Skip to main content
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Microbiology Resource Announcements
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems
  • Log in
  • My alerts
  • My Cart

Main menu

  • Home
  • Articles
    • Latest Articles
    • Archive
  • Types of Resources
    • Amplicon Sequence Collections
    • Culture Collections/Mutant Libraries
    • Databases and Software
    • Omics Data Sets
    • Other Genetic Resources
    • Genome Sequences
  • For Authors
    • Getting Started
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About MRA
    • Editor in Chief
    • Board of Editors
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Microbiology Resource Announcements
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems

User menu

  • Log in
  • My alerts
  • My Cart

Search

  • Advanced search
Microbiology Resource Announcements
publisher-logosite-logo

Advanced Search

  • Home
  • Articles
    • Latest Articles
    • Archive
  • Types of Resources
    • Amplicon Sequence Collections
    • Culture Collections/Mutant Libraries
    • Databases and Software
    • Omics Data Sets
    • Other Genetic Resources
    • Genome Sequences
  • For Authors
    • Getting Started
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About MRA
    • Editor in Chief
    • Board of Editors
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
Prokaryotes

The Draft Genome Sequence of Sphingomonas sp. Strain FukuSWIS1, Obtained from Acidic Lake Grosse Fuchskuhle, Indicates Photoheterotrophy and a Potential for Humic Matter Degradation

Ivette Salka, Abhishek Srivastava, Martin Allgaier, Hans-Peter Grossart
Ivette Salka
aLeibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Abhishek Srivastava
aLeibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Martin Allgaier
aLeibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
bBerlin Center for Genomics in Biodiversity Research, Berlin, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Hans-Peter Grossart
aLeibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
cPotsdam University, Institute for Biochemistry and Biology, Potsdam, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/genomeA.01183-14
  • Article
  • Info & Metrics
  • PDF
Loading

ABSTRACT

Sphingomonas spp. are Alphaproteobacteria considered to be versatile bacteria that can utilize a variety of natural substrates available in terrestrial and aquatic systems. Sphingomonas sp. strain FukuSWIS1 was isolated from the eutrophic and acidic freshwater Lake Grosse Fuchskuhle in northeastern Germany. The strain has a genome size of 3.89 Mb, possesses a set of photosynthetic genes, and expresses photopigment BChl a under oxic conditions. Thus, this strain belongs to the aerobic anoxygenic phototrophic (AAP) bacteria, which are most likely involved in humic matter degradation as indicated by the presence of organic compound mineralizing genes.

GENOME ANNOUNCEMENT

Freshwater ecosystems were recently shown to possess a remarkable number of aerobic anoxygenic phototrophic (AAP) bacteria (1). These are heterotrophic bacteria that possess a photosystem allowing for anoxygenic photosynthesis under aerobic conditions, but simultaneously lack the ability to grow photoautotrophically (2). Several genomes of marine AAP bacteria provide insights into their metabolic capabilities. However, information on phylogenetic diversity and the genomic potential of freshwater AAP bacteria is still missing. A strain belonging to the genus Sphingomonas was isolated from the acidic, humic-rich Lake Grosse Fuchskuhle (53°105774N,12°98454553E) located in northeastern Germany. Here, we briefly outline the ecologically relevant information from the genome of the freshwater Sphingomonas sp. strain FukuSWIS1 to obtain insights into their metabolic capabilities.

Sphingomonas sp. strain FukuSWIS1 genome sequencing was performed at the Berlin Center for Genomics in Biodiversity Research (BeGenDiv, http://www.begendiv.de/) using the Illumina MiSeq system following the 2×150-bp paired-end sequencing workflow. Genomic sequencing libraries were prepared using an Illumina TruSeq DNA sample preparation kit following the manufacturer's instructions. Sequencing reads were de novo assembled using Velvet assembler (v1.2.10) (3) with k-mers of 63 for this genome. We generated 288 DNA scaffolds out of the shotgun assembly from the FukuSWIS1 genome, with N50 values of 30. The contigs of this genome were submitted to MG-RAST (4) and IMG-ER (5) for annotation and data analysis. This represents a draft genome size of 3.89 Mb, and the G+C content was found to be 65%. Strain FukuSWIS1 has 50 tRNA-coding genes and only one 5S rRNA gene, aside from one gene encoding for 16S rRNA and 23S rRNA. 16S rRNA gene sequence similarity was highest for the 16S rRNA gene sequence belonging to Sphingomonas sp. M3C203B-B obtained from Lake Vostok ice accretion in Antarctica (6).

The strain expresses photopigment BChl a under aerobic conditions and represents an orange-pigmented, rod-shaped Gram-negative alphaproteobacterium. Genes involved in the synthesis of the photosynthetic reaction centers (pufBALM genes) and bacteriochlorophyll a (bchCXYZ genes) biosynthesis are present in its genome, which suggest their capability to use light as an energy source. The presence of carotenoid genes (crtZW-CYIB) indicates the formation of beta-carotene, which potentially participates in the functionality of another photopigment coded in the genome, i.e., bacteriorhodopsin. Genes involved in autotrophic carbon fixation, however, are missing in the draft genome and might underline their photoheterotrophic character. This Sphingomonas strain possesses genes encoding for aromatic compound decomposition (like ring-cleavage extradiol dioxygenase-encoding and protocatechuate 3,4-dioxygenase-encoding genes) and harbor several genes coding for cell-wall degradation, e.g., cellulose 1,4-beta-cellobiosidase-, beta-xylosidase-, and xylanase-encoding genes. Therefore, humic-rich substrates in lakes may serve as a potential target for microbes to sustain their cellular metabolic processes. The presence of iron sequestering genes in its genome hints at their capability to counter iron-limited scenarios like in acidic and humic-matter-rich lake ecosystems. Overall, light energy not only seems to be directly harvested by Sphingomonas “light-harvesting-complexes,” but the photodegradation products of humic matter can also be channeled into the central metabolic pathway. A detailed genome comparison with other genomes (e.g., Sphingomonas sp. FukuSWIS6.2 from oligotrophic Lake Stechlin, Genbank accession number JPDP00000000) will shed more light upon the lifestyle exhibited by cosmopolitan Sphingomonas sp. strain FukuSWIS1.

Nucleotide sequence accession number.The whole-genome shotgun information for Sphingomonas sp. strain FukuSWIS1 was submitted to GenBank under the accession no. JPJC00000000.

ACKNOWLEDGMENTS

We thank Susan Mbedi and Solvig Pinnow for providing excellent technical support in the lab. We also thank Stefanie Hartmann for supporting the assembly of the two genomes. We are equally thankful to Juan Antonio García and Mitaly Srivastava for their help with file formatting.

This work was financially supported by the ESF project “FREDI” (DFG, GR 1540/17-1), the “REAL” project (pact for innovation and research of the Gottfried Wilhelm Leibniz scientific community), and the EU Marie Curie project HUMADE (FP-7 PEOPLE Programme, Marie Curie Actions, proposal 276680).

We declare no competing interests.

FOOTNOTES

    • Received 2 October 2014.
    • Accepted 3 October 2014.
    • Published 13 November 2014.
  • Copyright © 2014 Salka et al.

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

REFERENCES

  1. 1.↵
    1. Salka I,
    2. Cuperová Z,
    3. Mašín M,
    4. Koblížek M,
    5. Grossart HP
    . 2011. Rhodoferax-related pufM gene cluster dominates the aerobic anoxygenic phototrophic communities in German freshwater lakes. Environ. Microbiol. 13:2865–2875. doi:10.1111/j.1462-2920.2011.02562.x.
    OpenUrlCrossRefPubMedWeb of Science
  2. 2.↵
    1. Yurkov V,
    2. Csotonyi JT
    . 2009. New light on aerobic anoxygenic phototrophs. Adv. Photosynth. Res. 28:31–55. doi:10.1007/978-1-4020-8815-5_3.
    OpenUrlCrossRef
  3. 3.↵
    1. Zerbino DR,
    2. Birney E
    . 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821–829. doi:10.1101/gr.074492.107.
    OpenUrlAbstract/FREE Full Text
  4. 4.↵
    1. Meyer F,
    2. Paarmann D,
    3. D'souza M,
    4. Olson R,
    5. Glass EM,
    6. Kubal M,
    7. Paczian T,
    8. Rodriguez A,
    9. Stevens R,
    10. Wilke A,
    11. Wilkening J,
    12. Edwards RA
    . 2008. The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386. doi:10.1186/1471-2105-9-386.
    OpenUrlCrossRefPubMed
  5. 5.↵
    1. Markowitz VM,
    2. Chen IM,
    3. Palaniappan K,
    4. Chu K,
    5. Szeto E,
    6. Grechkin Y,
    7. Ratner A,
    8. Jacob B,
    9. Huang J,
    10. Williams P,
    11. Huntemann M,
    12. Anderson I,
    13. Mavromatis K,
    14. Ivanova NN,
    15. Kyrpides NC
    . 2012. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res. 40:D115–D122. doi:10.1093/nar/gkr1044.
    OpenUrlCrossRefPubMedWeb of Science
  6. 6.↵
    1. Christner BC,
    2. Mosley-Thompson E,
    3. Thompson LG,
    4. Reeve JN
    . 2001. Isolation of bacteria and 16S rDNAs from Lake Vostok accretion ice. Environ. Microbiol. 3:570–577. doi:10.1046/j.1462-2920.2001.00226.x.
    OpenUrlCrossRefPubMedWeb of Science
PreviousNext
Back to top
Download PDF
Citation Tools
The Draft Genome Sequence of Sphingomonas sp. Strain FukuSWIS1, Obtained from Acidic Lake Grosse Fuchskuhle, Indicates Photoheterotrophy and a Potential for Humic Matter Degradation
Ivette Salka, Abhishek Srivastava, Martin Allgaier, Hans-Peter Grossart
Genome Announcements Nov 2014, 2 (6) e01183-14; DOI: 10.1128/genomeA.01183-14

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Print
Alerts
Sign In to Email Alerts with your Email Address
Email

Thank you for sharing this Microbiology Resource Announcements article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
The Draft Genome Sequence of Sphingomonas sp. Strain FukuSWIS1, Obtained from Acidic Lake Grosse Fuchskuhle, Indicates Photoheterotrophy and a Potential for Humic Matter Degradation
(Your Name) has forwarded a page to you from Microbiology Resource Announcements
(Your Name) thought you would be interested in this article in Microbiology Resource Announcements.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
The Draft Genome Sequence of Sphingomonas sp. Strain FukuSWIS1, Obtained from Acidic Lake Grosse Fuchskuhle, Indicates Photoheterotrophy and a Potential for Humic Matter Degradation
Ivette Salka, Abhishek Srivastava, Martin Allgaier, Hans-Peter Grossart
Genome Announcements Nov 2014, 2 (6) e01183-14; DOI: 10.1128/genomeA.01183-14
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • GENOME ANNOUNCEMENT
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
  • Info & Metrics
  • PDF

Related Articles

Cited By...

About

  • About MRA
  • Editor in Chief
  • Board of Editors
  • Policies
  • For Reviewers
  • For the Media
  • For Librarians
  • For Advertisers
  • Alerts
  • RSS
  • FAQ
  • Permissions
  • Journal Announcements

Authors

  • Getting Started
  • Submit a Manuscript
  • Author Warranty
  • Ethics
  • Contact Us
  • ASM Author Center

Follow #MRAJournal

@ASMicrobiology

       

ASM Journals

ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.

About ASM | Contact Us | Press Room

 

ASM is a member of

Scientific Society Publisher Alliance

 

American Society for Microbiology
1752 N St. NW
Washington, DC 20036
Phone: (202) 737-3600

Copyright © 2021 American Society for Microbiology | Privacy Policy | Website feedback

Online ISSN: 2576-098X