DOCSLIB.ORG

Specialized Metabolites from Methylotrophic Proteobacteria Aaron W

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Specialized Metabolites from Methylotrophic Proteobacteria Aaron W Specialized Metabolites from Methylotrophic Proteobacteria Aaron W. Puri* Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, UT, USA. *Correspondence: [email protected] htps://doi.org/10.21775/cimb.033.211 Abstract these compounds and strategies for determining Biosynthesized small molecules known as special- their biological functions. ized metabolites ofen have valuable applications Te explosion in bacterial genome sequences in felds such as medicine and agriculture. Con- available in public databases as well as the availabil- sequently, there is always a demand for novel ity of bioinformatics tools for analysing them has specialized metabolites and an understanding of revealed that many bacterial species are potentially their bioactivity. Methylotrophs are an underex- untapped sources for new molecules (Cimerman- plored metabolic group of bacteria that have several cic et al., 2014). Tis includes organisms beyond growth features that make them enticing in terms those traditionally relied upon for natural product of specialized metabolite discovery, characteriza- discovery, and recent studies have shown that tion, and production from cheap feedstocks such examining the biosynthetic potential of new spe- as methanol and methane gas. Tis chapter will cies indeed reveals new classes of compounds examine the predicted biosynthetic potential of (Pidot et al., 2014; Pye et al., 2017). Tis strategy these organisms and review some of the specialized is complementary to synthetic biology approaches metabolites they produce that have been character- focused on activating BGCs that are not normally ized so far. expressed under laboratory conditions in strains traditionally used for natural product discovery, such as Streptomyces (Rutledge and Challis, 2015). Introduction Tis chapter will focus on the methylotrophic Specialized metabolites, also known as secondary Proteobacteria, which use reduced carbon com- metabolites or natural products, form the basis of pounds with no carbon–carbon bonds as their many bioactive compounds essential to modern sole sources of carbon and energy. Specifcally, the medicine and agriculture (Demain and Sanchez, Proteobacteria are some of the most well-studied 2009; Cantrell et al., 2012; Newman and Cragg, organisms within this metabolic group (Chis- 2016). Tis makes intuitive sense because produc- toserdova et al., 2009). While several molecules tion of these compounds is genetically encoded in have been isolated from methylotrophic Proteo- biosynthetic gene clusters (BGCs) and therefore bacteria that have had an impact on the feld of the resulting structures have had millennia to natural products (Kenney and Rosenzweig, 2018a; evolve their roles. Te great value of these mol- Khmelenina et al., 2015), our understanding of the ecules in manipulating biological systems means specialized metabolism of these organisms is still there is a constant demand for new sources of in its infancy. Curr. Issues Mol. Biol. (2019) Vol. 33 caister.com/cimb 212 | Puri Methylotrophic bacteria as an biosynthetic potential in a past analysis of bacte- underexplored resource for rial genomes (Cimermancic et al., 2014). Many specialized metabolite discovery Alphaproteobacteria including methylotrophic Methylotrophic bacteria are an atractive source for species rely on the ethylmalonyl-CoA pathway to the discovery of new specialized metabolites for assimilate acetyl-CoA into central metabolism, and several reasons. this pathway involves high fux through CoA-linked intermediates that are also ofen used in the synthe- 1 Obligate methylotrophs, including many spe- sis of specialized metabolites such as polyketides cies of methane-oxidizing bacteria, may have (Alber, 2011). Tis makes the exploration of the been overlooked during traditional ‘grind and specialized metabolism of these organisms particu- fnd’ searches for new compounds that focused larly intriguing. on the isolation of specifc genera like Strepto- Bacteriocin and terpene BGCs were most myces using rich media. commonly predicted within the categories clas- 2 Te lack of complex carbon substrate in sifed by the antibiotic and secondary metabolite methylotroph growth medium can aid in the analysis shell (antiSMASH) (Blin et al., 2017). rapid analysis of new compounds produced However, the majority of predicted clusters were by a culture without laborious prefractiona- detected using ClusterFinder, which relies on more tion procedures, which may also help in high probabilistic (and less stringent) methods for BGC throughput screening approaches. identifcation (Cimermancic et al., 2014). Tis 3 Te chemically defned nature of the growth could suggest that methylotrophs produce diferent medium and simplicity of the carbon source compounds than those made by traditionally stud- also allows substrates with heavy labels such as ied organisms, which would be promising for the 15 13 13 NO3 and CH4 or CH3OH to be used for discovery of new classes of compounds. However, minimal cost, which can aid in structural elu- sequence homology-based comparisons to char- cidation using mass spectrometry and NMR. acterized BGCs and experimental verifcation will 4 If a molecule with atractive properties is be essential to exploring the hypothesis that these identifed, its methylotroph producer can gene clusters are producing novel products. be grown at scale using a feedstock such as methane or methanol, both of which have recently re-emerged as substrates of interest in Intercellular chemical industrial microbiology (Schrader et al., 2009; communication Henard and Guarnieri, 2018). Quorum sensing It is therefore worthwhile to discover more Quorum sensing (QS) allows bacteria to con- molecules produced by this ecologically important trol gene expression in a cell density-dependent group of bacteria. manner. In Proteobacteria, a canonical QS signal Genome sequencing eforts supported by enti- is the acyl-homoserine lactone (acyl-HSL), which ties including the Joint Genome Institute (JGI) can vary in its acyl chain length, saturation, and oxi- and Organization for Methanotroph Genome dation. Tese signals are produced by LuxI-family Analysis (OMeGA) have enabled a detailed exami- acyl-HSL synthases, and detected by LuxR-family nation of the predicted biosynthetic potential of receptor/transcription factors. For reviews please many methylotrophic species (Fig. 12.1). Amongst see Papenfort and Bassler (2016) as well as White- the strains analysed here, more BGCs are generally ley et al. (2017). predicted in methanotroph genomes compared Te frst QS system to be characterized in a meth- with the genomes of non-methanotrophic ylotroph was in the model strain Methylobacterium methylotrophs. Overall the Alphaproteobacteria, extorquens AM1 (Penalver et al., 2006). Research- including members of the Methylobacterium genus ers found that AM1 possesses two LuxI-family among the non-methanotrophs, appear to possess synthases, termed MlaI and MsaI. While MsaI pro- a large number of predicted BGCs. Te Methylobac- duces the short chain acyl-HSLs C6- and C8-HSL, terium genus was also highlighted for its substantial MlaI produces the more unusual unsaturated long Curr. Issues Mol. Biol. (2019) Vol. 33 caister.com/cimb | Figure 1. Methylotroph Specialized Metabolites 213 Figure 12.1 Predicted biosynthetic gene clusters in genomes of methylotrophic Proteobacteria. Predictions were made using antiSMASH 4.1.0 (Blin et al., 2017) with ClusterFinder (CF) (Cimermancic et al., 2014) enabled with default settings. HSL, homoserine lactone; NRPS, non-ribosomal peptide synthetase; PKS, polyketide synthase. Curr. Issues Mol. Biol. (2019) Vol. 33 caister.com/cimb 214 | Puri chain molecules 7Z-C14-HSL and 2E,7Z-C14-HSL tundrenone (see below) (Puri et al., 2018). Te fact only when AM1 is grown on methanol (Table that tundrenone is produced in a QS-dependent 12.1). Te short chain acyl-HSLs produced by M. manner fts the paradigm that QS systems ofen extorquens AM1 increase the production of exopol- activate the production of extracellular factors such ysaccharide (Penalver et al., 2006), and therefore as antibiotics (McGowan et al., 1995; Duerkop could have a role in bioflm formation. In support et al., 2009) and proteases (Pearson et al., 1997), of this, recently a highly homologous QS system in thereby allowing bacteria to afect their surround- a Methylobacterium populi strain was found to regu- ing environment at high cell density. late the structure and adherence of bioflms made It will be exciting to characterize more methy- by this organism (Morohoshi et al., 2018). lotroph QS systems in the future and determine Many Methylobacterium species have been their biological roles. It should be noted that found to produce acyl-HSLs as detected by bio- methylotrophs occupy diverse ecological niches, assays (Poonguzhali et al., 2007). In one study including both acidic (Dedysh et al., 2000) and researchers found that the orange tree symbiont alkaline (Khmelenina et al., 1997) environments. Methylobacterium mesophilicum SR 1.6/6 produces Te HSL ring is subject to base-catalysed hydroly- several signals, including novel variants (Table sis (Schaefer et al., 2000; Dong et al., 2001), which 12.1) (Pomini et al., 2009). Tere is some evidence may provide one explanation for why methylo- that increased concentrations of these molecules trophs isolated from alkaline environments such as may regulate the transcription of metabolic genes some Methylomicrobium species do not possess
Load more

Recommended publications
  • Identification of Active Methylotroph Populations in an Acidic Forest Soil
    Microbiology (2002), 148, 2331–2342 Printed in Great Britain Identification of active methylotroph populations in an acidic forest soil by stable- isotope probing Stefan Radajewski,1 Gordon Webster,2† David S. Reay,3‡ Samantha A. Morris,1 Philip Ineson,4 David B. Nedwell,3 James I. Prosser2 and J. Colin Murrell1 Author for correspondence: J. Colin Murrell. Tel: j44 24 7652 2553. Fax: j44 24 7652 3568. e-mail: cmurrell!bio.warwick.ac.uk 1 Department of Biological Stable-isotope probing (SIP) is a culture-independent technique that enables Sciences, University of the isolation of DNA from micro-organisms that are actively involved in a Warwick, Coventry CV4 7AL, UK specific metabolic process. In this study, SIP was used to characterize the active methylotroph populations in forest soil (pH 35) microcosms that were exposed 2 Department of Molecular 13 13 13 13 and Cell Biology, to CH3OH or CH4. Distinct C-labelled DNA ( C-DNA) fractions were resolved University of Aberdeen, from total community DNA by CsCl density-gradient centrifugation. Analysis of Institute of Medical 16S rDNA sequences amplified from the 13C-DNA revealed that bacteria related Sciences, Foresterhill, Aberdeen AB25 2ZD, UK to the genera Methylocella, Methylocapsa, Methylocystis and Rhodoblastus had assimilated the 13C-labelled substrates, which suggested that moderately 3 Department of Biological Sciences, University of acidophilic methylotroph populations were active in the microcosms. Essex, Wivenhoe Park, Enrichments targeted towards the active proteobacterial CH3OH utilizers were Colchester, Essex CO4 3SQ, successful, although none of these bacteria were isolated into pure culture. A UK parallel analysis of genes encoding the key enzymes methanol dehydrogenase 4 Department of Biology, and particulate methane monooxygenase reflected the 16S rDNA analysis, but University of York, PO Box 373, YO10 5YW, UK unexpectedly revealed sequences related to the ammonia monooxygenase of ammonia-oxidizing bacteria (AOB) from the β-subclass of the Proteobacteria.
    [Show full text]
  • Adaptive Laboratory Evolution Enhances Methanol Tolerance and Conversion in Engineered Corynebacterium Glutamicum
    ARTICLE https://doi.org/10.1038/s42003-020-0954-9 OPEN Adaptive laboratory evolution enhances methanol tolerance and conversion in engineered Corynebacterium glutamicum Yu Wang 1, Liwen Fan1,2, Philibert Tuyishime1, Jiao Liu1, Kun Zhang1,3, Ning Gao1,3, Zhihui Zhang1,3, ✉ ✉ 1234567890():,; Xiaomeng Ni1, Jinhui Feng1, Qianqian Yuan1, Hongwu Ma1, Ping Zheng1,2,3 , Jibin Sun1,3 & Yanhe Ma1 Synthetic methylotrophy has recently been intensively studied to achieve methanol-based biomanufacturing of fuels and chemicals. However, attempts to engineer platform micro- organisms to utilize methanol mainly focus on enzyme and pathway engineering. Herein, we enhanced methanol bioconversion of synthetic methylotrophs by improving cellular tolerance to methanol. A previously engineered methanol-dependent Corynebacterium glutamicum is subjected to adaptive laboratory evolution with elevated methanol content. Unexpectedly, the evolved strain not only tolerates higher concentrations of methanol but also shows improved growth and methanol utilization. Transcriptome analysis suggests increased methanol con- centrations rebalance methylotrophic metabolism by down-regulating glycolysis and up- regulating amino acid biosynthesis, oxidative phosphorylation, ribosome biosynthesis, and parts of TCA cycle. Mutations in the O-acetyl-L-homoserine sulfhydrylase Cgl0653 catalyzing formation of L-methionine analog from methanol and methanol-induced membrane-bound transporter Cgl0833 are proven crucial for methanol tolerance. This study demonstrates the importance of
    [Show full text]
  • Isolation and Characterisation of Methylocystis Spp. for Poly-3
    Rumah et al. AMB Expr (2021) 11:6 https://doi.org/10.1186/s13568-020-01159-4 ORIGINAL ARTICLE Open Access Isolation and characterisation of Methylocystis spp. for poly-3-hydroxybutyrate production using waste methane feedstocks Bashir L. Rumah† , Christopher E. Stead† , Benedict H. Claxton Stevens , Nigel P. Minton , Alexander Grosse‑Honebrink and Ying Zhang* Abstract Waste plastic and methane emissions are two anthropogenic by‑products exacerbating environmental pollution. Methane‑oxidizing bacteria (methanotrophs) hold the key to solving these problems simultaneously by utilising otherwise wasted methane gas as carbon source and accumulating the carbon as poly‑3‑hydroxybutyrate, a biode‑ gradable plastic polymer. Here we present the isolation and characterisation of two novel Methylocystis strains with the ability to produce up to 55.7 1.9% poly‑3‑hydroxybutyrate of cell dry weight when grown on methane from diferent waste sources such as landfll± and anaerobic digester gas. Methylocystis rosea BRCS1 isolated from a recrea‑ tional lake and Methylocystis parvus BRCS2 isolated from a bog were whole genome sequenced using PacBio and Illumina genome sequencing technologies. In addition to potassium nitrate, these strains were also shown to grow on ammonium chloride, glutamine and ornithine as nitrogen source. Growth of Methylocystis parvus BRCS2 on Nitrate Mineral Salt (NMS) media with 0.1% methanol vapor as carbon source was demonstrated. The genetic tractability by conjugation was also determined with conjugation efciencies up to 2.8 10–2 and 1.8 10–2 for Methylocystis rosea BRCS1 and Methylocystis parvus BRCS2 respectively using a plasmid with ColE1× origin of ×replication. Finally, we show that Methylocystis species can produce considerable amounts of poly‑3‑hydroxybutyrate on waste methane sources without impaired growth, a proof of concept which opens doors to their use in integrated bio‑facilities like landflls and anaerobic digesters.
    [Show full text]
  • Downloaded from the Fungene Database (
    bioRxiv preprint doi: https://doi.org/10.1101/2020.09.21.307504; this version posted September 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Enhancement of nitrous oxide emissions in soil microbial consortia via copper competition between proteobacterial methanotrophs and denitrifiers Jin Chang,a,b Daehyun Daniel Kim,a Jeremy D. Semrau,b Juyong Lee,a Hokwan Heo,a Wenyu Gu,b* Sukhwan Yoona# aDepartment of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea bDepartment of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, 48109 Running Title: Methanotrophic influence on N2O emissions #Address correspondence to Sukhwan Yoon, [email protected]. *Present address: Department of Civil & Environmental Engineering, Stanford University, Palo Alto CA, 94305 bioRxiv preprint doi: https://doi.org/10.1101/2020.09.21.307504; this version posted September 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Unique means of copper scavenging have been identified in proteobacterial methanotrophs, particularly the use of methanobactin, a novel ribosomally synthesized post-translationally modified polypeptide that binds copper with very high affinity. The possibility that copper sequestration strategies of methanotrophs may interfere with copper uptake of denitrifiers in situ and thereby enhance N2O emissions was examined using a suite of laboratory experiments performed with rice paddy microbial consortia. Addition of purified methanobactin from Methylosinus trichosporium OB3b to denitrifying rice paddy soil microbial consortia resulted in substantially increased N2O production, with more pronounced responses observed for soils with lower copper content.
    [Show full text]
  • Isolation, Characterization and Substrate-Transport Studies of a New, Unique Methylotroph
    RICE UNIVERSITY ISOLATION, CHARACTERIZATION AND SUBSTRATE-TRANSPORT STUDIES OF A NEW, UNIQUE METHYLOTROPH by Thomas Alan Keuer A THESIS SUBMITTED IN PARTIAL FULFULLMENT OF THE REQUIREMENTS FOR THE DEGREE Master of Science APPROVED, THESIS COMMITTEE: E. Terry Papoutsakis, Assistant Professor of Chemical Engineering LarryOf. Mclntire, Professor and Chairman of Chemical Engineering <03^ ' Roger Storck, Professor of Biology Houston, Texas April, 1984 3 1272 00289 0232 ABSTRACT Keuer, Thomas A. M.S. Rice University, April 1984. Isolation, Characterization and Substrate-Transport Studies of a New, Unique Methylotroph. Major Professor: E. T. Papoutsakis. Methylotrophic bacteria which assimilate carbon via the Ribulose Monophosphate Pathway are bioenergetically superior to other methylotrophs. The dehydrogenases which catalyze the oxidation of formaldehyde to formate and formate to CO2 in RMP bacteria produce much of the ATP required for biosynthesis. A strain, designated T15, has been isolated on the basis of high In vitro activities of the above two key enzymes, and has been biochemically characterized. The new strain exhibits high yields (up to 0.63 g cells/g MeOH) and growth rates (up to 0.46 hr“^) in batch culture? however, the yields and growth rates in continuous culture are significantly lower. Study of the transport mechanisms has provided valuable insight into the relationship between substrate uptake and the growth characteristics of T15. Experi¬ ments with radiolabelled substrates have indicated that methanol enters the cells primarily by diffusion? consequently, the bacteria are not able to accumulate methanol internally in order to support efficient Ill continuous growth. Formaldehyde, on the other hand, is accumulated by an active transport system which depends on the A pH component of the membrane proton-motive force.
    [Show full text]
  • Bacterial Metabolism of Methylated Amines and Identification of Novel Methylotrophs in Movile Cave
    The ISME Journal (2015) 9, 195–206 & 2015 International Society for Microbial Ecology All rights reserved 1751-7362/15 www.nature.com/ismej ORIGINAL ARTICLE Bacterial metabolism of methylated amines and identification of novel methylotrophs in Movile Cave Daniela Wischer1, Deepak Kumaresan1,4, Antonia Johnston1, Myriam El Khawand1, Jason Stephenson2, Alexandra M Hillebrand-Voiculescu3, Yin Chen2 and J Colin Murrell1 1School of Environmental Sciences, University of East Anglia, Norwich, UK; 2School of Life Sciences, University of Warwick, Coventry, UK and 3Department of Biospeleology and Karst Edaphobiology, Emil Racovit¸a˘ Institute of Speleology, Bucharest, Romania Movile Cave, Romania, is an unusual underground ecosystem that has been sealed off from the outside world for several million years and is sustained by non-phototrophic carbon fixation. Methane and sulfur-oxidising bacteria are the main primary producers, supporting a complex food web that includes bacteria, fungi and cave-adapted invertebrates. A range of methylotrophic bacteria in Movile Cave grow on one-carbon compounds including methylated amines, which are produced via decomposition of organic-rich microbial mats. The role of methylated amines as a carbon and nitrogen source for bacteria in Movile Cave was investigated using a combination of cultivation studies and DNA stable isotope probing (DNA-SIP) using 13C-monomethylamine (MMA). Two newly developed primer sets targeting the gene for gamma-glutamylmethylamide synthetase (gmaS), the first enzyme of the recently-discovered indirect MMA-oxidation pathway, were applied in functional gene probing. SIP experiments revealed that the obligate methylotroph Methylotenera mobilis is one of the dominant MMA utilisers in the cave. DNA-SIP experiments also showed that a new facultative methylotroph isolated in this study, Catellibacterium sp.
    [Show full text]
  • Use of Endophytic and Rhizosphere Bacteria to Improve
    Use of Endophytic and Rhizosphere Bacteria To Improve Phytoremediation of Arsenic-Contaminated Industrial Soils by Autochthonous Betula celtiberica Victoria Mesa, Alejandro Navazas, Ricardo González, Aida González, Nele Weyens, Béatrice Lauga, Jose Luis R. Gallego, Jesús Sánchez, Ana Isabel Peláez To cite this version: Victoria Mesa, Alejandro Navazas, Ricardo González, Aida González, Nele Weyens, et al.. Use of Endophytic and Rhizosphere Bacteria To Improve Phytoremediation of Arsenic-Contaminated Indus- trial Soils by Autochthonous Betula celtiberica. Applied and Environmental Microbiology, American Society for Microbiology, 2017, 83 (8), 10.1128/AEM.03411-16. hal-01644095 HAL Id: hal-01644095 https://hal.archives-ouvertes.fr/hal-01644095 Submitted on 11 Jan 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. ENVIRONMENTAL MICROBIOLOGY crossm Use of Endophytic and Rhizosphere Bacteria To Improve Phytoremediation of Arsenic-Contaminated Industrial Soils Downloaded from by Autochthonous Betula celtiberica Victoria Mesa,a Alejandro Navazas,b,c Ricardo González-Gil,b Aida González,b Nele Weyens,c Béatrice Lauga,d Jose Luis R. Gallego,e Jesús Sánchez,a Ana Isabel Peláeza a Departamento de Biología Funcional–IUBA, Universidad de Oviedo, Oviedo, Spain ; Departamento de Biología http://aem.asm.org/ de Organismos y Sistemas–IUBA, Universidad de Oviedo, Oviedo, Spainb; Centre for Environmental Sciences (CMK), Hasselt University, Hasselt, Belgiumc; Equipe Environnement et Microbiologie (EEM), CNRS/Univ.
    [Show full text]
  • Characterization of Bacterial Communities Associated
    www.nature.com/scientificreports OPEN Characterization of bacterial communities associated with blood‑fed and starved tropical bed bugs, Cimex hemipterus (F.) (Hemiptera): a high throughput metabarcoding analysis Li Lim & Abdul Hafz Ab Majid* With the development of new metagenomic techniques, the microbial community structure of common bed bugs, Cimex lectularius, is well‑studied, while information regarding the constituents of the bacterial communities associated with tropical bed bugs, Cimex hemipterus, is lacking. In this study, the bacteria communities in the blood‑fed and starved tropical bed bugs were analysed and characterized by amplifying the v3‑v4 hypervariable region of the 16S rRNA gene region, followed by MiSeq Illumina sequencing. Across all samples, Proteobacteria made up more than 99% of the microbial community. An alpha‑proteobacterium Wolbachia and gamma‑proteobacterium, including Dickeya chrysanthemi and Pseudomonas, were the dominant OTUs at the genus level. Although the dominant OTUs of bacterial communities of blood‑fed and starved bed bugs were the same, bacterial genera present in lower numbers were varied. The bacteria load in starved bed bugs was also higher than blood‑fed bed bugs. Cimex hemipterus Fabricus (Hemiptera), also known as tropical bed bugs, is an obligate blood-feeding insect throughout their entire developmental cycle, has made a recent resurgence probably due to increased worldwide travel, climate change, and resistance to insecticides1–3. Distribution of tropical bed bugs is inclined to tropical regions, and infestation usually occurs in human dwellings such as dormitories and hotels 1,2. Bed bugs are a nuisance pest to humans as people that are bitten by this insect may experience allergic reactions, iron defciency, and secondary bacterial infection from bite sores4,5.
    [Show full text]
  • Widespread Soil Bacterium That Oxidizes Atmospheric Methane
    Widespread soil bacterium that oxidizes atmospheric methane Alexander T. Tveita,1, Anne Grethe Hestnesa,1, Serina L. Robinsona, Arno Schintlmeisterb, Svetlana N. Dedyshc, Nico Jehmlichd, Martin von Bergend,e, Craig Herboldb, Michael Wagnerb, Andreas Richterf, and Mette M. Svenninga,2 aDepartment of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, 9037 Tromsoe, Norway; bCenter of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria; cWinogradsky Institute of Microbiology, Research Center of Biotechnology of Russian Academy of Sciences, 117312 Moscow, Russia; dDepartment of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; eFaculty of Life Sciences, Institute of Biochemistry, University of Leipzig, 04109 Leipzig, Germany; and fCenter of Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, 1090 Vienna, Austria Edited by Mary E. Lidstrom, University of Washington, Seattle, WA, and approved March 7, 2019 (received for review October 22, 2018) The global atmospheric level of methane (CH4), the second most as-yet-uncultured clades within the Alpha- and Gammaproteobacteria important greenhouse gas, is currently increasing by ∼10 million (16–18) which were designated as upland soil clusters α and γ tons per year. Microbial oxidation in unsaturated soils is the only (USCα and USCγ, respectively). Interest in soil atmMOB has known biological process that removes CH4 from the atmosphere, increased significantly since then because they are responsible but so far, bacteria that can grow on atmospheric CH4 have eluded for the only known biological removal of atmospheric CH4 all cultivation efforts.
    [Show full text]
  • Global Molecular Analyses of Methane Metabolism in Methanotrophic Alphaproteobacterium, Methylosinus Trichosporium Ob3b
    ORIGINAL RESEARCH ARTICLE published: 03 April 2013 doi: 10.3389/fmicb.2013.00070 Global molecular analyses of methane metabolism in methanotrophic Alphaproteobacterium, Methylosinus trichosporium OB3b. Part II. metabolomics and 13C-labeling study SongYang 1, Janet B. Matsen1, Michael Konopka1, Abigail Green-Saxena2, Justin Clubb1, Martin Sadilek 3, Victoria J. Orphan4, David Beck 1,5 and Marina G. Kalyuzhnaya6* 1 Department of Chemical Engineering, University of Washington, Seattle, WA, USA 2 Division of Biology, California Institute of Technology, Pasadena, CA, USA 3 Department of Chemistry, University of Washington, Seattle, WA, USA 4 Division of Geological and Planetary Sciences; California Institute of Technology, Pasadena, CA, USA 5 eScience Institute, University of Washington, Seattle, WA, USA 6 Department of Microbiology, University of Washington, Seattle, WA, USA Edited by: In this work we use metabolomics and 13C-labeling data to refine central metabolic Amy V. Callaghan, University of pathways for methane utilization in Methylosinus trichosporium OB3b, a model alphapro- Oklahoma, USA teobacterial methanotrophic bacterium. We demonstrate here that similar to non-methane Reviewed by: Alan A. DiSpirito, Ohio State utilizing methylotrophic alphaproteobacteria the core metabolism of the microbe is rep- University, USA resented by several tightly connected metabolic cycles, such as the serine pathway, the Amy V. Callaghan, University of ethylmalonyl-CoA (EMC) pathway, and the citric acid (TCA) cycle. Both in silico estimations Oklahoma, USA and stable isotope labeling experiments combined with single cell (NanoSIMS) and bulk *Correspondence: biomass analyses indicate that a significantly larger portion of the cell carbon (over 60%) is Marina G. Kalyuzhnaya, Department 13 of Microbiology, University of derived from CO2 in this methanotroph.
    [Show full text]
  • Large Scale Biogeography and Environmental Regulation of 2 Methanotrophic Bacteria Across Boreal Inland Waters
    1 Large scale biogeography and environmental regulation of 2 methanotrophic bacteria across boreal inland waters 3 running title : Methanotrophs in boreal inland waters 4 Sophie Crevecoeura,†, Clara Ruiz-Gonzálezb, Yves T. Prairiea and Paul A. del Giorgioa 5 aGroupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), 6 Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Québec, Canada 7 bDepartment of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, 8 Catalunya, Spain 9 Correspondence: Sophie Crevecoeur, Canada Centre for Inland Waters, Water Science and Technology - 10 Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, 11 Burlington, Ontario, Canada, e-mail: [email protected] 12 † Current address: Canada Centre for Inland Waters, Water Science and Technology - Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Burlington, Ontario, Canada 1 13 Abstract 14 Aerobic methanotrophic bacteria (methanotrophs) use methane as a source of carbon and energy, thereby 15 mitigating net methane emissions from natural sources. Methanotrophs represent a widespread and 16 phylogenetically complex guild, yet the biogeography of this functional group and the factors that explain 17 the taxonomic structure of the methanotrophic assemblage are still poorly understood. Here we used high 18 throughput sequencing of the 16S rRNA gene of the bacterial community to study the methanotrophic 19 community composition and the environmental factors that influence their distribution and relative 20 abundance in a wide range of freshwater habitats, including lakes, streams and rivers across the boreal 21 landscape. Within one region, soil and soil water samples were additionally taken from the surrounding 22 watersheds in order to cover the full terrestrial-aquatic continuum.
    [Show full text]
  • The Methanol Dehydrogenase Gene, Mxaf, As a Functional and Phylogenetic Marker for Proteobacterial Methanotrophs in Natural Environments
    The Methanol Dehydrogenase Gene, mxaF, as a Functional and Phylogenetic Marker for Proteobacterial Methanotrophs in Natural Environments The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Lau, Evan, Meredith C. Fisher, Paul A. Steudler, and Colleen Marie Cavanaugh. 2013. The methanol dehydrogenase gene, mxaF, as a functional and phylogenetic marker for proteobacterial methanotrophs in natural environments. PLoS ONE 8(2): e56993. Published Version doi:10.1371/journal.pone.0056993 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:11807572 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Open Access Policy Articles, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#OAP The Methanol Dehydrogenase Gene, mxaF,asa Functional and Phylogenetic Marker for Proteobacterial Methanotrophs in Natural Environments Evan Lau1,2*, Meredith C. Fisher2, Paul A. Steudler3, Colleen M. Cavanaugh2 1 Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America, 2 Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America, 3 The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America Abstract The mxaF gene, coding for the large (a) subunit of methanol dehydrogenase, is highly conserved among distantly related methylotrophic species in the Alpha-, Beta- and Gammaproteobacteria. It is ubiquitous in methanotrophs, in contrast to other methanotroph-specific genes such as the pmoA and mmoX genes, which are absent in some methanotrophic proteobacterial genera.
    [Show full text]