A Molecular Systematic Survey of Cultured Microbial Associates of Deep-Water Marine Invertebrates

Karen S. Sfanos; Dedra K. Harmody; Phat Dang; Angela Ledger; Shirley A. Pomponi; Peter McCarthy; Jose V Lopez

doi:10.1016/j.syapm.2004.12.002

A Molecular Systematic Survey of Cultured Microbial Associates of Deep-Water Marine Invertebrates

Karen S. Sfanos
, Dedra K. Harmody
, Phat Dang
, Angela Ledger
, Shirley A. Pomponi
, Peter McCarthy
, Jose V Lopez

Research output: Contribution to journal › Article › peer-review

101 Scopus citations

Abstract

A taxonomic survey was conducted to determine the microbial diversity held within the Harbor Branch Oceanographic Marine Microbial Culture Collection (HBMMCC). The collection consists of approximately 17,000 microbial isolates, with 11,000 from a depth of greater than 150 ft seawater. A total of 2273 heterotrophic bacterial isolates were inventoried using the DNA fingerprinting technique amplified rDNA restriction analysis on approximately 750–800 base pairs (bp) encompassing hypervariable regions in the 5′ portion of the small subunit (SSU) 16S rRNA gene. Restriction fragment length polymorphism patterns obtained from restriction digests with RsaI, HaeIII, and HhaI were used to infer taxonomic similarity. SSU 16S rDNA fragments were sequenced from a total of 356 isolates for more definitive taxonomic analysis. Sequence results show that this subset of the HBMMCC contains 224 different phylotypes from six major bacterial clades (Proteobacteria (Alpha, Beta, Gamma), Cytophaga, Flavobacteria, and Bacteroides (CFB), Gram+ high GC content, Gram+ low GC content). The 2273 microorganisms surveyed encompass 834 α-Proteobacteria (representing 60 different phylotypes), 25 β-Proteobacteria (3 phylotypes), 767 γ-Proteobacteria (77 phylotypes), 122 CFB (17 phylotypes), 327 Gram+ high GC content (43 phylotypes), and 198 Gram+ low GC content isolates (24 phylotypes). Notably, 11 phylotypes were ⩽93% similar to the closest sequence match in the GenBank database even after sequencing a larger portion of the 16S rRNA gene (∼1400 bp), indicating the likely discovery of novel microbial taxa. Furthermore, previously reported “uncultured” microbes, such as sponge-specific isolates, are part of the HBMMCC. The results of this research will be available online as a searchable taxonomic database (www.hboi.edu/dbmr/dbmr_hbmmd.html).

Original language	American English
Pages (from-to)	242-264
Number of pages	23
Journal	Systematic and Applied Microbiology
Volume	28
Issue number	3
DOIs	https://doi.org/10.1016/j.syapm.2004.12.002
State	Published - Apr 22 2005
Externally published	Yes

Funding

This material is based upon work supported by the National Science Foundation under Grant No. DEB-0103668 to JVL and PJM. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation. This research was also supported by a Gertrude E. Skelly Charitable Foundation graduate fellowship to KSS. We thank Christine Politz, Katie Olds, Nicolas Joannin, Kathleen Janda, Dr. Amy Wright, and John Reed, and Harbor Branch Oceanographic Institution for their assistance and support. The manuscript was improved by comments on early drafts by Cheryl Peterson and Dr. Ute Hentschel, Dr. Wolfram Bruck and Dr. Robert Thacker. This manuscript is Harbor Branch Oceanographic Institution contribution HBOI #1569.

Funders
Gertrude E. Skelly Charitable Foundation
National Science Foundation

ASJC Scopus Subject Areas

Applied Microbiology and Biotechnology
Ecology, Evolution, Behavior and Systematics
Microbiology

Keywords

16S
Alphaproteobacteria
Bacteria
Bacterial DNA
Bacteroides
Betaproteobacteria
Cytophaga
DNA
DNA fingerprinting
Flavobacteriaceae
Gammaproteobacteria
Genes
Geologic sediments
Molecular sequence data
Non-U.S. government research
Phylogeny
Polymorphism
RNA
Research support
Restriction fragment length
Ribosomal genetics
Seawater
Sequence analysis
rRNA
16S rRNA
Culture collection
Marine microorganisms
Sponge symbiosis

Disciplines

Biology
Genetics
Genetics and Genomics
Life Sciences
Marine Biology
Other Genetics and Genomics

Access to Document

10.1016/j.syapm.2004.12.002

Cite this

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title = "A Molecular Systematic Survey of Cultured Microbial Associates of Deep-Water Marine Invertebrates",

abstract = "A taxonomic survey was conducted to determine the microbial diversity held within the Harbor Branch Oceanographic Marine Microbial Culture Collection (HBMMCC). The collection consists of approximately 17,000 microbial isolates, with 11,000 from a depth of greater than 150 ft seawater. A total of 2273 heterotrophic bacterial isolates were inventoried using the DNA fingerprinting technique amplified rDNA restriction analysis on approximately 750–800 base pairs (bp) encompassing hypervariable regions in the 5′ portion of the small subunit (SSU) 16S rRNA gene. Restriction fragment length polymorphism patterns obtained from restriction digests with RsaI, HaeIII, and HhaI were used to infer taxonomic similarity. SSU 16S rDNA fragments were sequenced from a total of 356 isolates for more definitive taxonomic analysis. Sequence results show that this subset of the HBMMCC contains 224 different phylotypes from six major bacterial clades (Proteobacteria (Alpha, Beta, Gamma), Cytophaga, Flavobacteria, and Bacteroides (CFB), Gram+ high GC content, Gram+ low GC content). The 2273 microorganisms surveyed encompass 834 α-Proteobacteria (representing 60 different phylotypes), 25 β-Proteobacteria (3 phylotypes), 767 γ-Proteobacteria (77 phylotypes), 122 CFB (17 phylotypes), 327 Gram+ high GC content (43 phylotypes), and 198 Gram+ low GC content isolates (24 phylotypes). Notably, 11 phylotypes were ⩽93\% similar to the closest sequence match in the GenBank database even after sequencing a larger portion of the 16S rRNA gene (∼1400 bp), indicating the likely discovery of novel microbial taxa. Furthermore, previously reported “uncultured” microbes, such as sponge-specific isolates, are part of the HBMMCC. The results of this research will be available online as a searchable taxonomic database (www.hboi.edu/dbmr/dbmr\_hbmmd.html).",

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author = "Sfanos, \{Karen S.\} and Harmody, \{Dedra K.\} and Phat Dang and Angela Ledger and Pomponi, \{Shirley A.\} and Peter McCarthy and Lopez, \{Jose V\}",

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doi = "10.1016/j.syapm.2004.12.002",

language = "American English",

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AU - Sfanos, Karen S.

AU - Harmody, Dedra K.

AU - Dang, Phat

AU - Ledger, Angela

AU - Pomponi, Shirley A.

AU - McCarthy, Peter

AU - Lopez, Jose V

PY - 2005/4/22

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N2 - A taxonomic survey was conducted to determine the microbial diversity held within the Harbor Branch Oceanographic Marine Microbial Culture Collection (HBMMCC). The collection consists of approximately 17,000 microbial isolates, with 11,000 from a depth of greater than 150 ft seawater. A total of 2273 heterotrophic bacterial isolates were inventoried using the DNA fingerprinting technique amplified rDNA restriction analysis on approximately 750–800 base pairs (bp) encompassing hypervariable regions in the 5′ portion of the small subunit (SSU) 16S rRNA gene. Restriction fragment length polymorphism patterns obtained from restriction digests with RsaI, HaeIII, and HhaI were used to infer taxonomic similarity. SSU 16S rDNA fragments were sequenced from a total of 356 isolates for more definitive taxonomic analysis. Sequence results show that this subset of the HBMMCC contains 224 different phylotypes from six major bacterial clades (Proteobacteria (Alpha, Beta, Gamma), Cytophaga, Flavobacteria, and Bacteroides (CFB), Gram+ high GC content, Gram+ low GC content). The 2273 microorganisms surveyed encompass 834 α-Proteobacteria (representing 60 different phylotypes), 25 β-Proteobacteria (3 phylotypes), 767 γ-Proteobacteria (77 phylotypes), 122 CFB (17 phylotypes), 327 Gram+ high GC content (43 phylotypes), and 198 Gram+ low GC content isolates (24 phylotypes). Notably, 11 phylotypes were ⩽93% similar to the closest sequence match in the GenBank database even after sequencing a larger portion of the 16S rRNA gene (∼1400 bp), indicating the likely discovery of novel microbial taxa. Furthermore, previously reported “uncultured” microbes, such as sponge-specific isolates, are part of the HBMMCC. The results of this research will be available online as a searchable taxonomic database (www.hboi.edu/dbmr/dbmr_hbmmd.html).

AB - A taxonomic survey was conducted to determine the microbial diversity held within the Harbor Branch Oceanographic Marine Microbial Culture Collection (HBMMCC). The collection consists of approximately 17,000 microbial isolates, with 11,000 from a depth of greater than 150 ft seawater. A total of 2273 heterotrophic bacterial isolates were inventoried using the DNA fingerprinting technique amplified rDNA restriction analysis on approximately 750–800 base pairs (bp) encompassing hypervariable regions in the 5′ portion of the small subunit (SSU) 16S rRNA gene. Restriction fragment length polymorphism patterns obtained from restriction digests with RsaI, HaeIII, and HhaI were used to infer taxonomic similarity. SSU 16S rDNA fragments were sequenced from a total of 356 isolates for more definitive taxonomic analysis. Sequence results show that this subset of the HBMMCC contains 224 different phylotypes from six major bacterial clades (Proteobacteria (Alpha, Beta, Gamma), Cytophaga, Flavobacteria, and Bacteroides (CFB), Gram+ high GC content, Gram+ low GC content). The 2273 microorganisms surveyed encompass 834 α-Proteobacteria (representing 60 different phylotypes), 25 β-Proteobacteria (3 phylotypes), 767 γ-Proteobacteria (77 phylotypes), 122 CFB (17 phylotypes), 327 Gram+ high GC content (43 phylotypes), and 198 Gram+ low GC content isolates (24 phylotypes). Notably, 11 phylotypes were ⩽93% similar to the closest sequence match in the GenBank database even after sequencing a larger portion of the 16S rRNA gene (∼1400 bp), indicating the likely discovery of novel microbial taxa. Furthermore, previously reported “uncultured” microbes, such as sponge-specific isolates, are part of the HBMMCC. The results of this research will be available online as a searchable taxonomic database (www.hboi.edu/dbmr/dbmr_hbmmd.html).

KW - 16S

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KW - Betaproteobacteria

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KW - DNA

KW - DNA fingerprinting

KW - Flavobacteriaceae

KW - Gammaproteobacteria

KW - Genes

KW - Geologic sediments

KW - Molecular sequence data

KW - Non-U.S. government research

KW - Phylogeny

KW - Polymorphism

KW - RNA

KW - Research support

KW - Restriction fragment length

KW - Ribosomal genetics

KW - Seawater

KW - Sequence analysis

KW - rRNA

KW - 16S rRNA

KW - Culture collection

KW - Marine microorganisms

KW - Sponge symbiosis

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JO - Systematic and Applied Microbiology

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A Molecular Systematic Survey of Cultured Microbial Associates of Deep-Water Marine Invertebrates

Abstract

Funding

ASJC Scopus Subject Areas

Keywords

Disciplines

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