Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2014 Feb 13;12(2):899-925.
doi: 10.3390/md12020899.

Bioprospecting From Marine Sediments of New Brunswick, Canada: Exploring the Relationship Between Total Bacterial Diversity and Actinobacteria Diversity

Affiliations
Free PMC article

Bioprospecting From Marine Sediments of New Brunswick, Canada: Exploring the Relationship Between Total Bacterial Diversity and Actinobacteria Diversity

Katherine Duncan et al. Mar Drugs. .
Free PMC article

Abstract

Actinomycetes are an important resource for the discovery of natural products with therapeutic properties. Bioprospecting for actinomycetes typically proceeds without a priori knowledge of the bacterial diversity present in sampled habitats. In this study, we endeavored to determine if overall bacterial diversity in marine sediments, as determined by 16S rDNA amplicon pyrosequencing, could be correlated with culturable actinomycete diversity, and thus serve as a powerful tool in guiding future bioprospecting efforts. Overall bacterial diversity was investigated in eight marine sediments from four sites in New Brunswick, Canada, resulting in over 44,000 high quality sequences (x = 5610 per sample). Analysis revealed all sites exhibited significant diversity (H' = 5.4 to 6.7). Furthermore, statistical analysis of species level bacterial communities (D = 0.03) indicated community composition varied according to site and was strongly influenced by sediment physiochemical composition. In contrast, cultured actinomycetes (n = 466, 98.3% Streptomyces) were ubiquitously distributed among all sites and distribution was not influenced by sediment composition, suggesting that the biogeography of culturable actinomycetes does not correlate with overall bacterial diversity in the samples examined. These actinomycetes provide a resource for future secondary metabolite discovery, as exemplified by the antimicrobial activity observed from preliminary investigation.

Figures

Figure 1
Figure 1
Phylum level comparison of bacterial community composition for eight sediment samples (“Rare Phyla” include all phyla comprising <1% of the total bacterial community composition).
Figure 2
Figure 2
Complete-linkage cluster analysis (based on Bray-Curtis similarity matrix with square root standardization) comparing species level bacterial communities between eight sediment samples. Sediments collected at high, mid or low tidemark indicated by H, M and L, respectively.
Figure 3
Figure 3
Complete-linkage cluster analysis (based on Bray-Curtis similarity matrix with square root standardization) comparing the chemical composition of eight sediment samples. Sediments collected at high, mid or low tidemark indicated by H, M and L, respectively.
Figure 4
Figure 4
Family level bacterial community composition within the order Actinomycetales of eight sediment samples. Numbers in brackets indicate the total number of Actinomycetales sequences in each sample.
Figure 5
Figure 5
Neighbor-joining tree showing the phylogenetic relationship of cultured actinomycetes obtained from New Brunswick sediments. Numbers at nodes indicate the degree of bootstrap support (%) based on 1000 iterations, only values ≥50% are shown. The scale bar represents percent sequence similarity. The sequence of Nocardiopsis lucentensis (NR024362.1) was used as an out-group. Collection site (1B, 2B, 3B, 4B, 5B, 6B, 7B, 8B) and antimicrobial activity of crude fermentation extracts against the microbial pathogens MRSA (“M” colored red), VRE (“V” colored yellow) and C. albicans (“C” colored green) are displayed adjacent to each subclade. The antimicrobial activity results are represented by the first number being the number of active (>50% cell lysis) strains, with the second number (after the slash) the total number of isolates tested from that clade and ‘nt’ represents not tested. The tree branches within the phylogenetic tree correspond to an individual isolate, a consensus sequence or a clade comprised of both. The number in brackets after clade name is total number of isolates in each clade or contig group. Consensus sequences from sequence groups sharing >99% sequence similarities to other isolates are labeled with a “NB\” prefix. The numbers of isolates in these sequence groups are shown in brackets after the NB\ group number.

Similar articles

See all similar articles

Cited by 15 articles

See all "Cited by" articles

References

    1. Bérdy J. Bioactive microbial metabolites. J. Antibiot. (Tokyo) 2005;58:1–26. doi: 10.1038/ja.2005.1. - DOI - PubMed
    1. Kieser T., Bibb M.J., Buttner M.J., Chater K.F., Hopwood D.A. Practical Streptomyces Genetics. 2nd ed. John Innes Foundation; Norwich, UK: 2000.
    1. Fischbach M.A., Walsh C.T. Antibiotics for emerging pathogens. Science. 2009;325:1089–1093. doi: 10.1126/science.1176667. - DOI - PMC - PubMed
    1. Koehn F.E., Carter G.T. Rediscovering natural products as a source of new drugs. Discov. Med. 2005;5:159–164. - PubMed
    1. Bredholt H., Fjaervik E., Johnsen G., Zotchev S.B. Actinomycetes from sediments in the Trondheim Fjord, Norway: Diversity and biological activity. Mar. Drugs. 2008;6:12–24. doi: 10.3390/md6010012. - DOI - PMC - PubMed

Publication types

LinkOut - more resources

Feedback