Composition and predicted functional ecology of mussel - associated bacteria in Indonesian marine lakes

D.F.R. Cleary, L.E. Becking, A. Polonia, R.M. Freitas, N. Gomes

Research output: Contribution to journalArticleAcademicpeer-review

29 Citations (Scopus)

Abstract

In the present study, we sampled bacterial communities associated with mussels inhabiting two distinct coastal marine ecosystems in Kalimantan, Indonesia, namely, marine lakes and coastal mangroves. We used 16S rRNA gene pyrosequencing and predicted metagenomic analysis to compare microbial composition and function. Marine lakes are small landlocked bodies of seawater isolated to varying degrees from the open sea environment. They contain numerous endemic taxa and represent natural laboratories of speciation. Our primary goals were to (1) use BLAST search to identify closely related organisms to dominant bacterial OTUs in our mussel dataset and (2) to compare bacterial communities and enrichment in the predicted bacterial metagenome among lakes. Our sequencing effort yielded 3553 OTUs belonging to 44 phyla, 99 classes and 121 orders. Mussels in the largest marine lake (Kakaban) and the coastal mangrove habitat were dominated by bacteria belonging to the phylum Proteobacteria whereas smaller lakes, located on the island of Maratua, were dominated by bacteria belonging to the phyla Firmicutes and Tenericutes. The single most abundant OTU overall was assigned to the genus Mycoplasma. There were several significant differences among locations with respect to metabolic pathways. These included enrichment of xenobiotic biodegradation pathways in the largest marine lake and coastal mangrove. These locations were also the most enriched with respect to nitrogen metabolism. The presence of genes related to isoquinoline alkaloids, polyketides, hydrolases, mono and dioxygenases in the predicted analysis of functional pathways is an indication that the bacterial communities of Brachidontes mussels may be potentially important sources of new marine medicines and enzymes of industrial interest. Future work should focus on measuring how mussel microbial communities influence nutrient dynamics within the marine lake environment and isolating microbes with potential biotechnological applications.
Original languageEnglish
Pages (from-to)821-834
JournalAntonie van Leeuwenhoek: : Nederlandsch tijdschrift voor hygiëne, microbiologie en serologie
Volume107
Issue number3
DOIs
Publication statusPublished - 2015

Fingerprint

Bivalvia
Lakes
Ecology
Bacteria
Ecosystem
Tenericutes
Metagenome
Polyketides
Dioxygenases
Metagenomics
Proteobacteria
Occupational Medicine
Indonesia
Mycoplasma
Seawater
Hydrolases
Xenobiotics
Metabolic Networks and Pathways
rRNA Genes
Alkaloids

Keywords

  • microbial communities
  • brachidontes-exustus
  • scorched mussel
  • species complex
  • mytilidae
  • bivalvia
  • mycoplasma
  • diversity
  • islands
  • sequences

Cite this

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title = "Composition and predicted functional ecology of mussel - associated bacteria in Indonesian marine lakes",
abstract = "In the present study, we sampled bacterial communities associated with mussels inhabiting two distinct coastal marine ecosystems in Kalimantan, Indonesia, namely, marine lakes and coastal mangroves. We used 16S rRNA gene pyrosequencing and predicted metagenomic analysis to compare microbial composition and function. Marine lakes are small landlocked bodies of seawater isolated to varying degrees from the open sea environment. They contain numerous endemic taxa and represent natural laboratories of speciation. Our primary goals were to (1) use BLAST search to identify closely related organisms to dominant bacterial OTUs in our mussel dataset and (2) to compare bacterial communities and enrichment in the predicted bacterial metagenome among lakes. Our sequencing effort yielded 3553 OTUs belonging to 44 phyla, 99 classes and 121 orders. Mussels in the largest marine lake (Kakaban) and the coastal mangrove habitat were dominated by bacteria belonging to the phylum Proteobacteria whereas smaller lakes, located on the island of Maratua, were dominated by bacteria belonging to the phyla Firmicutes and Tenericutes. The single most abundant OTU overall was assigned to the genus Mycoplasma. There were several significant differences among locations with respect to metabolic pathways. These included enrichment of xenobiotic biodegradation pathways in the largest marine lake and coastal mangrove. These locations were also the most enriched with respect to nitrogen metabolism. The presence of genes related to isoquinoline alkaloids, polyketides, hydrolases, mono and dioxygenases in the predicted analysis of functional pathways is an indication that the bacterial communities of Brachidontes mussels may be potentially important sources of new marine medicines and enzymes of industrial interest. Future work should focus on measuring how mussel microbial communities influence nutrient dynamics within the marine lake environment and isolating microbes with potential biotechnological applications.",
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Composition and predicted functional ecology of mussel - associated bacteria in Indonesian marine lakes. / Cleary, D.F.R.; Becking, L.E.; Polonia, A.; Freitas, R.M.; Gomes, N.

In: Antonie van Leeuwenhoek: : Nederlandsch tijdschrift voor hygiëne, microbiologie en serologie, Vol. 107, No. 3, 2015, p. 821-834.

Research output: Contribution to journalArticleAcademicpeer-review

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T1 - Composition and predicted functional ecology of mussel - associated bacteria in Indonesian marine lakes

AU - Cleary, D.F.R.

AU - Becking, L.E.

AU - Polonia, A.

AU - Freitas, R.M.

AU - Gomes, N.

PY - 2015

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KW - brachidontes-exustus

KW - scorched mussel

KW - species complex

KW - mytilidae

KW - bivalvia

KW - mycoplasma

KW - diversity

KW - islands

KW - sequences

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DO - 10.1007/s10482-014-0375-1

M3 - Article

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SP - 821

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JO - Antonie van Leeuwenhoek: : Nederlandsch tijdschrift voor hygiëne, microbiologie en serologie

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SN - 0003-6072

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