TY - JOUR
T1 - A molecular systematic survey of cultured microbial associates of deep-water marine invertebrates
AU - Sfanos, Karen
AU - Harmody, Dedra
AU - Dang, Phat
AU - Ledger, Angela
AU - Pomponi, Shirley
AU - McCarthy, Peter
AU - Lopez, Jose
N1 - Funding Information:
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.
PY - 2005/4/22
Y1 - 2005/4/22
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 rRNA
KW - Culture collection
KW - Marine microorganisms
KW - Sponge symbiosis
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U2 - 10.1016/j.syapm.2004.12.002
DO - 10.1016/j.syapm.2004.12.002
M3 - Article
C2 - 15900971
AN - SCOPUS:16244420113
SN - 0723-2020
VL - 28
SP - 242
EP - 264
JO - Systematic and Applied Microbiology
JF - Systematic and Applied Microbiology
IS - 3
ER -