For Publishers
DiscoveryMetadataPeer reviewHostingPublishing
For Researchers
JoinPublishReviewCollect
Register
Blog
About
Search
Advanced search
My ScienceOpen
Search
For Publishers
For Researchers
Blog
About
13
views
9
references
 Top references
cited by
0
    
0 reviews
 Review
0
comments
 Comment
0
recommends
+1 Recommend
0 collections
    0
    shares
      77
      similar
       All similar
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Draft Genome Sequence of Methanol-Utilizing Methylophilus sp. Strain OH31, Isolated from Pond Sediment in Hokkaido, Japan

      brief-report

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Methylophilus sp. strain OH31 was isolated from the sediment of the Ohno pond at Hokkaido University. Strain OH31 utilizes methanol as its energy source. Here, we present the draft genome sequence of Methylophilus sp. strain OH31.

          Related collections

          Most cited references9

          • Record: found
          • Abstract: not found
          • Article: not found

          tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence

          T. M. Lowe, S. Eddy (1997)
          Article 0 comments Cited 816 times – based on 0 reviews     Review now
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Molecular phylogeny of type II methane-oxidizing bacteria isolated from various environments.

            Jürgen Heyer, Valery F Galchenko, Peter F Dunfield (2002)
            Type II methane-oxidizing bacteria (MOB) were isolated from diverse environments, including rice paddies, pristine and polluted freshwaters and sediments, mangrove roots, upland soils, brackish water ecosystems, moors, oil wells, water purification systems and livestock manure. Isolates were identified based on morphological traits as either Methylocystis spp., Methylosinus sporium or Methylosinus trichosporium. Molecular phylogenies were constructed based on nearly complete 16S rRNA gene sequences, and on partial sequences of genes encoding PmoA (a subunit of particulate methane monooxygenase), MxaF (a subunit of methanol dehydrogenase) and MmoX (a subunit of soluble methane monooxygenase). The maximum pairwise 16S rDNA difference between isolates was 4.2%, and considerable variability was evident within the Methylocystis (maximum difference 3.6%). Due to this variability, some of the published 'specific' oligonucleotide primers for type II MOB exhibit multiple mismatches with gene sequences from some isolates. The phylogenetic tree constructed from pmoA gene sequences closely mirrored that constructed from 16S rDNA sequences, and both supported the presently accepted taxonomy of type II MOB. Contrary to previously published phylogenetic trees, morphologically distinguishable species were generally monophyletic based on pmoA or 16S rRNA gene sequences. This was not true for phylogenies constructed from mmoX and mxaF gene sequences. The phylogeny of mxaF gene sequences suggested that horizontal transfer of this gene may have occurred across type II MOB species. Soluble methane monooxygenase could not be detected in many Methylocystis strains either by an enzyme activity test (oxidation of naphthalene) or by PCR-based amplification of an mmoX gene.
            Article 0 comments Cited 21 times – based on 0 reviews     Review now
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Acidophilic methanotrophic communities from Sphagnum peat bogs.

              N Panikov, J Tiedje, Svetlana N. Dedysh (1998)
              Highly enriched methanotrophic communities (> 25 serial transfers) were obtained from acidic ombrotrophic peat bogs from four boreal forest sites. The enrichment strategy involved using media conditions that were associated with the highest rates of methane uptake by the original peat samples, namely, the use of diluted mineral medium of low buffering capacity, moderate incubation temperature (20 degrees C), and pH values of 3 to 6. Enriched communities contained a mixture of rod-shaped bacteria arranged in aggregates with a minor contribution of Hyphomicrobium-like cells. The growth stoichiometry of isolates was characteristic of methanotrophic bacteria (CH4/O2/CO2 = 1:1.1:0.59), with an average apparent yield of 0.41 +/- 0.03 g of biomass C/g of CH4-C. DNA from each enrichment yielded a PCR product of the expected size with primers for both mmoX and mmoY genes of soluble methane monooxygenase. Two types of sequences were obtained for PCR-amplified fragments of mmoX. One of them exhibited high identity to the mmoX protein of the Methylocystis-Methylosinus group, whereas the other showed an equal level of divergence from both the Methylosinus-Methylocystis group and Methylococcus capsulatus (Bath) and formed a distinct branch. The pH optimum for growth and for CH4 uptake was 4.5 to 5.5, which is very similar to that for the optimum CH4 uptake observed in the original peat samples. These methanotrophs are moderate acidophiles rather than acidotolerant organisms, since their growth rate and methane uptake were much lower at neutral pH. The growth of the methanotrophic community was enhanced by using media with a very low salt content (20 to 200 mg/liter), more typical of their natural environment. All four enriched communities grew on N-free medium.
              Article 0 comments Cited 18 times – based on 0 reviews     Review now
                Bookmark
                All references

                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Announc
                Journal ID (iso-abbrev): Genome Announc
                Journal ID (hwp): ga
                Journal ID (pmc): ga
                Journal ID (publisher-id): GA
                Title: Genome Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2169-8287
                Publication date (Electronic): 10 April 2014
                Publication date Collection: Mar-Apr 2014
                Volume: 2
                Issue: 2
                Electronic Location Identifier: e00274-14
                Affiliations
                [a ]Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
                [b ]Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
                Author notes
                Address correspondence to Wataru Kitagawa, w-kitagawa@ 123456aist.go.jp .
                [†]

                Deceased.

                Article
                Publisher ID: genomeA00274-14
                DOI: 10.1128/genomeA.00274-14
                PMC ID: 3983305
                PubMed ID: 24723716
                SO-VID: e6cf1e12-1ee9-413e-b030-dfe39e941188
                Copyright © Copyright © 2014 Kugo et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.

                History
                Date received : 11 March 2014
                Date accepted : 21 March 2014
                Page count
                Pages: 2
                Categories
                Subject: Prokaryotes
                Custom metadata
                cover-date March/April 2014
                access-type free

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

                Comments

                Comment on this article