publication . Article . Conference object . Other literature type . 2017

Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization

Slaby, Beate M; Hackl, Thomas; Horn, Hannes; Bayer, Kristina; Hentschel, Ute;
Open Access
  • Published: 11 Jul 2017
  • Country: Germany
Abstract
Marine sponges are ancient metazoans that are populated by distinct and highly diverse microbial communities. In order to obtain deeper insights into the functional gene repertoire of the Mediterranean sponge Aplysina aerophoba, we combined Illumina short-read and PacBio long-read sequencing followed by un-targeted metagenomic binning. We identified a total of 37 high-quality bins representing 11 bacterial phyla and two candidate phyla. Statistical comparison of symbiont genomes with selected reference genomes revealed a significant enrichment of genes related to bacterial defense (restriction-modification systems, toxin-antitoxin systems) as well as genes invol...
Subjects
free text keywords: European Union (EU), Horizon 2020, Grant Agreement No 679849, an integrated approach towards their preservation and sustainable exploitation [Deep-sea Sponge Grounds Ecosystems of the North Atlantic], SponGES, Original Article, Ecology, Evolution, Behavior and Systematics, Microbiology, Genome, Microbiome, Phylum, Bacterial phyla, Environmental biotechnology, Sponge, biology.organism_classification, biology, Metagenomics, Phylogenetics, Ecology
Funded by
EC| SEABIOTECH
Project
SEABIOTECH
From sea-bed to test-bed: harvesting the potential of marine microbes for industrial biotechnology
  • Funder: European Commission (EC)
  • Project Code: 311932
  • Funding stream: FP7 | SP1 | KBBE
,
EC| SponGES
Project
SponGES
Deep-sea Sponge Grounds Ecosystems of the North Atlantic: an integrated approach towards their preservation and sustainable exploitation
  • Funder: European Commission (EC)
  • Project Code: 679849
  • Funding stream: H2020 | RIA
Communities
EuroMarine
European Marine Science
Download fromView all 8 versions
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Article . 2017
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Provider: OceanRep
79 references, page 1 of 6

Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH. (2013). Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol 31: 533–538.23707974 [PubMed]

Alexander BE, Liebrand K, Osinga R, Van Der Geest HG, Admiraal W, Cleutjens JPM et al (2014). Cell turnover and detritus production in marine sponges from tropical and temperate benthic ecosystems. PLoS One 9: e109486.25289641 [OpenAIRE] [PubMed]

Alneberg J, Bjarnason BS, de Bruijn I, Schirmer M, Quick J, Ijaz UZ et al (2014). Binning metagenomic contigs by coverage and composition. Nat Methods 11: 1144–1150.25218180 [OpenAIRE] [PubMed]

Ankenbrand MJ, Hohlfeld S, Hackl T, Förster F. (2017). AliTV-interactive visualization of whole genome comparisons. PeerJ Comput Sci 3: e116.

Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kuliko v AS et al (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19: 455–477.22506599 [OpenAIRE] [PubMed]

Beims H, Wittmann J, Bunk B, Spröer C, Rohde C, Günther G et al (2015). Paenibacillus larvae-directed bacteriophage HB10c2 and its application in American foulbrood-affected honey bee larvae. Appl Environ Microbiol 81: AEM.00804–15.

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. (2007). GenBank. Nucleic Acids Res 35: D21–D25.17202161 [OpenAIRE] [PubMed]

Bordenstein SR, Theis KR. (2015). Host biology in light of the microbiome: Ten principles of holobionts and hologenomes. PLOS Biol 13: e1002226.26284777 [OpenAIRE] [PubMed]

Burgsdorf I, Slaby BM, Handley KM, Haber M, Blom J, Marshall CW et al (2015). Lifestyle evolution in cyanobacterial symbionts of sponges. MBio 6: e00391–15.26037118 [OpenAIRE] [PubMed]

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoul os J, Bealer K et al (2009). BLAST+: Architecture and applications. BMC Bioinformatics 10: 421.20003500 [OpenAIRE] [PubMed]

Chaisson MJ, Tesler G. (2012). Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics 13: 238.22988817 [OpenAIRE] [PubMed]

Chen Y. (2007).Functional genomics of the unicellular cyanobacterium Synechococcus elongatus PCC 7942. PhD thesis. Texas A&M University, Kingsville, TX, USA.

De Goeij JM, De Kluijver A, Van Duyl FC, Vacelet J, Wijffels RH, De Goeij AFPM et al (2009). Cell kinetics of the marine sponge Halisarca caerulea reveal rapid cell turnover and shedding. J Exp Biol 212: 3892–3900.19915132 [OpenAIRE] [PubMed]

DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K et al (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069–5072.16820507 [OpenAIRE] [PubMed]

Easson CG, Thacker RW. (2014). Phylogen etic signal in the community structure of host-specific microbiomes of tropical marine sponges. Front Microbiol 5: 1–11.24478763 [OpenAIRE] [PubMed]

79 references, page 1 of 6
Abstract
Marine sponges are ancient metazoans that are populated by distinct and highly diverse microbial communities. In order to obtain deeper insights into the functional gene repertoire of the Mediterranean sponge Aplysina aerophoba, we combined Illumina short-read and PacBio long-read sequencing followed by un-targeted metagenomic binning. We identified a total of 37 high-quality bins representing 11 bacterial phyla and two candidate phyla. Statistical comparison of symbiont genomes with selected reference genomes revealed a significant enrichment of genes related to bacterial defense (restriction-modification systems, toxin-antitoxin systems) as well as genes invol...
Subjects
free text keywords: European Union (EU), Horizon 2020, Grant Agreement No 679849, an integrated approach towards their preservation and sustainable exploitation [Deep-sea Sponge Grounds Ecosystems of the North Atlantic], SponGES, Original Article, Ecology, Evolution, Behavior and Systematics, Microbiology, Genome, Microbiome, Phylum, Bacterial phyla, Environmental biotechnology, Sponge, biology.organism_classification, biology, Metagenomics, Phylogenetics, Ecology
Funded by
EC| SEABIOTECH
Project
SEABIOTECH
From sea-bed to test-bed: harvesting the potential of marine microbes for industrial biotechnology
  • Funder: European Commission (EC)
  • Project Code: 311932
  • Funding stream: FP7 | SP1 | KBBE
,
EC| SponGES
Project
SponGES
Deep-sea Sponge Grounds Ecosystems of the North Atlantic: an integrated approach towards their preservation and sustainable exploitation
  • Funder: European Commission (EC)
  • Project Code: 679849
  • Funding stream: H2020 | RIA
Communities
EuroMarine
European Marine Science
Download fromView all 8 versions
ZENODO
Article . 2017
Provider: ZENODO
OceanRep
Article . 2017
Provider: OceanRep
OceanRep
Conference object . 2017
Provider: OceanRep
79 references, page 1 of 6

Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH. (2013). Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol 31: 533–538.23707974 [PubMed]

Alexander BE, Liebrand K, Osinga R, Van Der Geest HG, Admiraal W, Cleutjens JPM et al (2014). Cell turnover and detritus production in marine sponges from tropical and temperate benthic ecosystems. PLoS One 9: e109486.25289641 [OpenAIRE] [PubMed]

Alneberg J, Bjarnason BS, de Bruijn I, Schirmer M, Quick J, Ijaz UZ et al (2014). Binning metagenomic contigs by coverage and composition. Nat Methods 11: 1144–1150.25218180 [OpenAIRE] [PubMed]

Ankenbrand MJ, Hohlfeld S, Hackl T, Förster F. (2017). AliTV-interactive visualization of whole genome comparisons. PeerJ Comput Sci 3: e116.

Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kuliko v AS et al (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19: 455–477.22506599 [OpenAIRE] [PubMed]

Beims H, Wittmann J, Bunk B, Spröer C, Rohde C, Günther G et al (2015). Paenibacillus larvae-directed bacteriophage HB10c2 and its application in American foulbrood-affected honey bee larvae. Appl Environ Microbiol 81: AEM.00804–15.

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. (2007). GenBank. Nucleic Acids Res 35: D21–D25.17202161 [OpenAIRE] [PubMed]

Bordenstein SR, Theis KR. (2015). Host biology in light of the microbiome: Ten principles of holobionts and hologenomes. PLOS Biol 13: e1002226.26284777 [OpenAIRE] [PubMed]

Burgsdorf I, Slaby BM, Handley KM, Haber M, Blom J, Marshall CW et al (2015). Lifestyle evolution in cyanobacterial symbionts of sponges. MBio 6: e00391–15.26037118 [OpenAIRE] [PubMed]

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoul os J, Bealer K et al (2009). BLAST+: Architecture and applications. BMC Bioinformatics 10: 421.20003500 [OpenAIRE] [PubMed]

Chaisson MJ, Tesler G. (2012). Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics 13: 238.22988817 [OpenAIRE] [PubMed]

Chen Y. (2007).Functional genomics of the unicellular cyanobacterium Synechococcus elongatus PCC 7942. PhD thesis. Texas A&M University, Kingsville, TX, USA.

De Goeij JM, De Kluijver A, Van Duyl FC, Vacelet J, Wijffels RH, De Goeij AFPM et al (2009). Cell kinetics of the marine sponge Halisarca caerulea reveal rapid cell turnover and shedding. J Exp Biol 212: 3892–3900.19915132 [OpenAIRE] [PubMed]

DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K et al (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069–5072.16820507 [OpenAIRE] [PubMed]

Easson CG, Thacker RW. (2014). Phylogen etic signal in the community structure of host-specific microbiomes of tropical marine sponges. Front Microbiol 5: 1–11.24478763 [OpenAIRE] [PubMed]

79 references, page 1 of 6
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publication . Article . Conference object . Other literature type . 2017

Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization

Slaby, Beate M; Hackl, Thomas; Horn, Hannes; Bayer, Kristina; Hentschel, Ute;