Comparative actinomycete diversity in marine sediments

Abstract

The diversity of cultured actinomycete bacteria was compared between near-and offshore marine sediments. Strains were tested for the effects of seawater on growth and analyzed for 16S rRNA gene sequence diversity. In total, 623 strains representing 6 families in the order Actinomycetales were cultured. These strains were binned into 16 to 63 operational taxonomic units (OTUs) over a range of 97 to 100% sequence identity. The majority of the OTUs were closely related (> 98% sequence identity) to strains previously reported from non-marine sources, indicating that most are not restricted to the sea. However, new OTUs averaged 96.6% sequence identity with previously cultured strains and ca. one-third of the OTUs were marine-specific, suggesting that sediment communities include considerable actinomycete diversity that does not occur on land. Marine specificity did not increase at the off-shore sites, indicating high levels of terrestrial influence out to 125 km from shore. The requirement of seawater for growth was observed among < 6% of the strains, while all members of 9 OTUs possessed this trait, revealing a high degree of marine adaptation among some lineages. Statistical analyses predicted greater OTU diversity at the off-shore sites and provided a rationale for expanded exploration of deep-sea samples. A change in community composition was observed, with the number of Micromonospora OTUs increasing in the off-shore samples. UniFrac (see http://bmf2.colorado.edu/unifrac) statistics support a difference in community composition between near-and off-shore locations. Overall, 123 of 176 strains had distinct 16S rRNA gene sequences, indicating a high level of actinomycete diversity in marine sediments.

Phylogenetic and Chemical Diversity of a Hybrid-Isoprenoid-Producing Streptomycete Lineage

“…An additional 15 strains, isolated as part of prior studies (9,12,19) and considered candidates for the MAR4 clade on the basis of preliminary sequence data or secondary metabolite analysis, were also confirmed to be members of this lineage. To further expand the search, 13 diverse MAR4 sequences were used as queries of the NCBI database.…”

“…Phylogenetic analyses included previously identified MAR4 16S rRNA gene sequences (13), as well as strains cultured as part of the present study and strains cultured as part of prior studies (9,12,19) that were subsequently considered MAR4 candidates on the basis of sequence data or the production of HI secondary metabolites. Diverse MAR4 sequence representatives (accession numbers KC261629, KC261602, EF121313, KC261627, KC261626, X87316, NR041166, EF538742, KC261604, JF346436, EF581384, KC261611, and KC261615) were additionally used as BLASTn queries of the NCBI database.…”

“…They are also widely distributed in marine sediments (5,6), form symbiotic relationships with plants (7) and insects (8), and are observed in association with marine sponges (8). Some streptomycete lineages have been observed broadly both in soils and in marine sediments (9), suggesting a high degree of environmental flexibility.…”

Diacidene, a Polyene Dicarboxylic Acid from a Micromonospora Isolate from the German Wadden Sea

“…Marine sediments have proven a profi table habitat for the isolation of high numbers of Micromonosporaceae (Bredholt et al, 2008;Maldonado et al, 2008;Prieto-Davó et al, 2008). Our isolate, Micromonospora strain DB620, originated from the German Wadden Sea, a unique ecosystem characterized by large areas of tidal fl ats.…”

Diacidene, a Polyene Dicarboxylic Acid from a Micromonospora Isolate from the German Wadden Sea

“…Marine sediments have proven a profi table habitat for the isolation of high numbers of Micromonosporaceae (Bredholt et al, 2008;Maldonado et al, 2008;Prieto-Davó et al, 2008). Our isolate, Micromonospora strain DB620, originated from the German Wadden Sea, a unique ecosystem characterized by large areas of tidal fl ats.…”