DOCSLIB.ORG

Seasonal and Ecohydrological Regulation of Active Microbial Populations Involved in DOC, CO2, and CH4 fluxes in Temperate Rainforest Soil

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Seasonal and Ecohydrological Regulation of Active Microbial Populations Involved in DOC, CO2, and CH4 fluxes in Temperate Rainforest Soil The ISME Journal https://doi.org/10.1038/s41396-018-0334-3 ARTICLE Seasonal and ecohydrological regulation of active microbial populations involved in DOC, CO2, and CH4 fluxes in temperate rainforest soil 1,2 2,3 1,2 4 5 David J. Levy-Booth ● Ian J. W. Giesbrecht ● Colleen T. E. Kellogg ● Thierry J. Heger ● David V. D’Amore ● 6 1 1 Patrick J. Keeling ● Steven J. Hallam ● William W. Mohn Received: 9 February 2018 / Revised: 12 October 2018 / Accepted: 3 December 2018 © The Author(s) 2019. This article is published with open access Abstract The Pacific coastal temperate rainforest (PCTR) is a global hot-spot for carbon cycling and export. Yet the influence of microorganisms on carbon cycling processes in PCTR soil is poorly characterized. We developed and tested a conceptual model of seasonal microbial carbon cycling in PCTR soil through integration of geochemistry, micro-meteorology, and eukaryotic and prokaryotic ribosomal amplicon (rRNA) sequencing from 216 soil DNA and RNA libraries. Soil moisture and pH increased during the wet season, with significant correlation to net CO2 flux in peat bog and net CH4 flux in bog 1234567890();,: 1234567890();,: forest soil. Fungal succession in these sites was characterized by the apparent turnover of Archaeorhizomycetes phylotypes accounting for 41% of ITS libraries. Anaerobic prokaryotes, including Syntrophobacteraceae and Methanomicrobia increased in rRNA libraries during the wet season. Putatively active populations of these phylotypes and their biogeochemical marker genes for sulfate and CH4 cycling, respectively, were positively correlated following rRNA and metatranscriptomic network analysis. The latter phylotype was positively correlated to CH4 fluxes (r = 0.46, p < 0.0001). Phylotype functional assignments were supported by metatranscriptomic analysis. We propose that active microbial populations respond primarily to changes in hydrology, pH, and nutrient availability. The increased microbial carbon export observed over winter may have ramifications for climate–soil feedbacks in the PCTR. Introduction Soils of the Pacific coastal temperate rainforest (PCTR) of North America sequester globally important amounts of carbon (~198–900 Mg C ha−1)[1] and contribute some of Supplementary information The online version of this article (https:// the highest rates of dissolved organic carbon (DOC) export doi.org/10.1038/s41396-018-0334-3) contains supplementary − − material, which is available to authorized users. to coastal margins in the world (10.5–29.9 g C m 2 y 1) [2]. Soil CH fluxes in the PCTR range from uptake * 4 William W. Mohn (0.05–0.55 mg C m−2 h−1) in upland forests to strong [email protected] emissions (0–1.08 mg C m−2 h−1) from ombrotrophic peat 1 Department of Microbiology & Immunology, Life Sciences bogs [3]. Microbial communities regulate the flow of Institute, University of British Columbia, Vancouver, BC, Canada carbon through coastal ecosystems via decomposition 2 Hakai Institute, Tula Foundation, Heriot Bay, BC, Canada of plant biomass [4, 5], yet the controls on microbial carbon 3 School of Resource and Environmental Management, Simon cycling in hydric soils, such those in the PCTR, are little Fraser University, Burnaby, BC, Canada understood. 4 The University of Applied Sciences Western Switzerland, Nutrient limitation, low O2, and acidic soil in the PCTR CHANGINS, Delémont, Switzerland restrict organic matter degradation [6]. The carbohydrate- 5 U.S. Department of Agriculture, Forest Service, Pacific Northwest active enzymes (CAZy) database [7] can facilitate investi- Research Station, Juneau, Alaska, USA gation of carbon cycling in soil communities [8, 9], and fl 6 Department of Botany, University of British Columbia, reveal the ow of carbon and energy through peatlands Vancouver, British Columbia, Canada from biopolymer degradation to C1 metabolism [10]. D. J. Levy-Booth et al. It remains to be seen how environmental conditions in Material and Methods distinct seasons and ecohydrological classes affects micro- bial organic matter degradation and carbon cycling. Study location and site description Anaerobic metabolic pathways play a major role in the mineralization of organic carbon in waterlogged soils. The Calvert Island Field Station is located on an outer- Anaerobic degradation in these environments can overcome coast island in the Perhumid PCTR (Supplementary thermodynamic limitations through the maintenance of Figure 1), in the very wet hypermaritime coastal western low H2 concentrations by coupling fermentation by sulfate- hemlock zone (CWH vh2) zone [20]. The bog forest reducing bacteria (SRB) to the reduction CO2 to CH4 site (TSN2; N51°39′08″, W128°07′47″) is within CWH by hydrogenotrophic methanogens [11, 12]. This syntrophic vh2 site series 11. It contained shallow, nutrient poor interaction is a major component of metabolism in organic soils (80–125 cm depth) with distinct L, F, anaerobic bog soil [13], which may be stimulated by winter and H layers over Of, Om layers, and some unstructured precipitation in the PCTR. Quantifying carbon balance mineral material. The primary canopy contains Pinus due to these processes is imperative for reconciling annual contorta, Chamaecyparis nootkatensis, and Thuja plicata. terrestrial carbon budgets. The deep, ombrotrophic peat bog site (TSN3; N51°39′05″, Quantifying active microbial populations can reveal W128°07′43″) is in BEC CWH vh2 site series 32. It how communities respond to changing environmental contained deep (>2 m) peat-derived organic soil, with conditions and contribute to nutrient cycles. However, sparse P. contorta, C. nootkatensis, and T. plicata and limitations of methods of assessing active microbial groups abundant ericaceous shrubs on Sphagnum spp. lawns and must be addressed. Sufficient mRNA is difficult to extract hummocks. We use the term ecohydrological class for and purify from high-organic soils. Ribosomal RNA these sites to distinguish areas of discrete vegetation, soil (rRNA) can be recovered using high-throughput methods, depth, soil type, and hydrology. Peat bog and bog forest but cellular concentration is not well correlated with growth sites were chosen on the basis of terrestrial ecosystem rates in mixed communities [14]. Further, dormant cells mapping methods, to target ecohydrological classes that can contain detectable rRNA [15]. Yet, rRNA analysis are prevalent in the PCTR [21]. can potentially reduce bias due to dead or dormant cells [16]. As ribosome concentration indicates potential for Terrestrial sensor nodes protein synthesis and thus cellular activity, the analysis of rRNA may provide ecologically-meaningful insights Both sites contained: an HC-S3 air temperature and relative into dynamics of putatively active microbial community humidity probe and a TB4 rain-gauge controlled with a members [10, 17–19]. CR1000 datalogger (Campbell Scientific (Canada) Corp., To characterize in situ total (DNA libraries) and puta- Edmonton, Canada) and powered by solar arrays. Three tively active (rRNA libraries) microorganisms and their subplots per site each contained: three 109-L soil tem- role in DOC, CO2, and CH4 cycling and export we perature probes (Campbell Scientific (Canada) Corp.), three sequenced amplicons of archaeal and bacterial 16S rRNA, platinum soil redox potential probes with XR300 Ag/AgCl fungal ITS, and eukaryotic 18S rRNA (focused on soil Reference Electrodes (Radiometer America Inc., Brea, protists). Metatranscriptomics (mRNA) validated phylotype USA). Soil temperature and redox potential probes were functional assignment. We hypothesized that soil conditions placed at depths of 10, 25, and 40 cm in the bog forest in distinct ecohydrological classes (peat bog and bog site and 10, 20, and 30 cm in the peat bog site, with the forest) would structure total microbial communities (H1); depths corresponding to approximate median water table that putatively active microbial populations would addi- depth and the bounds of annual water table variability. tionally respond to micro-climactic variables in distinct seasons (H2); and that winter periods would increase Soil, water, and gas sampling and analysis anaerobic metabolic processes leading to increased net CH4 flux (H3). We demonstrated seasonal differences in On June 18, 2015 (early summer), July 23, 2015, July 25, the structure of putatively active microbial community 2015 (summer), October 28, 2015 (fall), February 28, 2016 members, including a response to previously uncharacter- (winter), and April 18, 2016 (spring), soil was sampled in ized increased pH and inorganic nitrogen concentrations each subplot at depths corresponding to sensor placement, in winter, resulting in enhanced net flux of both CO2 using a screw auger and peat coring device. Two cores per and CH4. Together, these data allowed us to develop subplot were pooled to give 216 total soil samples analyzed and assess a conceptual model of seasonal changes in for this work. Subsamples (5 g) for DNA and RNA microbial carbon cycling in major PCTR ecohydrological extraction were immediately frozen on dry ice. Frozen soil classes (Fig. 1a). was transferred to a V900 CryoPro Vapor Shipper (VWR Seasonal and ecohydrological regulation of active microbial populations involved in DOC,. A Ecohydrology B DOC Fluxes C Soil Microclimate -2 Bog Forest Ombrotrophic Peat Bog 3 At time of sampling 0.4 to 1.8 mg C m h CO 0 to 0.025 CH o 15 CO 0.3 to 2.1 mg C m h mg C 2 m h 10 CH -0.004 to 0 mg C m h Decomp. 1 5 Denitrifcation Monthly DOC g m 0 -1 2015-062015-072015-102016-022016-04 0 Methano-
Load more

Recommended publications
  • Evolution of Methanotrophy in the Beijerinckiaceae&Mdash
    The ISME Journal (2014) 8, 369–382 & 2014 International Society for Microbial Ecology All rights reserved 1751-7362/14 www.nature.com/ismej ORIGINAL ARTICLE The (d)evolution of methanotrophy in the Beijerinckiaceae—a comparative genomics analysis Ivica Tamas1, Angela V Smirnova1, Zhiguo He1,2 and Peter F Dunfield1 1Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada and 2Department of Bioengineering, School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, China The alphaproteobacterial family Beijerinckiaceae contains generalists that grow on a wide range of substrates, and specialists that grow only on methane and methanol. We investigated the evolution of this family by comparing the genomes of the generalist organotroph Beijerinckia indica, the facultative methanotroph Methylocella silvestris and the obligate methanotroph Methylocapsa acidiphila. Highly resolved phylogenetic construction based on universally conserved genes demonstrated that the Beijerinckiaceae forms a monophyletic cluster with the Methylocystaceae, the only other family of alphaproteobacterial methanotrophs. Phylogenetic analyses also demonstrated a vertical inheritance pattern of methanotrophy and methylotrophy genes within these families. Conversely, many lateral gene transfer (LGT) events were detected for genes encoding carbohydrate transport and metabolism, energy production and conversion, and transcriptional regulation in the genome of B. indica, suggesting that it has recently acquired these genes. A key difference between the generalist B. indica and its specialist methanotrophic relatives was an abundance of transporter elements, particularly periplasmic-binding proteins and major facilitator transporters. The most parsimonious scenario for the evolution of methanotrophy in the Alphaproteobacteria is that it occurred only once, when a methylotroph acquired methane monooxygenases (MMOs) via LGT.
    [Show full text]
  • Methanotrophic Bacterial Biomass As Potential Mineral Feed Ingredients for Animals
    International Journal of Environmental Research and Public Health Article Methanotrophic Bacterial Biomass as Potential Mineral Feed Ingredients for Animals Agnieszka Ku´zniar 1,*, Karolina Furtak 2 , Kinga Włodarczyk 1, Zofia St˛epniewska 1 and Agnieszka Woli ´nska 1 1 Department of Biochemistry and Environmental Chemistry, The John Paul II Catholic University of Lublin, Konstantynów St. 1 I, 20-708 Lublin, Poland 2 Department of Agriculture Microbiology, Institute of Soil Sciences and Plant Cultivation State Research Institute, Czartoryskich St. 8, 24-100 Puławy, Poland * Correspondence: [email protected]; Tel.: +48-81-454-5461 Received: 14 June 2019; Accepted: 23 July 2019; Published: 26 July 2019 Abstract: Microorganisms play an important role in animal nutrition, as they can be used as a source of food or feed. The aim of the study was to determine the nutritional elements and fatty acids contained in the biomass of methanotrophic bacteria. Four bacterial consortia composed of Methylocystis and Methylosinus originating from Sphagnum flexuosum (Sp1), S. magellanicum (Sp2), S. fallax II (Sp3), S. magellanicum IV (Sp4), and one composed of Methylocaldum, Methylosinus, and Methylocystis that originated from coalbed rock (Sk108) were studied. Nutritional elements were determined using the flame atomic absorption spectroscopy technique after a biomass mineralization stage, whereas the fatty acid content was analyzed with the GC technique. Additionally, the growth of biomass and dynamics of methane consumption were monitored. It was found that the methanotrophic biomass 1 contained high concentrations of K, Mg, and Fe, i.e., approx. 9.6–19.1, 2.2–7.6, and 2.4–6.6 g kg− , respectively.
    [Show full text]
  • Denitrification and the Hypoxic Response in Obligate Aerobic Methane-Oxidizing Bacteria
    Denitrification and the hypoxic response in obligate aerobic methane-oxidizing bacteria By Kerim Dimitri Kits A thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Microbiology and Biotechnology Department of Biological Sciences University of Alberta Kerim Dimitri Kits, 2016 Abstract Aerobic methanotrophic bacteria lessen the impact of the greenhouse gas methane (CH4) not only because they are a sink for atmospheric methane but also because they oxidize it before it is emitted to the atmospheric reservoir. Aerobic methanotrophs, unlike anaerobic methane oxidizing archaea, have a dual need for molecular oxygen (O2) for respiration and CH4 oxidation. Nevertheless, methanotrophs are highly abundant and active in environments that are extremely hypoxic and even anaerobic. While the O2 requirement in these organisms for CH4 oxidation is inflexible, recent genome sequencing efforts have uncovered the presence of putative denitrification genes in many aerobic methanotrophs. Being able to use two different terminal electron acceptors – hybrid respiration – would be massively advantageous to aerobic methanotrophs as it would allow them to halve their O2 requirement. But, the function of these genes that hint at an undiscovered respiratory anaerobic metabolism is unknown. Moreover, past work on pure cultures of aerobic methanotrophs ruled out the possibility that these organisms - denitrify. An organism that can couple CH4 oxidation to NO3 respiration so far does not exist in pure culture. So while the role of aerobic methanotrophs in the carbon cycle is appreciated, the hypoxic metabolism and contribution of these specialized microorganisms to the nitrogen cycle is not understood. Here we demonstrate using cultivation dependent approaches, microrespirometry, and whole genome, transcriptome, and proteome analysis that an aerobic - methanotroph – Methylomonas denitrificans FJG1 – couples CH4 oxidation to NO3 respiration - with N2O as the terminal product via the intermediates NO2 and NO.
    [Show full text]
  • Computational and Experimental Approaches for Evaluating the Genetic Basis of Mitochondrial Disorders
    Computational and Experimental Approaches For Evaluating the Genetic Basis of Mitochondrial Disorders The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters. Lieber, Daniel Solomon. 2013. Computational and Experimental Citation Approaches For Evaluating the Genetic Basis of Mitochondrial Disorders. Doctoral dissertation, Harvard University. Accessed April 17, 2018 4:10:16 PM EDT Citable Link http://nrs.harvard.edu/urn-3:HUL.InstRepos:11158264 This article was downloaded from Harvard University's DASH Terms of Use repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA (Article begins on next page) Computational and Experimental Approaches For Evaluating the Genetic Basis of Mitochondrial Disorders A dissertation presented by Daniel Solomon Lieber to The Committee on Higher Degrees in Systems Biology in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Systems Biology Harvard University Cambridge, Massachusetts April 2013 © 2013 - Daniel Solomon Lieber All rights reserved. Dissertation Adviser: Professor Vamsi K. Mootha Daniel Solomon Lieber Computational and Experimental Approaches For Evaluating the Genetic Basis of Mitochondrial Disorders Abstract Mitochondria are responsible for some of the cell’s most fundamental biological pathways and metabolic processes, including aerobic ATP production by the mitochondrial respiratory chain. In humans, mitochondrial dysfunction can lead to severe disorders of energy metabolism, which are collectively referred to as mitochondrial disorders and affect approximately 1:5,000 individuals. These disorders are clinically heterogeneous and can affect multiple organ systems, often within a single individual.
    [Show full text]
  • Phd Thesis F.M. Kerckhof: the Methanotrophic Interactome
    The methanotrophic interactome: Microbial partnerships for sustainable methane cycling ir. Frederiek-Maarten Kerckhof 1 Notation index Promotors: Prof. dr. ir. Nico Boon Department of Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium. Dr. Kim Heylen Department of biochemistry and microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium. Members of the examination committee: Prof. dr. ir. Koen Dewettinck (Chairman) Laboratory of food technology and engineering, Faculty of bioscience engineering, Ghent University, Gent, Belgium Prof. dr. ir. Diederik Rousseau (Secretary) Laboratory of industrial water- and ecotechnology, Faculty of bioscience engineering, Ghent University, Kortrijk, Belgium Prof. dr. ir. Pascal Boeckx ISOFYS, Faculty of bioscience engineering, Ghent University, Gent, Belgium Prof. dr. Paul De Vos Laboratory of microbiology (LM-Ugent), Faculty of sciences, Ghent University, Ghent, Belgium Dr. Paul Bodelier Department of microbial ecology, Netherlands institute of ecology (NIOO-KNAW), Wageningen, The Netherlands Dr. Hannah Marchant Department of biogeochemistry, Max-Planck Institute (MPI) for Marine Microbiology, Bremen, Germany Dean Faculty of Bioscience Engineering Prof. dr. ir. Marc van Meirvenne Rector Ghent University Prof. dr. Anne De Paepe 2 The methanotrophic interactome: Microbial partnerships for sustainable methane cycling ir. Frederiek-Maarten Kerckhof Thesis submitted in fulfilment of the requirements for the degree of Doctor (Ph.D.) in Applied Biological Sciences 3 Notation index Titel van het doctoraat in het Nederlands: Het methanotroof interactoom: microbiële relaties voor een duurzame methaancyclus. Cover illustration by Tim Lacoere (www.timternet.be) “Sustainable interactomes” Chapter illustrations by Maarten Van Praet (www.maartenisdemax.be) Please refer to this work as: Kerckhof F.M. (2016). The methanotrophic interactome: microbial partnerships for sustainable methane cycling.
    [Show full text]
  • Metabolic Features of Aerobic Methanotrophs: News and Views Valentina N
    Metabolic Features of Aerobic Methanotrophs: News and Views Valentina N. Khmelenina*, Sergey Y. But, Olga N. Rozova and Yuri A. Trotsenko G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia. *Correspondence: [email protected] htps://doi.org/10.21775/cimb.033.085 Abstract halotolerant representatives are especially Tis review is focused on recent studies of carbon promising for industrial applications, as they are metabolism in aerobic methanotrophs that spe- genetically tractable due to the availability of a cifcally addressed the properties, distribution and variety of genetic manipulation tools (Kalyuzh- phylogeny of some of the key enzymes involved naya et al., 2015; Mustakhimov et al., 2015; Fu and in assimilation of carbon from methane. Tese Lidstrom, 2017; Garg et al., 2018). Te adaptation include enzymes involved in sugar synthesis and of halo- and thermotolerant methanotrophs to cleavage, conversion of intermediates of the tricar- extreme environmental conditions includes the boxylic acid cycle, as well as in osmoadaptation in acquisition of the specifc mechanisms for syn- halotolerant methanotrophs. thesis and reutilization of the compatible solutes. Tis review focuses on the recent studies of carbon metabolism in three model species of the aerobic Introduction methanotrophs Methylomicrobium alcaliphilum Methanotrophs inhabit a variety of ecosystems 20Z, Methylosinus trichosporium OB3b, and Methy- including soils, fresh and marine waters and sedi- lococcus capsulatus Bath. ments, saline and alkaline lakes, hot springs, rice paddies, peatlands, and tissues of higher organisms. Tey play a major role in both global carbon and The carbon assimilation global nitrogen cycles (Hanson and Hanson, 1996; pathways McDonald et al., 2008, Etwig et al., 2010; Khadem Methanotrophs obtain energy for growth pre- et al., 2010).
    [Show full text]
  • A New Cell Morphotype Among Methane Oxidizers: a Spiral-Shaped Obligately Microaerophilic Methanotroph from Northern Low-Oxygen Environments
    The ISME Journal (2016) 10, 2734–2743 © 2016 International Society for Microbial Ecology All rights reserved 1751-7362/16 www.nature.com/ismej ORIGINAL ARTICLE A new cell morphotype among methane oxidizers: a spiral-shaped obligately microaerophilic methanotroph from northern low-oxygen environments Olga V Danilova1, Natalia E Suzina2, Jodie Van De Kamp3, Mette M Svenning4, Levente Bodrossy3 and Svetlana N Dedysh1 1Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia; 2G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia; 3CSIRO Oceans and Atmosphere, Hobart, Tasmania, Australia and 4UiT The Arctic University of Norway, Department of Arctic and Marine Biology, Tromsø, Norway Although representatives with spiral-shaped cells are described for many functional groups of bacteria, this cell morphotype has never been observed among methanotrophs. Here, we show that spiral-shaped methanotrophic bacteria do exist in nature but elude isolation by conventional approaches due to the preference for growth under micro-oxic conditions. The helical cell shape may enable rapid motility of these bacteria in water-saturated, heterogeneous environments with high microbial biofilm content, therefore offering an advantage of fast cell positioning under desired high methane/low oxygen conditions. The pmoA genes encoding a subunit of particulate methane monooxygenase from these methanotrophs form a new genus-level lineage within the family Methylococcaceae, type Ib methanotrophs. Application of a pmoA-based microarray detected these bacteria in a variety of high-latitude freshwater environments including wetlands and lake sediments. As revealed by the environmental pmoA distribution analysis, type Ib methanotrophs tend to live very near the methane source, where oxygen is scarce.
    [Show full text]
  • Genome-Scale Metabolic Reconstruction and Metabolic Versatility of an Obligate Methanotroph Methylococcus Capsulatus Str. Bath
    bioRxiv preprint doi: https://doi.org/10.1101/349191; this version posted June 18, 2018. 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. 1 Genome-scale metabolic reconstruction and metabolic versatility of 2 an obligate methanotroph Methylococcus capsulatus str. Bath 3 4 Authors : Ankit Gupta1†, Ahmad Ahmad2†, Dipesh Chothwe1†, Midhun K. Madhu1, 5 Shireesh Srivastava2*, Vineet K. Sharma1* 6 7 Affiliation 8 1 Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, INDIA 9 2 International Centre For Genetic Engineering And Biotechnology, New Delhi, INDIA 10 †These authors have contributed equally to this work 11 *Corresponding Authors 12 13 Correspondence to be addressed: 14 Dr. Vineet K. Sharma 15 Address: IISER Bhopal, Bhopal By-Pass Road, Bhauri, Bhopal, Madhya Pradesh - 462066, 16 INDIA 17 Telephone: +91-755-6691401 18 Email-id: [email protected] 19 20 Dr. Shireesh Srivastava, Systems Biology for Biofuels Group, ICGEB Campus, Aruna Asaf 21 Ali Marg, New Delhi 110067 22 Telephone: +91-11-26741361 x 450 23 Email: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/349191; this version posted June 18, 2018. 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. 24 Abstract 25 The increase in greenhouse gases with high global warming potential such as methane is a 26 matter of concern and requires multifaceted efforts to reduce its emission and increase its 27 mitigation from the environment.
    [Show full text]
  • Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on Pmoa As Molecular Marker
    REVIEW published: 15 December 2015 doi: 10.3389/fmicb.2015.01346 Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker Claudia Knief* Institute of Crop Science and Resource Conservation – Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of Edited by: aerobic methanotrophs has resulted in thousands of sequences representing “unknown Svetlana N. Dedysh, methanotrophic bacteria.” This limits data interpretation due to restricted information Winogradsky Institute of Microbiology, Russia Academy of Science, Russia about these uncultured methanotrophs. A few groups of uncultivated methanotrophs Reviewed by: are assumed to play important roles in methane oxidation in specific habitats, while Marc Gregory Dumont, the biology behind other sequence clusters remains still largely unknown. The discovery University of Southampton, UK of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA Levente Bodrossy, CSIRO Ocean and Atmosphere, paralogs in methanotrophs requires that sequence clusters of uncultivated organisms Australia have to be interpreted with care. This review article describes the present diversity Paul Bodelier, Netherlands Institute of Ecology, of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene Netherlands sequence diversity. It summarizes current knowledge about cultivated and major clusters *Correspondence: of uncultivated methanotrophic bacteria and evaluates habitat specificity of these Claudia Knief bacteria at different levels of taxonomic resolution.
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2016/0237398 A1 Kalyuzhnaya Et Al
    US 2016O237398A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2016/0237398 A1 Kalyuzhnaya et al. (43) Pub. Date: Aug. 18, 2016 (54) METHODS OF MICROBIAL PRODUCTION (86). PCT No.: PCT/US1.4f61304 OF EXCRETED PRODUCTS FROM S371 (c)(1) METHANE AND RELATED BACTERIAL (2) Date: Apr. 15, 2016 STRANS Related U.S. Application Data (71) Applicant: UNIVERSITY OF WASHINGTON THROUGHTS CENTERFOR (60) Eyal application No. 61/892,909, filed on Oct. COMMERCIALIZATION, Seattle, s WA (US) Publication Classification (72) Inventors: Marina Kalyuzhnaya, Seattle, WA (51) Int. Cl. (US); Mary E. Lidstrom, Seattle, WA CI2N I/20 (2006.01) (US) CI2P 7/02 (2006.01) CI2P 7/40 (2006.01) (52) U.S. Cl. (73) Assignee: UNIVERSITY OF WASHINGTON CPC. CI2N 1/20 (2013.01); C12P 7/40 (2013.01); THROUGHTS CENTERFOR CI2P 7/02 (2013.01) COMMERCIALIZATION, Seattle, WA (US) (57) ABSTRACT The present disclosure is directed to methods of producing (21) Appl. No.: 15/029,968 excreted products through the fermentation of methane with methanotrophs. In certain embodiments, the methods are per (22) PCT Fled: Oct. 20, 2014 formed at low oxygen levels. Patent Application Publication Aug. 18, 2016 Sheet 1 of 16 US 2016/0237398 A1 ########~## 3#######~## {######################$$$ ########## #######~###3 ######### ("~~~~q)+":"~~~~q) ####§§§ VI"OI) sess ex www.ww.wn M w.rwise-- s - 8 s es se Patent Application Publication Aug. 18, 2016 Sheet 2 of 16 US 2016/0237398 A1 i s w s s as: s s vex &x s iii) Patent Application Publication Aug. 18, 2016 Sheet 3 of 16 US 2016/0237398 A1 -- ..
    [Show full text]
  • Contribution of Genome Characteristics to Assessment of Taxonomy of Obligate Methanotrophs J
    INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Apr. 1991, p. 301-305 Vol. 41, No. 2 0020-7713/91/020301-05$02.00/0 Copyright 0 1991, International Union of Microbiological Societies Contribution of Genome Characteristics to Assessment of Taxonomy of Obligate Methanotrophs J. P. BOWMAN,” L. I. SLY, AND A. C. HAYWARD Department of Microbiology, University of Queensland, Brisbane, Queensland, Australia 4072 The DNAs of a variety of obligate methanotrophic bacteria were analyzed for base composition and nucleotide distribution. Genome molecular weights were determined for representative strains. Similarity ‘\, maps attained by plotting DNA base composition versus nucleotide distribution and genome molecular weight showed that related species formed distinct clusters. Group I methanotrophs were found to form three clusters in both nucleotide distribution and genome size analyses. The first cluster consisted of five Methylomonas species, Methylomonas methanica, Methylomonas fodinarum, Methylomonas aurantiaca, “Methylomonas ru- bra,” and “Methylomonas agile.” The other clusters included both Methylomonas species and Methylococcus species, indicating the heterogeneity within these genera. One cluster contained low-G+ C-content Methylo- coccus strains and included Methylococcus whittenburyi, Methylococcus bovis, Methylococcus vinelandii, Methylococcus luteus, and ‘4Methylococcus ucrainicus. ” The type strains of Methylomonas pelagica and “Methylomonas alba” and a marine methanotrophic strain also clustered with the low-G+C-content Methylococcus
    [Show full text]
  • Cultivation of Methanotrophic Bacteria in Opposing Gradients of Methane and Oxygen Ingeborg Bussmann, Monali Rahalkar & Bernhard Schink
    Cultivation of methanotrophic bacteria in opposing gradients of methane and oxygen Ingeborg Bussmann, Monali Rahalkar & Bernhard Schink LS Mikrobielle O¨ kologie, Fachbereich Biologie, Universitat¨ Konstanz, Konstanz, Germany Correspondence: Ingeborg Bussmann, LS Abstract Mikrobielle O¨ kologie, Fachbereich Biologie, Universitat¨ Konstanz, Fach M 654, 78457 In sediments, methane-oxidizing bacteria live in opposing gradients of methane Konstanz, Germany. Tel.: 149 7531 883249; and oxygen. In such a gradient system, the fluxes of methane and oxygen are fax: 149 7531 884047; e-mail: controlled by diffusion and consumption rates, and the rate-limiting substrate is [email protected] maintained at a minimum concentration at the layer of consumption. Opposing gradients of methane and oxygen were mimicked in a specific cultivation set-up in Received 6 July 2005; revised 31 October 2005; which growth of methanotrophic bacteria occurred as a sharp band at either c.5or accepted 6 November 2005. 20 mm below the air-exposed end. Two new strains of methanotrophic bacteria First published online 24 January 2006. were isolated with this system. One isolate, strain LC 1, belonged to the Methylomonas genus (type I methantroph) and contained soluble methane doi:10.1111/j.1574-6941.2006.00076.x mono-oxygenase. Another isolate, strain LC 2, was related to the Methylobacter Editor: Gary King group (type I methantroph), as determined by 16S rRNA gene and pmoA sequence similarities. However, the partial pmoA sequence was only 86% related to cultured Keywords Methylobacter species. This strain accumulated significant amounts of formalde- freshwater sediment; gradient cultivation; Lake hyde in conventional cultivation with methane and oxygen, which may explain Constance; methanotrophs; Methylobacter ; why it is preferentially enriched in a gradient cultivation system.
    [Show full text]