Biology Faculty Articles
Title
A Molecular Systematic Survey of Cultured Microbial Associates of Deep-Water Marine Invertebrates
Document Type
Article
Publication Date
4-22-2005
Publication Title
Systematic and Applied Microbiology
Keywords
Alphaproteobacteria, Bacteria, Bacteroides, Betaproteobacteria, Cytophaga, DNA fingerprinting, DNA, Bacterial DNA, Ribosomal genetics, Flavobacteriaceae, Gammaproteobacteria, Genes, rRNA, Geologic sediments, Molecular sequence data, Phylogeny, Polymorphism, Restriction fragment length, RNA, 16S, Research support, Non-U.S. government research, Seawater, Sequence analysis, DNA
ISSN
0723-2020
Volume
28
Issue/No.
3
First Page
242
Last Page
264
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).
NSUWorks Citation
Sfanos, Karen S.; Dedra K. Harmody; Phat Dang; Angela Ledger; Shirley A. Pomponi; Peter McCarthy; and Jose V. Lopez. 2005. "A Molecular Systematic Survey of Cultured Microbial Associates of Deep-Water Marine Invertebrates." Systematic and Applied Microbiology 28, (3): 242-264. doi:10.1016/j.syapm.2004.12.002.
ORCID ID
0000-0002-1637-4125
ResearcherID
F-8809-2011
DOI
10.1016/j.syapm.2004.12.002
Comments
©2004 Elsevier GmbH. All rights reserved.