev, Beer Sheva, 8499000, Israel
| | - Rachel M Wilson
- Department of Earth, Ocean & Atmospheric Science, Florida State University, Tallahassee, FL 32304, United States
| | - Jason K Keller
- Schmid College of Science and Technology, Chapman University, 1 University Dr, Orange, CA 92866, United States
| | - Jose L Rolando
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Jeffrey P Chanton
- Department of Earth, Ocean & Atmospheric Science, Florida State University, Tallahassee, FL 32304, United States
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30318, United States
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, United States
| |
Collapse
|
4
|
Cooper RE, Finck J, Chan C, Küsel K. Mixotrophy broadens the ecological niche range of the iron oxidizer Sideroxydans sp. CL21 isolated from an iron-rich peatland. FEMS Microbiol Ecol 2023; 99:6979798. [PMID: 36623865 PMCID: PMC9925335 DOI: 10.1093/femsec/fiac156] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/17/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
Sideroxydans sp. CL21 is a microaerobic, acid-tolerant Fe(II)-oxidizer, isolated from the Schlöppnerbrunnen fen. Since the genome size of Sideroxydans sp. CL21 is 21% larger than that of the neutrophilic Sideroxydans lithotrophicus ES-1, we hypothesized that strain CL21 contains additional metabolic traits to thrive in the fen. The common genomic content of both strains contains homologs of the putative Fe(II) oxidation genes, mtoAB and cyc2. A large part of the accessory genome in strain CL21 contains genes linked to utilization of alternative electron donors, including NiFe uptake hydrogenases, and genes encoding lactate uptake and utilization proteins, motility and biofilm formation, transposable elements, and pH homeostasis mechanisms. Next, we incubated the strain in different combinations of electron donors and characterized the fen microbial communities. Sideroxydans spp. comprised 3.33% and 3.94% of the total relative abundance in the peatland soil and peatland water, respectively. Incubation results indicate Sideroxydans sp. CL21 uses H2 and thiosulfate, while lactate only enhances growth when combined with Fe, H2, or thiosulfate. Rates of H2 utilization were highest in combination with other substrates. Thus, Sideroxydans sp. CL21 is a mixotroph, growing best by simultaneously using substrate combinations, which helps to thrive in dynamic and complex habitats.
Collapse
Affiliation(s)
- Rebecca E Cooper
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Jessica Finck
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Clara Chan
- School of Marine Science and Policy, University of Delaware, Newark, DE 19716, United States,Delaware Biotechnology Institute, University of Delaware, Newark, DE 19713, United States,Department of Earth Sciences, University of Delaware, Newark, DE 19716, United States
| | - Kirsten Küsel
- Corresponding author. Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany. Tel: +49 3641 949461; Fax: +49 3641 949462; E-mail:
| |
Collapse
|
5
|
Meier AB, Oppermann S, Drake HL, Schmidt O. The root zone of graminoids: A niche for H2-consuming acetogens in a minerotrophic peatland. Front Microbiol 2022; 13:978296. [PMID: 35992704 PMCID: PMC9391049 DOI: 10.3389/fmicb.2022.978296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
The importance of acetogens for H2 turnover and overall anaerobic degradation in peatlands remains elusive. In the well-studied minerotrophic peatland fen Schlöppnerbrunnen, H2-consuming acetogens are conceptualized to be largely outcompeted by iron reducers, sulfate reducers, and hydrogenotrophic methanogens in bulk peat soil. However, in root zones of graminoids, fermenters thriving on rhizodeposits and root litter might temporarily provide sufficient H2 for acetogens. In the present study, root-free peat soils from around the roots of Molinia caerulea and Carex rostrata (i.e., two graminoids common in fen Schlöpnnerbrunnen) were anoxically incubated with or without supplemental H2 to simulate conditions of high and low H2 availability in the fen. In unsupplemented soil treatments, H2 concentrations were largely below the detection limit (∼10 ppmV) and possibly too low for acetogens and methanogens, an assumption supported by the finding that neither acetate nor methane substantially accumulated. In the presence of supplemental H2, acetate accumulation exceeded CH4 accumulation in Molinia soil whereas acetate and methane accumulated equally in Carex soil. However, reductant recoveries indicated that initially, additional unknown processes were involved either in H2 consumption or the consumption of acetate produced by H2-consuming acetogens. 16S rRNA and 16S rRNA gene analyses revealed that potential acetogens (Clostridium, Holophagaceae), methanogens (Methanocellales, Methanobacterium), iron reducers (Geobacter), and physiologically uncharacterized phylotypes (Acidobacteria, Actinobacteria, Bacteroidetes) were stimulated by supplemental H2 in soil treatments. Phylotypes closely related to clostridial acetogens were also active in soil-free Molinia and Carex root treatments with or without supplemental H2. Due to pronounced fermentation activities, H2 consumption was less obvious in root treatments, and acetogens likely thrived on root organic carbon and fermentation products (e.g., ethanol) in addition to H2. Collectively, the data highlighted that in fen Schlöppnerbrunnen, acetogens are associated to graminoid roots and inhabit the peat soil around the roots, where they have to compete for H2 with methanogens and iron reducers. Furthermore, the study underscored that the metabolically flexible acetogens do not rely on H2, potentially a key advantage over other H2 consumers under the highly dynamic conditions characteristic for the root-zones of graminoids in peatlands.
Collapse
Affiliation(s)
- Anja B. Meier
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Sindy Oppermann
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Harold L. Drake
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Oliver Schmidt
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
- *Correspondence: Oliver Schmidt,
| |
Collapse
|
6
|
Ding H, Liu T, Hu Q, Liu M, Cai M, Jiang Y, Cao C. Effect of microbial community structures and metabolite profile on greenhouse gas emissions in rice varieties. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119365. [PMID: 35489537 DOI: 10.1016/j.envpol.2022.119365] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 04/01/2022] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
Rice paddy fields are major sources of atmospheric methane (CH4) and nitrous oxide (N2O). Rice variety is an important factor affecting CH4 and N2O emissions. However, the interactive effects of rice metabolites and microorganisms on CH4 and N2O emissions in paddy fields are not clearly understood. In this study, a high greenhouse gas-emitting cultivar (YL 6) and a low greenhouse gas-emitting cultivar (YY 1540) were used as experimental materials. Metabolomics was used to examine the roots, root exudates, and bulk soil metabolites. High-throughput sequencing was used to determine the microbial community composition. YY 1540 had more secondary metabolites (flavonoids and isoflavonoids) in root exudates than YL 6. It was enriched with the uncultured members of the families Gemmatimonadanceae and Rhizobiales_Incertae_Sedis in bulk soil, and genera Burkholderia-Caballeronia-Paraburkholderia, Magnetospirillum, Aeromonas, and Anaeromyxobacter in roots, contributing to increased expression of pmoA and nosZ genes and reducing CH4 and N2O emissions. YL 6 roots and root exudates contained higher contents of carbohydrates [e.g., 6-O- acetylarbutin and 2-(3- hydroxyphenyl) ethanol 1'-glucoside] than those of YY 1540. They were enriched with genera RBG-16-58-14 in bulk soil and Exiguobacterium, and uncultured member of the Kineosporiaceae family in roots, which contributed to increased expression of mcrA, ammonia-oxidizing archaea, ammonia-oxidizing bacteria, nirS, and nirK genes and greenhouse gas emissions. In general, these results established a link between metabolites, microorganisms, microbial functional genes, and greenhouse gas emissions. The metabolites of root exudates and roots regulated CH4 and N2O emissions by influencing the microbial community composition in bulk soil and roots.
Collapse
Affiliation(s)
- Huina Ding
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Tianqi Liu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Quanyi Hu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Min Liu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Mingli Cai
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yang Jiang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Cougui Cao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| |
Collapse
|
7
|
Meier AB, Oppermann S, Drake HL, Schmidt O. Organic carbon from graminoid roots as a driver of fermentation in a fen. FEMS Microbiol Ecol 2021; 97:6412523. [PMID: 34718537 DOI: 10.1093/femsec/fiab143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Fen Schlöppnerbrunnen is a moderately acidic methane-emitting peatland overgrown by Molinia caerulea and other wetland graminoids (e.g. Carex rostrata). Recently, the accumulation of H2, an indicator for fermentation, was observed with anoxically incubated C. rostrata roots but not with root-free fen soil. Based on this finding, we hypothesized that root-derived organic carbon has a higher capacity to promote fermentation processes than peat organic carbon from root-free fen soil. To address this hypothesis, C. rostrata and M. caerulea roots were anoxically incubated with or without fen soil and the product profiles of root treatments were compared with those of root-free soil treatments. Ethanol, acetate, propionate, butyrate, H2 and CO2 accumulated in root treatments and collective amounts of carbon in accumulating products were 20-200 times higher than those in root-free soil treatments, in which mainly CO2 accumulated. Analyses of 16S rRNA and 16S rRNA gene sequences revealed that Clostridium, Propionispira and Rahnella, representatives of butyrate, propionate and mixed acid fermenters, respectively, were relatively enriched in root treatments. In contrast, differences of the microbial community before and after incubation were marginal in root-free soil treatments. Collectively, these findings supported the assumed stimulatory effect of root-derived organic carbon on fen fermenters.
Collapse
Affiliation(s)
- Anja B Meier
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth 95440, Germany
| | - Sindy Oppermann
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth 95440, Germany
| | - Harold L Drake
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth 95440, Germany
| | - Oliver Schmidt
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth 95440, Germany
| |
Collapse
|
8
|
Morrison ES, Thomas P, Ogram A, Kahveci T, Turner BL, Chanton JP. Characterization of Bacterial and Fungal Communities Reveals Novel Consortia in Tropical Oligotrophic Peatlands. MICROBIAL ECOLOGY 2021; 82:188-201. [PMID: 31942666 DOI: 10.1007/s00248-020-01483-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
Despite their importance for global biogeochemical cycles and carbon sequestration, the microbiome of tropical peatlands remains under-determined. Microbial interactions within peatlands can regulate greenhouse gas production, organic matter turnover, and nutrient cycling. Here we analyze bacterial and fungal communities along a steep P gradient in a tropical peat dome and investigate community level traits and network analyses to better understand the composition and potential interactions of microorganisms in these understudied systems and their relationship to peatland biogeochemistry. We found that both bacterial and fungal community compositions were significantly different along the P gradient, and that the low-P bog plain was characterized by distinct fungal and bacterial families. At low P, the dominant fungal families were cosmopolitan parasites and endophytes, including Clavicipitaceae (19%) in shallow soils (0-4 cm), Hypocreaceae (50%) in intermediate-depth soils (4-8 cm), and Chaetothyriaceae (45%) in deep soils (24-30 cm). In contrast, high- and intermediate-P sites were dominated by saprotrophic families at all depths. Bacterial communities were consistently dominated by the acidophilic Koribacteraceae family, with the exception of the low-P bog site, which was dominated by Acetobacteraceae (19%) and Syntrophaceae (11%). These two families, as well as Rhodospirillaceae, Syntrophobacteraceae, Syntrophorhabdaceae, Spirochaetaceae, and Methylococcaceae appeared within low-P bacterial networks, suggesting the presence of a syntrophic-methanogenic consortium in these soils. Further investigation into the active microbial communities at these sites, when paired with CH4 and CO2 gas exchange, and the quantification of metabolic intermediates will validate these potential interactions and provide insight into microbially driven biogeochemical cycling within these globally important tropical peatlands.
Collapse
Affiliation(s)
- Elise S Morrison
- Soil and Water Sciences Department, University of Florida, Gainesville, FL, USA.
- Department of Geological Sciences, University of Florida, 241 Williamson Hall, PO Box 112120, Gainesville, FL, 32611, USA.
| | - P Thomas
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA
| | - A Ogram
- Soil and Water Sciences Department, University of Florida, Gainesville, FL, USA
| | - T Kahveci
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA
| | - B L Turner
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
| | - J P Chanton
- Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL, USA
| |
Collapse
|
9
|
Guerrero-Cruz S, Vaksmaa A, Horn MA, Niemann H, Pijuan M, Ho A. Methanotrophs: Discoveries, Environmental Relevance, and a Perspective on Current and Future Applications. Front Microbiol 2021; 12:678057. [PMID: 34054786 PMCID: PMC8163242 DOI: 10.3389/fmicb.2021.678057] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
Methane is the final product of the anaerobic decomposition of organic matter. The conversion of organic matter to methane (methanogenesis) as a mechanism for energy conservation is exclusively attributed to the archaeal domain. Methane is oxidized by methanotrophic microorganisms using oxygen or alternative terminal electron acceptors. Aerobic methanotrophic bacteria belong to the phyla Proteobacteria and Verrucomicrobia, while anaerobic methane oxidation is also mediated by more recently discovered anaerobic methanotrophs with representatives in both the bacteria and the archaea domains. The anaerobic oxidation of methane is coupled to the reduction of nitrate, nitrite, iron, manganese, sulfate, and organic electron acceptors (e.g., humic substances) as terminal electron acceptors. This review highlights the relevance of methanotrophy in natural and anthropogenically influenced ecosystems, emphasizing the environmental conditions, distribution, function, co-existence, interactions, and the availability of electron acceptors that likely play a key role in regulating their function. A systematic overview of key aspects of ecology, physiology, metabolism, and genomics is crucial to understand the contribution of methanotrophs in the mitigation of methane efflux to the atmosphere. We give significance to the processes under microaerophilic and anaerobic conditions for both aerobic and anaerobic methane oxidizers. In the context of anthropogenically influenced ecosystems, we emphasize the current and potential future applications of methanotrophs from two different angles, namely methane mitigation in wastewater treatment through the application of anaerobic methanotrophs, and the biotechnological applications of aerobic methanotrophs in resource recovery from methane waste streams. Finally, we identify knowledge gaps that may lead to opportunities to harness further the biotechnological benefits of methanotrophs in methane mitigation and for the production of valuable bioproducts enabling a bio-based and circular economy.
Collapse
Affiliation(s)
- Simon Guerrero-Cruz
- Catalan Institute for Water Research (ICRA), Girona, Spain
- Universitat de Girona, Girona, Spain
| | - Annika Vaksmaa
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, ’t Horntje, Netherlands
| | - Marcus A. Horn
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
| | - Helge Niemann
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, ’t Horntje, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
- Centre for Arctic Gas Hydrate, Environment and Climate, Department of Geosciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Maite Pijuan
- Catalan Institute for Water Research (ICRA), Girona, Spain
- Universitat de Girona, Girona, Spain
| | - Adrian Ho
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
- Division of Applied Life Sciences, Gyeongsang National University, Jinju, South Korea
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Liechty Z, Santos-Medellín C, Edwards J, Nguyen B, Mikhail D, Eason S, Phillips G, Sundaresan V. Comparative Analysis of Root Microbiomes of Rice Cultivars with High and Low Methane Emissions Reveals Differences in Abundance of Methanogenic Archaea and Putative Upstream Fermenters. mSystems 2020; 5:e00897-19. [PMID: 32071162 PMCID: PMC7029222 DOI: 10.1128/msystems.00897-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 01/22/2020] [Indexed: 02/01/2023] Open
Abstract
Rice cultivation worldwide accounts for ∼7 to 17% of global methane emissions. Methane cycling in rice paddies is a microbial process not only involving methane producers (methanogens) and methane metabolizers (methanotrophs) but also other microbial taxa that affect upstream processes related to methane metabolism. Rice cultivars vary in their rates of methane emissions, but the influence of rice genotypes on methane cycling microbiota has been poorly characterized. Here, we profiled the rhizosphere, rhizoplane, and endosphere microbiomes of a high-methane-emitting cultivar (Sabine) and a low-methane-emitting cultivar (CLXL745) throughout the growing season to identify variations in the archaeal and bacterial communities relating to methane emissions. The rhizosphere of the high-emitting cultivar was enriched in methanogens compared to that in the low emitter, whereas the relative abundances of methanotrophs between the cultivars were not significantly different. Further analysis of cultivar-sensitive taxa identified families enriched in the high emitter that are associated with methanogenesis-related processes. The high emitter had greater relative abundances of sulfate-reducing and iron-reducing taxa which peak earlier in the season than methanogens and are necessary to lower soil oxidation reduction potential before methanogenesis can occur. The high emitter also had a greater abundance of fermentative taxa which produce methanogenesis precursors (acetate, CO2, and H2). Furthermore, the high emitter was enriched in taxa related to acetogenesis which compete with methanogens for CO2 and H2 These taxa were enriched in a spatio-specific manner and reveal a complex network of microbial interactions on which plant genotype-dependent factors can act to affect methanogenesis and methane emissions.IMPORTANCE Rice cultivation is a major source of anthropogenic emissions of methane, a greenhouse gas with a potentially severe impact on climate change. Emission variation between rice cultivars suggests the feasibility of breeding low-emission rice, but there is a limited understanding of how genotypes affect the microbiota involved in methane cycling. Here, we show that the root microbiome of the high-emitting cultivar is enriched both in methanogens and in taxa associated with fermentation, iron, and sulfate reduction and acetogenesis, processes that support methanogenesis. Understanding how cultivars affect microbes with methanogenesis-related functions is vital for understanding the genetic basis for methane emission in rice and can aid in the development of breeding programs that reduce the environmental impact of rice cultivation.
Collapse
Affiliation(s)
- Zachary Liechty
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | | | - Joseph Edwards
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Bao Nguyen
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - David Mikhail
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Shane Eason
- Department of Agriculture, Arkansas State University, Jonesboro, Arkansas, USA
| | - Gregory Phillips
- Department of Agriculture, Arkansas State University, Jonesboro, Arkansas, USA
| | - Venkatesan Sundaresan
- Department of Plant Biology, University of California, Davis, Davis, California, USA
- Department of Plant Sciences, University of California, Davis, Davis, California, USA
| |
Collapse
|
12
|
Yarwood SA. The role of wetland microorganisms in plant-litter decomposition and soil organic matter formation: a critical review. FEMS Microbiol Ecol 2019; 94:5087730. [PMID: 30169564 DOI: 10.1093/femsec/fiy175] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 08/29/2018] [Indexed: 02/06/2023] Open
Abstract
New soil organic matter (SOM) models highlight the role of microorganisms in plant litter decomposition and storage of microbial-derived carbon (C) molecules. Wetlands store more C per unit area than any other ecosystem, but SOM storage mechanisms such as aggregation and metal complexes are mostly untested in wetlands. This review discusses what is currently known about the role of microorganisms in SOM formation and C sequestrations, as well as, measures of microbial communities as they relate to wetland C cycling. Studies within the last decade have yielded new insights about microbial communities. For example, microbial communities appear to be adapted to short-term fluctuations in saturation and redox and researchers have observed synergistic pairings that in some cases run counter to thermodynamic theory. Significant knowledge gaps yet to be filled include: (i) What controls microbial access to and decomposition of plant litter and SOM? (ii) How does microbial community structure shape C fate, across different wetland types? (iii) What types of plant and microbial molecules contribute to SOM accumulation? Studies examining the active microbial community directly or that utilize multi-pronged approaches are shedding new light on microbial functional potential, however, and promise to improve wetland C models in the near future.
Collapse
Affiliation(s)
- Stephanie A Yarwood
- Environmental Science and Technology Department, University of Maryland, 1204 HJ Patterson Hall, College Park, MD 20742, USA
| |
Collapse
|
13
|
Kolton M, Marks A, Wilson RM, Chanton JP, Kostka JE. Impact of Warming on Greenhouse Gas Production and Microbial Diversity in Anoxic Peat From a Sphagnum-Dominated Bog (Grand Rapids, Minnesota, United States). Front Microbiol 2019; 10:870. [PMID: 31105668 PMCID: PMC6498409 DOI: 10.3389/fmicb.2019.00870] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 04/04/2019] [Indexed: 11/17/2022] Open
Abstract
Climate warming is predicted to increase heterotrophic metabolism in northern peatland soils leading to enhanced greenhouse gas emissions. However, the specific relationships between temperature and the greenhouse gas producing microbial communities are poorly understood. Thus, in this study, the temperature dependence of carbon dioxide (CO2) and methane (CH4) production rates along with abundance and composition of microbial communities were investigated in peat from a Sphagnum-dominated peatland, S1 bog (Minnesota, United States). Whereas CH4 production rates increased with temperature up to 30°C, CO2 production did not, resulting in a lower CO2:CH4 ratio with increasing temperature. CO2 production showed both psychrophilic and mesophilic maxima at 4 and 20°C, respectively, and appears to be mediated by two anaerobic microbial communities, one that operates under psychrophilic conditions that predominate for much of the year, and another that is more active under warmer conditions during the growing season. In incubations at 10°C above the ambient range, members of the Clostridiaceae and hydrogenotrophic methanogens of the Methanobacteriaceae dominated. Moreover, a significant negative correlation between temperature and microbial diversity was observed. Results indicate that the potential consequences of warming surface peat in northern peatlands include a large stimulation in CH4 production and a significant loss of microbial diversity.
Collapse
Affiliation(s)
- Max Kolton
- School of Biology, Georgia Institute of Technology, Atlanta, GA, United States
| | - Ansley Marks
- School of Biology, Georgia Institute of Technology, Atlanta, GA, United States
| | - Rachel M. Wilson
- Department of Earth, Ocean & Atmospheric Science, Florida State University, Tallahassee, FL, United States
| | - Jeffrey P. Chanton
- Department of Earth, Ocean & Atmospheric Science, Florida State University, Tallahassee, FL, United States
| | - Joel E. Kostka
- School of Biology, Georgia Institute of Technology, Atlanta, GA, United States
- School of Earth and Atmospheric Science, Georgia Institute of Technology, Atlanta, GA, United States
| |
Collapse
|
14
|
Hao X, Jiao S, Lu Y. Geographical pattern of methanogenesis in paddy and wetland soils across eastern China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 651:281-290. [PMID: 30243161 DOI: 10.1016/j.scitotenv.2018.09.167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/08/2018] [Accepted: 09/13/2018] [Indexed: 06/08/2023]
Abstract
Large variation of CH4 emissions from paddy and wetland ecosystems exists across different geographical locations in China. To obtain mechanistic understanding of this variation, we investigated the dynamics of methanogenesis over the course of glucose degradation in fourteen paddy field soils and five wetland soils collected from different regions of China. The results revealed that the maximal rate (2-3 mM per day) and the total amount (25-30 mM) of CH4 produced were similar across soil samples. The lag phase of methanogenesis, however, differed substantially with the shortest lag phase of 4 days in a paddy soil from north China and the longest of 32 days in a soil from south China, and this difference reflected a general geographical trend among all soils tested. Nitrate was reduced completely within 4 days in all soils. The reduction of Fe(III) and sulfate was completed after 21 days and 29 days, respectively. The depletion time of Fe(III) and sulfate were positively correlated with the lag phase of methanogenesis. Competition for common substrates between methanogens and iron and sulfate reducers, however, does not explain this coincidence because a slow production of CH4 was detected at the very beginning. It appears that the geographical variations in methanogenesis and the reduction of ferric iron and sulfate are related to the variation in soil pH but not to temperature, soil organic C and nutrient conditions in paddy and wetland soils across eastern China.
Collapse
Affiliation(s)
- Xin Hao
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Shuo Jiao
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, China.
| |
Collapse
|
15
|
Zhang W, Zhang J, Lu Y. Stimulation of carbon nanomaterials on syntrophic oxidation of butyrate in sediment enrichments and a defined coculture. Sci Rep 2018; 8:12185. [PMID: 30111866 PMCID: PMC6093938 DOI: 10.1038/s41598-018-30745-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/30/2018] [Indexed: 11/18/2022] Open
Abstract
It remains elusive if direct interspecies electron transfer (DIET) occurs in canonical syntrophy involving short-chain fatty acids oxidation. In the present study, we determined the effects of carbon nanomaterials on syntrophic oxidation of butyrate in two lake sediment enrichments and a defined coculture comprising Syntrophomonas wolfei and Methanococcus Maripaludis. After four continuous transfers of enrichment cultivation, Syntrophomonas dominated the bacterial populations in enrichments, and the dominated methanogens comprised Methanosarcina and Methanospirillum in one enrichment (from Weiming Lake) and Methanoregula and Methanospirillum in another (from Erhai Lake). Butyrate oxidation and CH4 production was significantly accelerated by carbon nanotubes (CNTs) in both enrichments. Replacement of CNTs by magnetite caused similar stimulating effect. For the defined coculture, two carbon nanomaterials, CNTs and reduced graphene oxide (rGO), were tested, both showed consistently stimulating effects on butyrate oxidation. Addition of kaolinite, an electric nonconductive clay mineral, however, revealed no effect. The test on M. maripaludis in pure culture showed no effect by rGO and a negative effect by CNTs (especially at a high concentration). Fluorescence in situ hybridization (FISH) and scanning electron microscopy (SEM) revealed that microbial cells were interwoven by CNTs forming cell-CNT mixture aggregates, and in case of rGO, cells were attached to surface or wrapped-up by rGO thin sheets. Collectively, our data suggest that the presence of conductive nanomaterials likely induces DIET in syntrophic butyrate oxidation.
Collapse
Affiliation(s)
- Wei Zhang
- College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Jianchao Zhang
- Institute of Surface-Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
| |
Collapse
|
16
|
Fu L, Song T, Zhang W, Zhang J, Lu Y. Stimulatory Effect of Magnetite Nanoparticles on a Highly Enriched Butyrate-Oxidizing Consortium. Front Microbiol 2018; 9:1480. [PMID: 30026737 PMCID: PMC6041394 DOI: 10.3389/fmicb.2018.01480] [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: 02/27/2018] [Accepted: 06/13/2018] [Indexed: 11/13/2022] Open
Abstract
Syntrophic oxidation of butyrate is catabolized by a few bacteria specialists in the presence of methanogens. In the present study, a highly enriched butyrate-oxidizing consortium was obtained from a wetland sediment in Tibetan Plateau. During continuous transfers of the enrichment, the addition of magnetite nanoparticles (nanoFe3O4) consistently enhanced butyrate oxidation and CH4 production. Molecular analysis revealed that all bacterial sequences from the consortium belonged to Syntrophomonas with the closest relative of Syntrophomonas wolfei and 96% of the archaeal sequences were related to Methanobacteria with the remaining sequences to Methanocella. Addition of graphite and carbon nanotubes for a replacement of nanoFe3O4 caused the similar stimulatory effect. Silica coating of nanoFe3O4 surface, however, completely eliminated the stimulatory effect. The control experiment with axenic cultivation of a Syntrophomonas strain and two methanogen strains showed no effect by nanoFe3O4. Together, the results in the present study support that syntrophic oxidation of butyrate is likely facilitated by direct interspecies electron transfer in the presence of conductive nanomaterials.
Collapse
Affiliation(s)
- Li Fu
- College of Urban and Environmental Sciences, Peking University, Beijing, China
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tianze Song
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Wei Zhang
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Jie Zhang
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| |
Collapse
|
17
|
Analysis of functional genomes from metagenomes: Revealing the accelerated electron transfer in microbial fuel cell with rhamnolipid addition. Bioelectrochemistry 2018; 119:59-67. [DOI: 10.1016/j.bioelechem.2017.08.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/19/2017] [Accepted: 08/24/2017] [Indexed: 11/20/2022]
|
18
|
Liu P, Pommerenke B, Conrad R. Identification ofSyntrophobacteraceaeas major acetate-degrading sulfate reducing bacteria in Italian paddy soil. Environ Microbiol 2017; 20:337-354. [DOI: 10.1111/1462-2920.14001] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/26/2017] [Accepted: 11/16/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Pengfei Liu
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10; Marburg 35043 Germany
| | - Bianca Pommerenke
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10; Marburg 35043 Germany
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10; Marburg 35043 Germany
| |
Collapse
|
19
|
Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO2/CH4 Production Ratios. Appl Environ Microbiol 2017; 83:AEM.02533-16. [PMID: 27913414 DOI: 10.1128/aem.02533-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/28/2016] [Indexed: 11/20/2022] Open
Abstract
Northern peatlands in general have high methane (CH4) emissions, but individual peatlands show considerable variation as CH4 sources. Particularly in nutrient-poor peatlands, CH4 production can be low and exceeded by carbon dioxide (CO2) production from unresolved anaerobic processes. To clarify the role anaerobic bacterial degraders play in this variation, we compared consumers of cellobiose-derived carbon in two fens differing in nutrient status and the ratio of CO2 to CH4 produced. After [13C]cellobiose amendment, the mesotrophic fen produced equal amounts of CH4 and CO2 The oligotrophic fen had lower CH4 production but produced 3 to 59 times more CO2 than CH4 RNA stable-isotope probing revealed that in the mesotrophic fen with higher CH4 production, cellobiose-derived carbon was mainly assimilated by various recognized fermenters of Firmicutes and by Proteobacteria The oligotrophic peat with excess CO2 production revealed a wider variety of cellobiose-C consumers, including Firmicutes and Proteobacteria, but also more unconventional degraders, such as Telmatobacter-related Acidobacteria and subphylum 3 of Verrucomicrobia Prominent and potentially fermentative Planctomycetes and Chloroflexi did not appear to process cellobiose-C. Our results show that anaerobic degradation resulting in different levels of CH4 production can involve distinct sets of bacterial degraders. By distinguishing cellobiose degraders from the total community, this study contributes to defining anaerobic bacteria that process cellulose-derived carbon in peat. Several of the identified degraders, particularly fermenters and potential Fe(III) or humic substance reducers in the oligotrophic peat, represent promising candidates for resolving the origin of excess CO2 production in peatlands. IMPORTANCE Peatlands are major sources of the greenhouse gas methane (CH4), yet in many peatlands, CO2 production from unresolved anaerobic processes exceeds CH4 production. Anaerobic degradation produces the precursors of CH4 production but also represents competing processes. We show that anaerobic degradation leading to high or low CH4 production involved distinct sets of bacteria. Well-known fermenters dominated in a peatland with high CH4 production, while novel and unconventional degraders could be identified in a site where CO2 production greatly exceeds CH4 production. Our results help identify and assign functions to uncharacterized bacteria that promote or inhibit CH4 production and reveal bacteria potentially producing the excess CO2 in acidic peat. This study contributes to understanding the microbiological basis for different levels of CH4 emission from peatlands.
Collapse
|
20
|
Hunger S, Schmidt O, Gößner AS, Drake HL. Formate-derived H2, a driver of hydrogenotrophic processes in the root-zone of a methane-emitting fen. Environ Microbiol 2016; 18:3106-19. [DOI: 10.1111/1462-2920.13301] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 03/12/2016] [Indexed: 02/04/2023]
Affiliation(s)
- Sindy Hunger
- Department of Ecological Microbiology; University of Bayreuth; 95440 Bayreuth Germany
| | - Oliver Schmidt
- Department of Ecological Microbiology; University of Bayreuth; 95440 Bayreuth Germany
| | - Anita S. Gößner
- Department of Ecological Microbiology; University of Bayreuth; 95440 Bayreuth Germany
| | - Harold L. Drake
- Department of Ecological Microbiology; University of Bayreuth; 95440 Bayreuth Germany
| |
Collapse
|
21
|
Hausmann B, Knorr KH, Schreck K, Tringe SG, Glavina Del Rio T, Loy A, Pester M. Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms. ISME JOURNAL 2016; 10:2365-75. [PMID: 27015005 PMCID: PMC4930147 DOI: 10.1038/ismej.2016.42] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 02/15/2016] [Accepted: 02/22/2016] [Indexed: 01/20/2023]
Abstract
Dissimilatory sulfate reduction in peatlands is sustained by a cryptic sulfur cycle and effectively competes with methanogenic degradation pathways. In a series of peat soil microcosms incubated over 50 days, we identified bacterial consortia that responded to small, periodic additions of individual fermentation products (formate, acetate, propionate, lactate or butyrate) in the presence or absence of sulfate. Under sulfate supplementation, net sulfate turnover (ST) steadily increased to 16–174 nmol cm–3 per day and almost completely blocked methanogenesis. 16S rRNA gene and cDNA amplicon sequencing identified microorganisms whose increases in ribosome numbers strongly correlated to ST. Natively abundant (⩾0.1% estimated genome abundance) species-level operational taxonomic units (OTUs) showed no significant response to sulfate. In contrast, low-abundance OTUs responded significantly to sulfate in incubations with propionate, lactate and butyrate. These OTUs included members of recognized sulfate-reducing taxa (Desulfosporosinus, Desulfopila, Desulfomonile, Desulfovibrio) and also members of taxa that are either yet unknown sulfate reducers or metabolic interaction partners thereof. Most responsive OTUs markedly increased their ribosome content but only weakly increased in abundance. Responsive Desulfosporosinus OTUs even maintained a constantly low population size throughout 50 days, which suggests a novel strategy of rare biosphere members to display activity. Interestingly, two OTUs of the non-sulfate-reducing genus Telmatospirillum (Alphaproteobacteria) showed strongly contrasting preferences towards sulfate in butyrate-amended microcosms, corroborating that closely related microorganisms are not necessarily ecologically coherent. We show that diverse consortia of low-abundance microorganisms can perform peat soil sulfate reduction, a process that exerts control on methane production in these climate-relevant ecosystems.
Collapse
Affiliation(s)
- Bela Hausmann
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Klaus-Holger Knorr
- Hydrology Group, Institute of Landscape Ecology, University of Münster, Münster, Germany
| | - Katharina Schreck
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria
| | - Susannah G Tringe
- Joint Genome Institute, US Department of Energy, Walnut Creek, CA, USA
| | | | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria
| | - Michael Pester
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria.,Department of Biology, University of Konstanz, Konstanz, Germany
| |
Collapse
|
22
|
Schmidt O, Hink L, Horn MA, Drake HL. Peat: home to novel syntrophic species that feed acetate- and hydrogen-scavenging methanogens. ISME JOURNAL 2016; 10:1954-66. [PMID: 26771931 DOI: 10.1038/ismej.2015.256] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/25/2015] [Accepted: 12/07/2015] [Indexed: 11/09/2022]
Abstract
Syntrophic bacteria drive the anaerobic degradation of certain fermentation products (e.g., butyrate, ethanol, propionate) to intermediary substrates (e.g., H2, formate, acetate) that yield methane at the ecosystem level. However, little is known about the in situ activities and identities of these syntrophs in peatlands, ecosystems that produce significant quantities of methane. The consumption of butyrate, ethanol or propionate by anoxic peat slurries at 5 and 15 °C yielded methane and CO2 as the sole accumulating products, indicating that the intermediates H2, formate and acetate were scavenged effectively by syntrophic methanogenic consortia. 16S rRNA stable isotope probing identified novel species/strains of Pelobacter and Syntrophomonas that syntrophically oxidized ethanol and butyrate, respectively. Propionate was syntrophically oxidized by novel species of Syntrophobacter and Smithella, genera that use different propionate-oxidizing pathways. Taxa not known for a syntrophic metabolism may have been involved in the oxidation of butyrate (Telmatospirillum-related) and propionate (unclassified Bacteroidetes and unclassified Fibrobacteres). Gibbs free energies (ΔGs) for syntrophic oxidations of ethanol and butyrate were more favorable than ΔGs for syntrophic oxidation of propionate. As a result of the thermodynamic constraints, acetate transiently accumulated in ethanol and butyrate treatments but not in propionate treatments. Aceticlastic methanogens (Methanosarcina, Methanosaeta) appeared to outnumber hydrogenotrophic methanogens (Methanocella, Methanoregula), reinforcing the likely importance of aceticlastic methanogenesis to the overall production of methane. ΔGs for acetogenesis from H2 to CO2 approximated to -20 kJ mol(-1) when acetate concentrations were low, indicating that acetogens may have contributed to the flow of carbon and reductant towards methane.
Collapse
Affiliation(s)
- Oliver Schmidt
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Linda Hink
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Marcus A Horn
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Harold L Drake
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| |
Collapse
|
23
|
Tveit AT, Urich T, Frenzel P, Svenning MM. Metabolic and trophic interactions modulate methane production by Arctic peat microbiota in response to warming. Proc Natl Acad Sci U S A 2015; 112:E2507-16. [PMID: 25918393 PMCID: PMC4434766 DOI: 10.1073/pnas.1420797112] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Arctic permafrost soils store large amounts of soil organic carbon (SOC) that could be released into the atmosphere as methane (CH4) in a future warmer climate. How warming affects the complex microbial network decomposing SOC is not understood. We studied CH4 production of Arctic peat soil microbiota in anoxic microcosms over a temperature gradient from 1 to 30 °C, combining metatranscriptomic, metagenomic, and targeted metabolic profiling. The CH4 production rate at 4 °C was 25% of that at 25 °C and increased rapidly with temperature, driven by fast adaptations of microbial community structure, metabolic network of SOC decomposition, and trophic interactions. Below 7 °C, syntrophic propionate oxidation was the rate-limiting step for CH4 production; above this threshold temperature, polysaccharide hydrolysis became rate limiting. This change was associated with a shift within the functional guild for syntrophic propionate oxidation, with Firmicutes being replaced by Bacteroidetes. Correspondingly, there was a shift from the formate- and H2-using Methanobacteriales to Methanomicrobiales and from the acetotrophic Methanosarcinaceae to Methanosaetaceae. Methanogenesis from methylamines, probably stemming from degradation of bacterial cells, became more important with increasing temperature and corresponded with an increased relative abundance of predatory protists of the phylum Cercozoa. We concluded that Arctic peat microbiota responds rapidly to increased temperatures by modulating metabolic and trophic interactions so that CH4 is always highly produced: The microbial community adapts through taxonomic shifts, and cascade effects of substrate availability cause replacement of functional guilds and functional changes within taxa.
Collapse
Affiliation(s)
- Alexander Tøsdal Tveit
- Department of Arctic and Marine Biology, University of Tromsø The Arctic University of Norway, 9037 Tromsø, Norway;
| | - Tim Urich
- Department of Ecogenomics and Systems Biology, University of Vienna, 1090 Vienna, Austria; Austrian Polar Research Institute, 1090, Vienna, Austria; and
| | - Peter Frenzel
- Department of Biochemistry, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Mette Marianne Svenning
- Department of Arctic and Marine Biology, University of Tromsø The Arctic University of Norway, 9037 Tromsø, Norway;
| |
Collapse
|
24
|
Hunger S, Gößner AS, Drake HL. Anaerobic trophic interactions of contrasting methane-emitting mire soils: processes versus taxa. FEMS Microbiol Ecol 2015; 91:fiv045. [PMID: 25877342 DOI: 10.1093/femsec/fiv045] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2015] [Indexed: 11/13/2022] Open
Abstract
Natural wetlands such as mires contribute up to 33% to the global emission of methane. The emission of methane is driven by trophic interactions of anaerobes that collectively degrade biopolymers. The hypothesis of this study was that these interactions in contrasting methane-emitting mire soils are functionally similar but linked to dissimilar taxa. This hypothesis was addressed by evaluating anaerobic processes and microbial taxa of eutrophic, mesotrophic and oligotrophic mire soils. Glucose was fermented to various products (e.g. H2, CO2, butyrate, acetate). Acetoclastic methanogenesis occurred, and acetogenesis and methanogenesis transformed H2-CO2 to acetate and methane, respectively. Although product profiles, cultivable cell numbers and gene copy numbers [mcrA (encodes alpha-subunit of methyl-CoM reductase) and 16S rRNA genes] were similar for all mire soils, only approximately 15% of detected family-level bacteria and species-level methanogens were shared by all mire soils. Approximately, 40% of the detected family-level taxa of each mire soil have no cultured isolates. Acidic conditions appeared to restrict the number of dominant phylotypes. The results indicated (a) that microbial processes which drive methanogenesis are similar but facilitated by dissimilar microbial communities in contrasting mire soils and (b) that mire soils harbor a large number of taxa with no cultured isolates.
Collapse
Affiliation(s)
- Sindy Hunger
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Anita S Gößner
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Harold L Drake
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| |
Collapse
|
25
|
Beulig F, Heuer VB, Akob DM, Viehweger B, Elvert M, Herrmann M, Hinrichs KU, Küsel K. Carbon flow from volcanic CO2 into soil microbial communities of a wetland mofette. ISME JOURNAL 2014; 9:746-59. [PMID: 25216086 DOI: 10.1038/ismej.2014.148] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/02/2014] [Accepted: 07/03/2014] [Indexed: 12/13/2022]
Abstract
Effects of extremely high carbon dioxide (CO2) concentrations on soil microbial communities and associated processes are largely unknown. We studied a wetland area affected by spots of subcrustal CO2 degassing (mofettes) with focus on anaerobic autotrophic methanogenesis and acetogenesis because the pore gas phase was largely hypoxic. Compared with a reference soil, the mofette was more acidic (ΔpH ∼0.8), strongly enriched in organic carbon (up to 10 times), and exhibited lower prokaryotic diversity. It was dominated by methanogens and subdivision 1 Acidobacteria, which likely thrived under stable hypoxia and acidic pH. Anoxic incubations revealed enhanced formation of acetate and methane (CH4) from hydrogen (H2) and CO2 consistent with elevated CH4 and acetate levels in the mofette soil. (13)CO2 mofette soil incubations showed high label incorporations with ∼512 ng (13)C g (dry weight (dw)) soil(-1) d(-1) into the bulk soil and up to 10.7 ng (13)C g (dw) soil(-1) d(-1) into almost all analyzed bacterial lipids. Incorporation of CO2-derived carbon into archaeal lipids was much lower and restricted to the first 10 cm of the soil. DNA-SIP analysis revealed that acidophilic methanogens affiliated with Methanoregulaceae and hitherto unknown acetogens appeared to be involved in the chemolithoautotrophic utilization of (13)CO2. Subdivision 1 Acidobacteriaceae assimilated (13)CO2 likely via anaplerotic reactions because Acidobacteriaceae are not known to harbor enzymatic pathways for autotrophic CO2 assimilation. We conclude that CO2-induced geochemical changes promoted anaerobic and acidophilic organisms and altered carbon turnover in affected soils.
Collapse
Affiliation(s)
- Felix Beulig
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Verena B Heuer
- Organic Geochemistry Group, Dept. of Geosciences and MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Denise M Akob
- 1] Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany [2] U.S. Geological Survey, Reston, VA, USA
| | - Bernhard Viehweger
- Organic Geochemistry Group, Dept. of Geosciences and MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- Organic Geochemistry Group, Dept. of Geosciences and MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Martina Herrmann
- 1] Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany [2] German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, Dept. of Geosciences and MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Kirsten Küsel
- 1] Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany [2] German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, Germany
| |
Collapse
|
26
|
Schmidt O, Horn MA, Kolb S, Drake HL. Temperature impacts differentially on the methanogenic food web of cellulose-supplemented peatland soil. Environ Microbiol 2014; 17:720-34. [PMID: 24813682 DOI: 10.1111/1462-2920.12507] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 05/07/2014] [Indexed: 11/29/2022]
Abstract
The impact of temperature on the largely unresolved intermediary ecosystem metabolism and associated unknown microbiota that link cellulose degradation and methane production in soils of a moderately acidic (pH 4.5) fen was investigated. Supplemental [(13) C]cellulose stimulated the accumulation of propionate, acetate and carbon dioxide as well as initial methane production in anoxic peat soil slurries at 15°C and 5°C. Accumulation of organic acids at 15°C was twice as fast as that at 5°C. 16S rRNA [(13) C]cellulose stable isotope probing identified novel unclassified Bacteria (79% identity to the next cultured relative Fibrobacter succinogenes), unclassified Bacteroidetes (89% identity to Prolixibacter bellariivorans), Porphyromonadaceae, Acidobacteriaceae and Ruminococcaceae as main anaerobic degraders of cellulose-derived carbon at both 15°C and 5°C. Holophagaceae and Spirochaetaceae were more abundant at 15°C. Clostridiaceae dominated the degradation of cellulose-derived carbon only at 5°C. Methanosarcina was the dominant methanogenic taxa at both 15°C and 5°C. Relative abundance of Methanocella increased at 15°C whereas that of Methanoregula and Methanosaeta increased at 5°C. Thaumarchaeota closely related to Nitrosotalea (presently not known to grow anaerobically) were abundant at 5°C but absent at 15°C indicating that Nitrosotalea sp. might be capable of anaerobic growth at low temperatures in peat.
Collapse
Affiliation(s)
- Oliver Schmidt
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, 95440, Germany
| | | | | | | |
Collapse
|
27
|
Microbial metabolic potential for carbon degradation and nutrient (nitrogen and phosphorus) acquisition in an ombrotrophic peatland. Appl Environ Microbiol 2014; 80:3531-40. [PMID: 24682299 DOI: 10.1128/aem.00206-14] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
This study integrated metagenomic and nuclear magnetic resonance (NMR) spectroscopic approaches to investigate microbial metabolic potential for organic matter decomposition and nitrogen (N) and phosphorus (P) acquisition in soils of an ombrotrophic peatland in the Marcell Experimental Forest (MEF), Minnesota, USA. This analysis revealed vertical stratification in key enzymatic pathways and taxa containing these pathways. Metagenomic analyses revealed that genes encoding laccases and dioxygenases, involved in aromatic compound degradation, declined in relative abundance with depth, while the relative abundance of genes encoding metabolism of amino sugars and all four saccharide groups increased with depth in parallel with a 50% reduction in carbohydrate content. Most Cu-oxidases were closely related to genes from Proteobacteria and Acidobacteria, and type 4 laccase-like Cu-oxidase genes were >8 times more abundant than type 3 genes, suggesting an important and overlooked role for type 4 Cu-oxidase in phenolic compound degradation. Genes associated with sulfate reduction and methanogenesis were the most abundant anaerobic respiration genes in these systems, with low levels of detection observed for genes of denitrification and Fe(III) reduction. Fermentation genes increased in relative abundance with depth and were largely affiliated with Syntrophobacter. Methylocystaceae-like small-subunit (SSU) rRNA genes, pmoA, and mmoX genes were more abundant among methanotrophs. Genes encoding N2 fixation, P uptake, and P regulons were significantly enriched in the surface peat and in comparison to other ecosystems, indicating N and P limitation. Persistence of inorganic orthophosphate throughout the peat profile in this P-limiting environment indicates that P may be bound to recalcitrant organic compounds, thus limiting P bioavailability in the subsurface. Comparative metagenomic analysis revealed a high metabolic potential for P transport and starvation, N2 fixation, and oligosaccharide degradation at MEF relative to other wetland and soil environments, consistent with the nutrient-poor and carbohydrate-rich conditions found in this Sphagnum-dominated boreal peatland.
Collapse
|
28
|
Microbial community stratification linked to utilization of carbohydrates and phosphorus limitation in a boreal peatland at Marcell Experimental Forest, Minnesota, USA. Appl Environ Microbiol 2014; 80:3518-30. [PMID: 24682300 DOI: 10.1128/aem.00205-14] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study investigated the abundance, distribution, and composition of microbial communities at the watershed scale in a boreal peatland within the Marcell Experimental Forest (MEF), Minnesota, USA. Through a close coupling of next-generation sequencing, biogeochemistry, and advanced analytical chemistry, a biogeochemical hot spot was revealed in the mesotelm (30- to 50-cm depth) as a pronounced shift in microbial community composition in parallel with elevated peat decomposition. The relative abundance of Acidobacteria and the Syntrophobacteraceae, including known hydrocarbon-utilizing genera, was positively correlated with carbohydrate and organic acid content, showing a maximum in the mesotelm. The abundance of Archaea (primarily crenarchaeal groups 1.1c and 1.3) increased with depth, reaching up to 60% of total small-subunit (SSU) rRNA gene sequences in the deep peat below the 75-cm depth. Stable isotope geochemistry and potential rates of methane production paralleled vertical changes in methanogen community composition to indicate a predominance of acetoclastic methanogenesis mediated by the Methanosarcinales in the mesotelm, while hydrogen-utilizing methanogens predominated in the deeper catotelm. RNA-derived pyrosequence libraries corroborated DNA sequence data to indicate that the above-mentioned microbial groups are metabolically active in the mid-depth zone. Fungi showed a maximum in rRNA gene abundance above the 30-cm depth, which comprised only an average of 0.1% of total bacterial and archaeal rRNA gene abundance, indicating prokaryotic dominance. Ratios of C to P enzyme activities approached 0.5 at the acrotelm and catotelm, indicating phosphorus limitation. In contrast, P limitation pressure appeared to be relieved in the mesotelm, likely due to P solubilization by microbial production of organic acids and C-P lyases. Based on path analysis and the modeling of community spatial turnover, we hypothesize that P limitation outweighs N limitation at MEF, and microbial communities are structured by the dominant shrub, Chamaedaphne calyculata, which may act as a carbon source for major consumers in the peatland.
Collapse
|
29
|
Kolb S, Stacheter A. Prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment. Front Microbiol 2013; 4:268. [PMID: 24046766 PMCID: PMC3763247 DOI: 10.3389/fmicb.2013.00268] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 08/19/2013] [Indexed: 01/06/2023] Open
Abstract
The commercial availability of next generation sequencing (NGS) technologies facilitated the assessment of functional groups of microorganisms in the environment with high coverage, resolution, and reproducibility. Soil methylotrophs were among the first microorganisms in the environment that were assessed with molecular tools, and nowadays, as well with NGS technologies. Studies in the past years re-attracted notice to the pivotal role of methylotrophs in global conversions of methanol, which mainly originates from plants, and is involved in oxidative reactions and ozone formation in the atmosphere. Aerobic methanol utilizers belong to Bacteria, yeasts, Ascomycota, and molds. Numerous bacterial methylotrophs are facultatively aerobic, and also contribute to anaerobic methanol oxidation in the environment, whereas strict anaerobic methanol utilizers belong to methanogens and acetogens. The diversity of enzymes catalyzing the initial oxidation of methanol is considerable, and comprises at least five different enzyme types in aerobes, and one in strict anaerobes. Only the gene of the large subunit of pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH; mxaF) has been analyzed by environmental pyrosequencing. To enable a comprehensive assessment of methanol utilizers in the environment, new primers targeting genes of the PQQ MDH in Methylibium (mdh2), of the nicotinamide adenine dinucleotide-dependent MDH (mdh), of the methanol oxidoreductase of Actinobacteria (mdo), of the fungal flavin adenine nucleotide-dependent alcohol oxidase (mod1, mod2, and homologs), and of the gene of the large subunit of the methanol:corrinoid methyltransferases (mtaC) in methanogens and acetogens need to be developed. Combined stable isotope probing of nucleic acids or proteins with amplicon-based NGS are straightforward approaches to reveal insights into functions of certain methylotrophic taxa in the global methanol cycle.
Collapse
Affiliation(s)
- Steffen Kolb
- Department of Ecological Microbiology, University of Bayreuth Bayreuth, Germany
| | | |
Collapse
|
30
|
Basiliko N, Henry K, Gupta V, Moore TR, Driscoll BT, Dunfield PF. Controls on bacterial and archaeal community structure and greenhouse gas production in natural, mined, and restored Canadian peatlands. Front Microbiol 2013; 4:215. [PMID: 23914185 PMCID: PMC3728569 DOI: 10.3389/fmicb.2013.00215] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 07/10/2013] [Indexed: 11/15/2022] Open
Abstract
Northern peatlands are important global C reservoirs, largely because of their slow rates of microbial C mineralization. Particularly in sites that are heavily influenced by anthropogenic disturbances, there is scant information about microbial ecology and whether or not microbial community structure influences greenhouse gas production. This work characterized communities of bacteria and archaea using terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of 16S rRNA and functional genes across eight natural, mined, or restored peatlands in two locations in eastern Canada. Correlations were explored among chemical properties of peat, bacterial and archaeal community structure, and carbon dioxide (CO2) and methane (CH4) production rates under oxic and anoxic conditions. Bacteria and archaea similar to those found in other peat soil environments were detected. In contrast to other reports, methanogen diversity was low in our study, with only 2 groups of known or suspected methanogens. Although mining and restoration affected substrate availability and microbial activity, these land-uses did not consistently affect bacterial or archaeal community composition. In fact, larger differences were observed between the two locations and between oxic and anoxic peat samples than between natural, mined, and restored sites, with anoxic samples characterized by less detectable bacterial diversity and stronger dominance by members of the phylum Acidobacteria. There were also no apparent strong linkages between prokaryote community structure and CH4 or CO2 production, suggesting that different organisms exhibit functional redundancy and/or that the same taxa function at very different rates when exposed to different peat substrates. In contrast to other earlier work focusing on fungal communities across similar mined and restored peatlands, bacterial and archaeal communities appeared to be more resistant or resilient to peat substrate changes brought about by these land uses.
Collapse
Affiliation(s)
- Nathan Basiliko
- Department of Geography, University of Toronto Mississauga Mississauga, ON, Canada ; Max-Planck-Institute for Terrestrial Microbiology Marburg, Germany
| | | | | | | | | | | |
Collapse
|
31
|
Bridgham SD, Cadillo-Quiroz H, Keller JK, Zhuang Q. Methane emissions from wetlands: biogeochemical, microbial, and modeling perspectives from local to global scales. GLOBAL CHANGE BIOLOGY 2013; 19:1325-1346. [PMID: 23505021 DOI: 10.1111/gcb.12131] [Citation(s) in RCA: 314] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Revised: 12/07/2012] [Accepted: 12/14/2012] [Indexed: 06/01/2023]
Abstract
Understanding the dynamics of methane (CH4 ) emissions is of paramount importance because CH4 has 25 times the global warming potential of carbon dioxide (CO2 ) and is currently the second most important anthropogenic greenhouse gas. Wetlands are the single largest natural CH4 source with median emissions from published studies of 164 Tg yr(-1) , which is about a third of total global emissions. We provide a perspective on important new frontiers in obtaining a better understanding of CH4 dynamics in natural systems, with a focus on wetlands. One of the most exciting recent developments in this field is the attempt to integrate the different methodologies and spatial scales of biogeochemistry, molecular microbiology, and modeling, and thus this is a major focus of this review. Our specific objectives are to provide an up-to-date synthesis of estimates of global CH4 emissions from wetlands and other freshwater aquatic ecosystems, briefly summarize major biogeophysical controls over CH4 emissions from wetlands, suggest new frontiers in CH4 biogeochemistry, examine relationships between methanogen community structure and CH4 dynamics in situ, and to review the current generation of CH4 models. We highlight throughout some of the most pressing issues concerning global change and feedbacks on CH4 emissions from natural ecosystems. Major uncertainties in estimating current and future CH4 emissions from natural ecosystems include the following: (i) A number of important controls over CH4 production, consumption, and transport have not been, or are inadequately, incorporated into existing CH4 biogeochemistry models. (ii) Significant errors in regional and global emission estimates are derived from large spatial-scale extrapolations from highly heterogeneous and often poorly mapped wetland complexes. (iii) The limited number of observations of CH4 fluxes and their associated environmental variables loosely constrains the parameterization of process-based biogeochemistry models.
Collapse
|
32
|
Paul Antony C, Kumaresan D, Hunger S, Drake HL, Murrell JC, Shouche YS. Microbiology of Lonar Lake and other soda lakes. THE ISME JOURNAL 2013; 7:468-76. [PMID: 23178675 PMCID: PMC3578565 DOI: 10.1038/ismej.2012.137] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 09/17/2012] [Accepted: 09/28/2012] [Indexed: 11/08/2022]
Abstract
Soda lakes are saline and alkaline ecosystems that are believed to have existed throughout the geological record of Earth. They are widely distributed across the globe, but are highly abundant in terrestrial biomes such as deserts and steppes and in geologically interesting regions such as the East African Rift valley. The unusual geochemistry of these lakes supports the growth of an impressive array of microorganisms that are of ecological and economic importance. Haloalkaliphilic Bacteria and Archaea belonging to all major trophic groups have been described from many soda lakes, including lakes with exceptionally high levels of heavy metals. Lonar Lake is a soda lake that is centered at an unusual meteorite impact structure in the Deccan basalts in India and its key physicochemical and microbiological characteristics are highlighted in this article. The occurrence of diverse functional groups of microbes, such as methanogens, methanotrophs, phototrophs, denitrifiers, sulfur oxidizers, sulfate reducers and syntrophs in soda lakes, suggests that these habitats harbor complex microbial food webs that (a) interconnect various biological cycles via redox coupling and (b) impact on the production and consumption of greenhouse gases. Soda lake microorganisms harbor several biotechnologically relevant enzymes and biomolecules (for example, cellulases, amylases, ectoine) and there is the need to augment bioprospecting efforts in soda lake environments with new integrated approaches. Importantly, some saline and alkaline lake ecosystems around the world need to be protected from anthropogenic pressures that threaten their long-term existence.
Collapse
Affiliation(s)
| | | | - Sindy Hunger
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Harold L Drake
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Yogesh S Shouche
- Microbial Culture Collection, National Centre for Cell Science, Pune, India
| |
Collapse
|
33
|
Wang J, Liu H, Fu B, Xu K, Chen J. Trophic link between syntrophic acetogens and homoacetogens during the anaerobic acidogenic fermentation of sewage sludge. Biochem Eng J 2013. [DOI: 10.1016/j.bej.2012.09.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
34
|
Zhou M, Hünerberg M, Beauchemin KA, McAllister TA, Okine EK, Guan LL. Individuality of ruminal methanogen/protozoa populations in beef cattle fed diets containing dried distillers' grain with solubles. ACTA AGR SCAND A-AN 2012. [DOI: 10.1080/09064702.2013.788206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
35
|
Montoya L, Celis LB, Razo-Flores E, Alpuche-Solís ÁG. Distribution of CO2 fixation and acetate mineralization pathways in microorganisms from extremophilic anaerobic biotopes. Extremophiles 2012; 16:805-17. [DOI: 10.1007/s00792-012-0487-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 09/27/2012] [Indexed: 11/28/2022]
|
36
|
Syntrophic oxidation of propionate in rice field soil at 15 and 30°C under methanogenic conditions. Appl Environ Microbiol 2012; 78:4923-32. [PMID: 22582054 DOI: 10.1128/aem.00688-12] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Propionate is one of the major intermediary products in the anaerobic decomposition of organic matter in wetlands and paddy fields. Under methanogenic conditions, propionate is decomposed through syntrophic interaction between proton-reducing and propionate-oxidizing bacteria and H(2)-consuming methanogens. Temperature is an important environmental regulator; yet its effect on syntrophic propionate oxidation has been poorly understood. In the present study, we investigated the syntrophic oxidation of propionate in a rice field soil at 15°C and 30°C. [U-(13)C]propionate (99 atom%) was applied to anoxic soil slurries, and the bacteria and archaea assimilating (13)C were traced by DNA-based stable isotope probing. Syntrophobacter spp., Pelotomaculum spp., and Smithella spp. were found significantly incorporating (13)C into their nucleic acids after [(13)C]propionate incubation at 30°C. The activity of Smithella spp. increased in the later stage, and concurrently that of Syntrophomonas spp. increased. Aceticlastic Methanosaetaceae and hydrogenotrophic Methanomicrobiales and Methanocellales acted as methanogenic partners at 30°C. Syntrophic oxidation of propionate also occurred actively at 15°C. Syntrophobacter spp. were significantly labeled with (13)C, whereas Pelotomaculum spp. were less active at this temperature. In addition, Methanomicrobiales, Methanocellales, and Methanosarcinaceae dominated the methanogenic community, while Methanosaetaceae decreased. Collectively, temperature markedly influenced the activity and community structure of syntrophic guilds degrading propionate in the rice field soil. Interestingly, Geobacter spp. and some other anaerobic organisms like Rhodocyclaceae, Acidobacteria, Actinobacteria, and Thermomicrobia probably also assimilated propionate-derived (13)C. The mechanisms for the involvement of these organisms remain unclear.
Collapse
|
37
|
Hädrich A, Heuer VB, Herrmann M, Hinrichs KU, Küsel K. Origin and fate of acetate in an acidic fen. FEMS Microbiol Ecol 2012; 81:339-54. [DOI: 10.1111/j.1574-6941.2012.01352.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 02/16/2012] [Accepted: 02/26/2012] [Indexed: 11/28/2022] Open
Affiliation(s)
- Anke Hädrich
- Aquatic Geomicrobiology Group; Institute of Ecology; Friedrich Schiller University Jena; Jena; Germany
| | - Verena B. Heuer
- Organic Geochemistry Group; Department of Geosciences and MARUM Center for Marine Environmental Sciences; University of Bremen; Bremen; Germany
| | - Martina Herrmann
- Aquatic Geomicrobiology Group; Institute of Ecology; Friedrich Schiller University Jena; Jena; Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group; Department of Geosciences and MARUM Center for Marine Environmental Sciences; University of Bremen; Bremen; Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology Group; Institute of Ecology; Friedrich Schiller University Jena; Jena; Germany
| |
Collapse
|
38
|
Key players and team play: anaerobic microbial communities in hydrocarbon-contaminated aquifers. Appl Microbiol Biotechnol 2012; 94:851-73. [PMID: 22476263 DOI: 10.1007/s00253-012-4025-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Revised: 03/13/2012] [Accepted: 03/14/2012] [Indexed: 02/06/2023]
Abstract
Biodegradation of anthropogenic pollutants in shallow aquifers is an important microbial ecosystem service which is mainly brought about by indigenous anaerobic microorganisms. For the management of contaminated sites, risk assessment and control of natural attenuation, the assessment of in situ biodegradation and the underlying microbial processes is essential. The development of novel molecular methods, "omics" approaches, and high-throughput techniques has revealed new insight into complex microbial communities and their functions in anoxic environmental systems. This review summarizes recent advances in the application of molecular methods to study anaerobic microbial communities in contaminated terrestrial subsurface ecosystems. We focus on current approaches to analyze composition, dynamics, and functional diversity of subsurface communities, to link identity to activity and metabolic function, and to identify the ecophysiological role of not yet cultured microbes and syntrophic consortia. We discuss recent molecular surveys of contaminated sites from an ecological viewpoint regarding degrader ecotypes, abiotic factors shaping anaerobic communities, and biotic interactions underpinning the importance of microbial cooperation for microbial ecosystem services such as contaminant degradation.
Collapse
|
39
|
Sun CL, Brauer SL, Cadillo-Quiroz H, Zinder SH, Yavitt JB. Seasonal changes in methanogenesis and methanogenic community in three peatlands, new york state. Front Microbiol 2012; 3:81. [PMID: 22408638 PMCID: PMC3294236 DOI: 10.3389/fmicb.2012.00081] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 02/17/2012] [Indexed: 11/24/2022] Open
Abstract
Fluctuating environmental conditions can promote diversity and control dominance in community composition. In addition to seasonal temperature and moisture changes, seasonal supply of metabolic substrates selects populations temporally. Here we demonstrate cascading effects in the supply of metabolic substrates on methanogenesis and community composition of anaerobic methanogenic archaea in three contrasting peatlands in upstate New York. Fresh samples of peat soils, collected about every 3 months for 20 months and incubated at 22 ± 2°C regardless of the in situ temperature, exhibited potential rates of methane (CH4) production of 0.02–0.2 mmol L−1 day−1 [380–3800 nmol g−1 (dry) day−1). The addition of acetate stimulated rates of CH4 production in a fen peatland soil, whereas addition of hydrogen (H2), and simultaneous inhibition of H2-consuming acetogenic bacteria with rifampicin, stimulated CH4 production in two acidic bog soils, especially, in autumn and winter. The methanogenic community structure was characterized using T-RFLP analyses of SSU rRNA genes. The E2 group of methanogens (Methanoregulaceae) dominated in the two acidic bog peatlands with relatively greater abundance in winter. In the fen peatland, the E1 group (Methanoregulaceae) and members of the Methanosaetaceae were co-dominant, with E1 having a high relative abundance in spring. Change in relative abundance profiles among methanogenic groups in response to added metabolic substrates was as predicted. The acetate-amendment increased abundance of Methanosarcinaceae, and H2-amendment enhanced abundance of E2 group in all peat soils studied, respectively. Additionally, addition of acetate increased abundance of Methanosaetaceae only in the bog soils. Variation in the supply of metabolic substrates helps explain the moderate diversity of methanogens in peatlands.
Collapse
Affiliation(s)
- Christine L Sun
- Department of Microbiology, Cornell University Ithaca, NY, USA
| | | | | | | | | |
Collapse
|
40
|
Kolb S, Horn MA. Microbial CH(4) and N(2)O Consumption in Acidic Wetlands. Front Microbiol 2012; 3:78. [PMID: 22403579 PMCID: PMC3291872 DOI: 10.3389/fmicb.2012.00078] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 02/15/2012] [Indexed: 01/21/2023] Open
Abstract
Acidic wetlands are global sources of the atmospheric greenhouse gases methane (CH(4)), and nitrous oxide (N(2)O). Consumption of both atmospheric gases has been observed in various acidic wetlands, but information on the microbial mechanisms underlying these phenomena is scarce. A substantial amount of CH(4) is consumed in sub soil by aerobic methanotrophs at anoxic-oxic interfaces (e.g., tissues of Sphagnum mosses, rhizosphere of vascular plant roots). Methylocystis-related species are likely candidates that are involved in the consumption of atmospheric CH(4) in acidic wetlands. Oxygen availability regulates the activity of methanotrophs of acidic wetlands. Other parameters impacting on the methanotroph-mediated CH(4) consumption have not been systematically evaluated. N(2)O is produced and consumed by microbial denitrification, thus rendering acidic wetlands as temporary sources or sinks for N(2)O. Denitrifier communities in such ecosystems are diverse, and largely uncultured and/or new, and environmental factors that control their consumption activity are unresolved. Analyses of the composition of N(2)O reductase genes in acidic wetlands suggest that acid-tolerant Proteobacteria have the potential to mediate N(2)O consumption in such soils. Thus, the fragmented current state of knowledge raises open questions concerning methanotrophs and denitrifiers that consume atmospheric CH(4) and N(2)O in acidic wetlands.
Collapse
Affiliation(s)
- Steffen Kolb
- Department of Ecological Microbiology, University of BayreuthBayreuth, Germany
| | - Marcus A. Horn
- Department of Ecological Microbiology, University of BayreuthBayreuth, Germany
| |
Collapse
|
41
|
Wilhelm RC, Niederberger TD, Greer C, Whyte LG. Microbial diversity of active layer and permafrost in an acidic wetland from the Canadian High Arctic. Can J Microbiol 2012; 57:303-15. [PMID: 21491982 DOI: 10.1139/w11-004] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The abundance and structure of archaeal and bacterial communities from the active layer and the associated permafrost of a moderately acidic (pH < 5.0) High Arctic wetland (Axel Heiberg Island, Nunavut, Canada) were investigated using culture- and molecular-based methods. Aerobic viable cell counts from the active layer were ∼100-fold greater than those from the permafrost (2.5 × 10(5) CFU·(g soil dry mass)(-1)); however, a greater diversity of isolates were cultured from permafrost, as determined by 16S rRNA gene sequencing. Isolates from both layers demonstrated growth characteristics of a psychrotolerant, halotolerant, and acidotolerant community. Archaea constituted 0.1% of the total 16S rRNA gene copy number and, in the 16S rRNA gene clone library, predominantly (71% and 95%) consisted of Crenarchaeota related to Group I. 1b. In contrast, bacterial communities were diverse (Shannon's diversity index, H = ∼4), with Acidobacteria constituting the largest division of active layer clones (30%) and Actinobacteria most abundant in permafrost (28%). Direct comparisons of 16S rRNA gene sequence data highlighted significant differences between the bacterial communities of each layer, with the greatest differences occurring within Actinobacteria. Comparisons of 16S rRNA gene sequences with those from other Arctic permafrost and cold-temperature wetlands revealed commonly occurring taxa within the phyla Chloroflexi, Acidobacteria, and Actinobacteria (families Intrasporangiaceae and Rubrobacteraceae).
Collapse
Affiliation(s)
- Roland C Wilhelm
- Department of Natural Resource Sciences, McGill University, Ste. Anne de Bellevue, QC, Canada
| | | | | | | |
Collapse
|
42
|
Hunger S, Schmidt O, Hilgarth M, Horn MA, Kolb S, Conrad R, Drake HL. Competing formate- and carbon dioxide-utilizing prokaryotes in an anoxic methane-emitting fen soil. Appl Environ Microbiol 2011; 77:3773-85. [PMID: 21478308 PMCID: PMC3127604 DOI: 10.1128/aem.00282-11] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 03/29/2011] [Indexed: 11/20/2022] Open
Abstract
Methanogenesis in wetlands is dependent on intermediary substrates derived from the degradation of biopolymers. Formate is one such substrate and is stimulatory to methanogenesis and acetogenesis in anoxic microcosms of soil from the fen Schlöppnerbrunnen. Formate dissimilation also yields CO(2) as a potential secondary substrate. The objective of this study was to resolve potential differences between anaerobic formate- and CO(2)-utilizing prokaryotes of this fen by stable isotope probing. Anoxic soil microcosms were pulsed daily with low concentrations of [(13)C]formate or (13)CO(2) (i.e., [(13)C]bicarbonate). Taxa were evaluated by assessment of 16S rRNA genes, mcrA (encoding the alpha-subunit of methyl-coenzyme M reductase), and fhs (encoding formyltetrahydrofolate synthetase). Methanogens, acetogens, and formate-hydrogen lyase-containing taxa appeared to compete for formate. Genes affiliated with Methanocellaceae, Methanobacteriaceae, Acetobacteraceae, and Rhodospirillaceae were (13)C enriched (i.e., labeled) in [(13)C]formate treatments, whereas genes affiliated with Methanosarcinaceae, Conexibacteraceae, and Solirubrobacteraceae were labeled in (13)CO(2) treatments. [(13)C]acetate was enriched in [(13)C]formate treatments, but labeling of known acetogenic taxa was not detected. However, several phylotypes were affiliated with acetogen-containing taxa (e.g., Sporomusa). Methanosaetaceae-affiliated methanogens appeared to participate in the consumption of acetate. Twelve and 58 family-level archaeal and bacterial 16S rRNA phylotypes, respectively, were detected, approximately half of which had no isolated representatives. Crenarchaeota constituted half of the detected archaeal 16S rRNA phylotypes. The results highlight the unresolved microbial diversity of the fen Schlöppnerbrunnen, suggest that differing taxa competed for the same substrate, and indicate that Methanocellaceae, Methanobacteriaceae, Methanosarcinaceae, and Methanosaetaceae were linked to the production of methane, but they do not clearly resolve the taxa responsible for the apparent conversion of formate to acetate.
Collapse
MESH Headings
- Anaerobiosis
- Biodiversity
- Carbon Dioxide/metabolism
- Carbon Isotopes/metabolism
- Cluster Analysis
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Formates/metabolism
- Genes, rRNA
- Methane/metabolism
- Molecular Sequence Data
- Phylogeny
- RNA, Archaeal/genetics
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil Microbiology
- Wetlands
Collapse
Affiliation(s)
- Sindy Hunger
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Oliver Schmidt
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Maik Hilgarth
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Marcus A. Horn
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Steffen Kolb
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Harold L. Drake
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| |
Collapse
|
43
|
Wieczorek AS, Drake HL, Kolb S. Organic acids and ethanol inhibit the oxidation of methane by mire methanotrophs. FEMS Microbiol Ecol 2011; 77:28-39. [DOI: 10.1111/j.1574-6941.2011.01080.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
|
44
|
Chemolithotrophic acetogenic H2/CO2 utilization in Italian rice field soil. ISME JOURNAL 2011; 5:1526-39. [PMID: 21368906 DOI: 10.1038/ismej.2011.17] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Acetate oxidation in Italian rice field at 50 °C is achieved by uncultured syntrophic acetate oxidizers. As these bacteria are closely related to acetogens, they may potentially also be able to synthesize acetate chemolithoautotrophically. Labeling studies using exogenous H(2) (80%) and (13)CO(2) (20%), indeed demonstrated production of acetate as almost exclusive primary product not only at 50 °C but also at 15 °C. Small amounts of formate, propionate and butyrate were also produced from (13)CO(2). At 50 °C, acetate was first produced but later on consumed with formation of CH(4). Acetate was also produced in the absence of exogenous H(2) albeit to lower concentrations. The acetogenic bacteria and methanogenic archaea were targeted by stable isotope probing of ribosomal RNA (rRNA). Using quantitative PCR, (13)C-labeled bacterial rRNA was detected after 20 days of incubation with (13)CO(2). In the heavy fractions at 15 °C, terminal restriction fragment length polymorphism, cloning and sequencing of 16S rRNA showed that Clostridium cluster I and uncultured Peptococcaceae assimilated (13)CO(2) in the presence and absence of exogenous H(2), respectively. A similar experiment showed that Thermoanaerobacteriaceae and Acidobacteriaceae were dominant in the (13)C treatment at 50 °C. Assimilation of (13)CO(2) into archaeal rRNA was detected at 15 °C and 50 °C, mostly into Methanocellales, Methanobacteriales and rice cluster III. Acetoclastic methanogenic archaea were not detected. The above results showed the potential for acetogenesis in the presence and absence of exogenous H(2) at both 15 °C and 50 °C. However, syntrophic acetate oxidizers seemed to be only active at 50 °C, while other bacterial groups were active at 15 °C.
Collapse
|
45
|
Typical methanogenic inhibitors can considerably alter bacterial populations and affect the interaction between fatty acid degraders and homoacetogens. Appl Microbiol Biotechnol 2010; 87:2267-79. [DOI: 10.1007/s00253-010-2708-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2010] [Revised: 05/30/2010] [Accepted: 05/30/2010] [Indexed: 10/19/2022]
|
46
|
Hitherto unknown [Fe-Fe]-hydrogenase gene diversity in anaerobes and anoxic enrichments from a moderately acidic fen. Appl Environ Microbiol 2010; 76:2027-31. [PMID: 20118375 DOI: 10.1128/aem.02895-09] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Newly designed primers for [Fe-Fe]-hydrogenases indicated that (i) fermenters, acetogens, and undefined species in a fen harbor hitherto unknown hydrogenases and (ii) Clostridium- and Thermosinus-related primary fermenters, as well as secondary fermenters related to sulfate or iron reducers might be responsible for hydrogen production in the fen. Comparative analysis of [Fe-Fe]-hydrogenase and 16S rRNA gene-based phylogenies indicated the presence of homologous multiple hydrogenases per organism and inconsistencies between 16S rRNA gene- and [Fe-Fe]-hydrogenase-based phylogenies, necessitating appropriate qualification of [Fe-Fe]-hydrogenase gene data for diversity analyses.
Collapse
|
47
|
Schellenberger S, Kolb S, Drake HL. Metabolic responses of novel cellulolytic and saccharolytic agricultural soil Bacteria to oxygen. Environ Microbiol 2009; 12:845-61. [DOI: 10.1111/j.1462-2920.2009.02128.x] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
48
|
Association of novel and highly diverse acid-tolerant denitrifiers with N2O fluxes of an acidic fen. Appl Environ Microbiol 2009; 76:1125-34. [PMID: 20023077 DOI: 10.1128/aem.02256-09] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Wetlands are sources of denitrification-derived nitrous oxide (N2O). Thus, the denitrifier community of an N2O-emitting fen (pH 4.7 to 5.2) was investigated. N2O was produced and consumed to subatmospheric concentrations in unsupplemented anoxic soil microcosms. Total cell counts and most probable numbers of denitrifiers approximated 10(11) cells x g(DW)(-1) (where DW is dry weight) and 10(8) cells x g(DW)(-1), respectively, in both 0- to 10-cm and 30- to 40-cm depths. Despite this uniformity, depth-related maximum reaction rate (v(max)) values for denitrification in anoxic microcosms ranged from 1 to 24 and -19 to -105 nmol N2O h(-1) x g(DW)(-1), with maximal values occurring in the upper soil layers. Denitrification was enhanced by substrates that might be formed via fermentation in anoxic microzones of soil. N2O approximated 40% of total nitrogenous gases produced at in situ pH, which was likewise the optimal pH for denitrification. Gene libraries of narG and nosZ (encoding nitrate reductase and nitrous oxide reductase, respectively) from fen soil DNA yielded 15 and 18 species-level operational taxonomic units, respectively, many of which displayed phylogenetic novelty and were not closely related to cultured organisms. Although statistical analyses of narG and nosZ sequences indicated that the upper 20 cm of soil contained the highest denitrifier diversity and species richness, terminal restriction fragment length polymorphism analyses of narG and nosZ revealed only minor differences in denitrifier community composition from a soil depth of 0 to 40 cm. The collective data indicate that the regional fen harbors novel, highly diverse, acid-tolerant denitrifier communities capable of complete denitrification and consumption of atmospheric N2O at in situ pH.
Collapse
|
49
|
McInerney MJ, Sieber JR, Gunsalus RP. Syntrophy in anaerobic global carbon cycles. Curr Opin Biotechnol 2009; 20:623-32. [PMID: 19897353 PMCID: PMC2790021 DOI: 10.1016/j.copbio.2009.10.001] [Citation(s) in RCA: 273] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Revised: 09/30/2009] [Accepted: 10/02/2009] [Indexed: 10/20/2022]
Abstract
Syntrophy is an essential intermediary step in the anaerobic conversion of organic matter to methane where metabolically distinct microorganisms are tightly linked by the need to maintain the exchanged metabolites at very low concentrations. Anaerobic syntrophy is thermodynamically constrained, and is probably a prime reason why it is difficult to culture microbes as these approaches disrupt consortia. Reconstruction of artificial syntrophic consortia has allowed uncultured syntrophic metabolizers and methanogens to be optimally grown and studied biochemically. The pathways for syntrophic acetate, propionate and longer chain fatty acid metabolism are mostly understood, but key steps involved in benzoate breakdown and cyclohexane carboxylate formation are unclear. Syntrophic metabolism requires reverse electron transfer, close physical contact, and metabolic synchronization of the syntrophic partners. Genomic analyses reveal that multiple mechanisms exist for reverse electron transfer. Surprisingly, the flagellum functions were implicated in ensuring close physical proximity and synchronization of the syntrophic partners.
Collapse
Affiliation(s)
- Michael J. McInerney
- Department of Botany and Microbiology, University of Oklahoma, 770 Van Vleet Oval, Norman, Oklahoma 73019, USA; phone: 405-325-6050; fax: 405-325-7619
| | - Jessica R. Sieber
- Department of Botany and Microbiology, University of Oklahoma, 770 Van Vleet Oval, Norman, Oklahoma 73019, USA; phone: 405-325-6050; fax: 405-325-7619
| | - Robert P. Gunsalus
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, 1602 Molecular Science Building, 609 Charles Young Drive East, Los Angeles, CA 90095-1489, USA phone: 310-206-8201; fax: 310-206-5231
| |
Collapse
|
50
|
Abstract
This special issue highlights several recent discoveries in the microbial methane cycle, including the diversity and activity of methanotrophic bacteria in special habitats, distribution and contribution of the newly discovered Verrucomicrobia, metabolism of methane and related one-carbon compounds such as methanol and methylamine in freshwater and marine environments, methanol and methane-dependent nitrate reduction, the relationships of methane cycle microorganisms with plants and animals, and the environmental factors that regulate microbial processes of the methane cycle. These articles also highlight the plethora of new organisms and metabolism relating to the methane cycle that have been discovered in recent years and outline the many questions in the methane cycle that still need to be addressed. It is clear that despite a tremendous amount of research on the biology of the methane cycle, the microbes involved in catalysing methane production and consumption harbour many secrets that need to be disclosed in order for us to fully understand how the biogeochemical methane cycle is regulated in the environment, and for us to make future predictions about the global sources and sinks of methane and how anthropogenic changes impact on the cycling of this important greenhouse gas.
Collapse
Affiliation(s)
- J Colin Murrell
- Department of Microbiology, Warwick University, Warwick, UK. Department of Microbiology, IWWR Radboud University, Nijmegen, The Netherlands. Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | | |
Collapse
|