Taxonomy and biotransformation activities of some deep-sea actinomycetes

Abstract

Deep-sea soft sediments from trench systems and depths in the northwestern Pacific Ocean ranging from less than 300 to 10,897 m in depth have been analyzed for three target genera of actinomycetes: Micromonospora, Rhodococcus, and Streptomyces. Only culturable strains, recovered at atmospheric pressure on selective isolation media, have been examined to date. Maximum recoveries of culturable bacteria were greater that 10(7)/ml wet g sediment, but actinomycetes comprised a small proportion of this population (usually less than 1%). The target actinomycetes were isolated at all depths except from the Mariana Trench sediments. Actinomycete colonies were defined initially on the basis of colony morphologies, and preliminary identification then was made by chemotaxonomic tests. Pyrolysis mass spectrometry (PyMS) of deep-sea mycolic acid-containing actinomycetes gave excellent correspondence with numerical (phenetic) taxonomic analyses and subsequently was adopted as a rapid procedure for assessing taxonomic diversity. PyMS analysis enabled several clusters of deep-sea rhodococci to be distinguished that are quite distinct from all type strains. 16S rRNA gene sequence analysis has revealed that several of these marine rhodococci have sequences that are very similar to certain terrestrial species of Rhodococcus and to Dietzia. There is evidence for the intrusion of terrestrial runoff into these deep trench systems, and the inconsistency of the phenotypic and molecular taxonomies may reflect recent speciatiion events in actinomycetes under the high-pressure conditions of the deep sea. The results of DNA-DNA pairing experiments point to the novelty of Rhodococcus strains recovered from hadal depths in the Izu Bonin Trench. Biotransformation studies of deep-sea bacteria have focused on nitrile compounds. Nitrile-metabolizing bacteria, closely related to rhodococci, have been isolated that grow well at low temperature, high salt concentrations, and high pressures, suggesting that they are of marine origin or have adapted to the deep-sea environment.

Comparative actinomycete diversity in marine sediments

“…As in other cultivation-based studies of actinomycetes in marine sediments (e.g. Pisano et al 1989, Colquhoun et al 1998, the dominant genera recovered were Streptomyces and Micromonospora. As has also been previously observed (Weyland 1981, Jensen et al 1991, there was a shift in community composition from Streptomyces to Micromonospora between near-and off-shore samples (Fig.…”

“…These microorganisms have been recovered from diverse environments including rain forests (Wang et al 1999), lake sediments (Terkina et al 2002), estuaries (Takizawa et al 1993), and deep ocean trenches (Colquhoun et al 1998). With respect to the marine environment, it has long been known that actinomycetes can be cultured from ocean samples including sediments collected at depths > 3 km (Weyland 1969).…”

Chemolithotrophic nitrate-dependent Fe(II)-oxidizing nature of actinobacterial subdivision lineage TM3

“…Previous culture-independent studies have revealed the presence of deeply branching phylogenetic groups of Actinobacteria from various terrestrial and marine environments (Liesack and Stackebrandt, 1992;Colquhoun et al, 1998;Wohl and McArthur, 1998). These actinobacterial groups from soil have been designated as TM, forming three major clusters TM1, TM2 and TM3 (Rheims et al, 1996).…”

Search and Discovery Strategies for Biotechnology: the Paradigm Shift

“…Even the most cursory glance at the literature illustrates the pace and range of new microorganism discovery: completely novel bacteria being found in such commonplace environments as activated sludge (7,178,347), caves (191), and the human gut (430); novel rickettsial endosymbionts in common soil and water amebae (145); and high bacterial and genetic diversity in deep-sea sediments (79,80,290,382). However, this brief survey also raises several general issues of importance for the biotechnology search activity.…”