Taxonomy and Biotransformation Activities of Some Deep-Sea Actinomycetes
Alan T. BULL*, Joy A. COLQUHOUN, and Stephen C. HEALD
Department of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
A major interest of our laboratory is the isolation of novel microorganisms for entry into biotechnology search and discovery programmes. The opportunity to collaborate with the DEEPSTAR Group of the Japan Marine Science and Technology Center has enabled us to explore deep sea soft sediments in this context. Sediments from trench systems and depths in the NW Pacific Ocean ranging from less than 300 m to the Challenger Deep in the Mariana Trench (10 897 m) have been analyzed for three target genera: Micromonospora, Rhodococcus and Streptomyces. Only culturable strains, isolated at atmospheric pressure, have been examined to date; a dispersion differential centrifugation procedure was used to maximize the recovery of bacteria from sediments. Maximum recoveries of culturable bacteria were greater that 106 per ml wet sediment but actinomycetes usually comprised a small proportion of this population (less than 1%). The target actinomycetes were isolated at all depths except from the Mariana Trench sediments. However, alkaliphilic bacteria closely related to Dietzia maris recently have been found even at this extreme depth (Takami, H., et al., FEMS Microbiol. Lett. 1997,152, 279). Actinomycete colonies were defined initially on the basis of colony morphologies and preliminary identification then made by chemotaxonomic tests. Pyrolysis mass spectrometry (PyMS) of deep- sea actinomycetes gave excellent correspondence with numerical taxonomic analyses and subsequently was adopted as a rapid procedure for assessing taxonomic diversity. PyMS analysis enabled several major clusters of deep sea rhodococci to be distinguished that are quite distinct from all type strains. However, 16S rDNA sequence analysis has revealed that most of these marine rhodococci have sequences that are very similar to certain terrestrial species of Rhodococcus and Dietzia. There is evidence for the intrusion of terrestrial run-off into these deep trench systems and we suggest that the inconsistency of the phenotypic and molecular taxonomies reflects recent speciation events in actinomycetes under the high pressure conditions of the deep-sea. 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 focussed on haloorganic and nitrile compounds. Dehalogenating bacteria have been isolated from abyssal and hadal sediments but none of them showed salt-dependency. Haloalcohol dehalogenating enzymes were identical to those from previously characterized terrestrial bacteria whereas haloalkanoic acid dehalogenases showed greater diversity (Heald, S.C., et al., submitted). In contrast 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. Some properties of their nitrile enzyme system will be described.
The studies made in our laboratory point to significant diversity of actinomycetes in deep-sea sedimentS. Our search for useful properties among microbial populations in the relatively unexplored deep-sea is on-going and the resource that they present for biotechnology innovation is at present incalculable.
