Salinispora arenicola gen. nov., sp. nov. and Salinispora tropica sp. nov., obligate marine actinomycetes belonging to the family Micromonosporaceae

Luís A. Maldonado1, William Fenical2, Paul R. Jensen2, Christopher A. Kauffman2, Tracy J. Mincer2, Alan C. Ward1, Alan T. Bull1, Michael Goodfellow1
1School of Biology, University of Newcastle, Newcastle upon Tyne, NE1 7RU, UK
2Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0204, USA

Tóm tắt

A taxonomic study was carried out to clarify the taxonomy of representatives of a group of marine actinomycetes previously designated MAR 1 and considered to belong to the family Micromonosporaceae. The organisms had phenotypic properties consistent with their assignment to this taxon. The strains formed a distinct taxon in the 16S rRNA Micromonosporaceae gene tree and shared a range of phenotypic properties that distinguished them from members of all of the genera with validly published names classified in this family. The name proposed for this novel taxon is Salinispora gen. nov. The genus contains two species recognized using a range of genotypic and phenotypic criteria, including comparative 16S–23S rRNA gene spacer region and DNA–DNA relatedness data. The names proposed for these taxa are Salinispora arenicola sp. nov., the type species, and Salinispora tropica sp. nov.; the type strains of these novel species have been deposited in service culture collections as strain CNH-643T (=ATCC BAA-917T=DSM 44819T) and strain CNB-440T (=ATCC BAA-916T=DSM 44818T), respectively.

Từ khóa


Tài liệu tham khảo

Asano, 1986, Catellatospora , a new genus of the Actinomycetales, Int J Syst Bacteriol, 36, 512, 10.1099/00207713-36-4-512

Asano, 1988, Catellatospora citrea subsp. methionotrophica subsp. nov., a methionine-deficient auxotroph of the Actinomycetales, Int J Syst Bacteriol, 38, 326, 10.1099/00207713-38-3-326

Asano, 1989, Catellatospora matsumotoense sp. nov. and C. tsunoense sp. nov., actinomycetes found in woodland soils, Int J Syst Bacteriol, 39, 309, 10.1099/00207713-39-3-309

Buchanan, 1917, Studies in the nomenclature and classification of the bacteria. II. The primary subdivisions of the schizomycetes, J Bacteriol, 2, 155, 10.1128/JB.2.2.155-164.1917

Bull, 2000, Search and discovery strategies for biotechnology: the paradigm shift, Microbiol Mol Biol Rev, 64, 573, 10.1128/MMBR.64.3.573-606.2000

Collins, 1994, Isoprenoid quinones, In Chemical Methods in Prokaryotic Systematics, 265

Colquhoun, 1998, Novel rhodococci and other mycolate actinomycetes from the deep sea, Antonie van Leeuwenhoek, 74, 27, 10.1023/A:1001743625912

Feling, 2003, Salinosporamide A: a highly cytotoxic proteasome inhibitor from a novel microbial source, a marine bacterium of the new genus Salinospora, Angew Chem Int Ed Engl, 42, 355, 10.1002/anie.200390115

Felsenstein, 1981, Evolutionary trees from DNA sequences: a maximum likelihood approach, J Mol Evol, 17, 368, 10.1007/BF01734359

Felsenstein, 1985, Confidence limits on phylogenies: an approach using the bootstrap, Evolution, 39, 783, 10.1111/j.1558-5646.1985.tb00420.x

Felsenstein, 1993, phylip (phylogeny inference package), version 3.5c. Department of Genome Sciences

Fiedler, 2005, Marine actinomycetes as a source of novel secondary metabolites, Antonie van Leeuwenhoek, 87, 37, 10.1007/s10482-004-6538-8

Fitch, 1967, Construction of phylogenetic trees, Science, 155, 279, 10.1126/science.155.3760.279

García-Martínez, 2001, RISSC: a novel database for ribosomal 16S-23S RNA gene spacer regions, Nucleic Acids Res, 29, 178, 10.1093/nar/29.1.178

Goodfellow, 1989, The actinomycetes. I. Suprageneric classification of actinomycetes, In Bergey's Manual of Systematic Bacteriology, vol. 4, 2333

Goodfellow, 1984, Actinomycetes in marine sediments, In Biological, Biochemical and Biomedical Aspects of Actinomycetes, 453, 10.1016/B978-0-12-528620-6.50039-2

Goodfellow, 1990, Numerical and chemical classification of Actinoplanes and some related actinomycetes, J Gen Microbiol, 136, 19, 10.1099/00221287-136-1-19

Gordon, 1967, The taxonomy of soil bacteria, In The Ecology of Soil Bacteria, 293

Groth, 2004, Five novel Kitasatospora species from soil: Kitasatospora arboriphila sp.nov., K. gansuensis sp. nov., K. nipponensis sp. nov., K. paranensis sp. nov., and K. terrestris sp. nov, Int J Syst Evol Microbiol, 54, 2121, 10.1099/ijs.0.63070-0

Gürtler, 1996, New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region, Microbiology, 142, 3, 10.1099/13500872-142-1-3

Han, 2003, Salinibacterium amurskyense gen. nov., sp. nov. a novel genus of the family Microbacteriaceae from the marine environment, Int J Syst Evol Microbiol, 53, 2061, 10.1099/ijs.0.02627-0

Helmke, 1984, Rhodococcus marinonascens sp. nov., an actinomycete from the sea, Int J Syst Bacteriol, 34, 127, 10.1099/00207713-34-2-127

Jensen, 1991, Distribution of actinomycetes in near-shore tropical marine sediments, Appl Environ Microbiol, 57, 1102, 10.1128/AEM.57.4.1102-1108.1991

Jones, 1949, Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic, J Bacteriol, 57, 141, 10.1128/JB.57.2.141-145.1949

Jones, 2004, Rhodococcus gordoniae sp. nov., an actinomycete isolated from clinical material and phenol-contaminated soil, Int J Syst Evol Microbiol, 54, 407, 10.1099/ijs.0.02756-0

Jukes, 1969, Evolution of protein molecules, In Mammalian Protein Metabolism, 21, 10.1016/B978-1-4832-3211-9.50009-7

Kim, 1998, Streptomyces thermocarboxydovorans sp. nov. and Streptomyces thermocarboxydus sp. nov., two moderately thermophilic carboxydotrophic species from soil, Int J Syst Bacteriol, 48, 59, 10.1099/00207713-48-1-59

Kim, 1999, Gordonia desulfuricans sp. nov., a benzothiophene-desulphurizing actinomycete, Int J Syst Bacteriol, 49, 1845, 10.1099/00207713-49-4-1845

Kluge, 1969, Quantitative phyletics and the evolution of anurans, Syst Zool, 18, 1, 10.2307/2412407

Koch, 1996, 16S ribosomal DNA analysis of the genera Micromonospora ,Actinoplanes , Catellatospora , Catenuloplanes , Couchioplanes , Dactylosporangium , and Pilimelia and emendation of the family Micromonosporaceae, Int J Syst Bacteriol, 46, 765, 10.1099/00207713-46-3-765

Komagata, 1987, Lipid and cell wall analysis in bacterial systematics, Methods Microbiol, 19, 161, 10.1016/S0580-9517(08)70410-0

Krasil'nikov, 1938, Ray Fungi and Related Organisms – Actinomycetales

Kroppenstedt, 1985, Fatty acid and menaquinone analysis of actinomycetes and related organisms, In Chemical Methods in Bacterial Systematics, 173

Kudo, 1999, Catenuloplanes crispus (Petrolini et al . 1993) comb. nov.: incorporation of the genus Planopolyspora Petrolini 1993 into the genus Catenuloplanes Yokota et al . 1993 with an emended description of the genus Catenuloplanes, Int J Syst Bacteriol, 49, 1853, 10.1099/00207713-49-4-1853

Lane, 1991, 16S/23S rRNA sequencing, In Nucleic Acid Techniques in Bacterial Systematics, 115

Lechevalier, 1970, Chemical composition as a criterion in the classification of aerobic actinomycetes, Int J Syst Bacteriol, 20, 435, 10.1099/00207713-20-4-435

Lechevalier, 1977, Chemotaxonomy of aerobic actinomycetes: phospholipid composition, Biochem Syst Ecol, 5, 249, 10.1016/0305-1978(77)90021-7

Lee, 2002, Proposal to transfer Catellatospora ferruginea and ‘ Catellatospora ishikariense ’ to Asanoa gen. nov. as Asanoa ferruginea comb. nov. and Asanoa ishikariensis sp. nov., with emended description of the genus Catellatospora, Int J Syst Evol Microbiol, 52, 967

Lee, 2000, Catellatospora koreensis sp. nov., a novel actinomycete isolated from a gold-mine cave, Int J Syst Evol Microbiol, 50, 1103, 10.1099/00207713-50-3-1103

Maldonado, 2005, Diversity of cultivable actinobacteria in geographically widespread marine sediments, Antonie van Leeuwenhoek, 87, 11, 10.1007/s10482-004-6525-0

Matsumoto, 2003, Longispora albida gen. nov., sp. nov., a novel genus of the family Micromonosporaceae, Int J Syst Evol Microbiol, 53, 1553, 10.1099/ijs.0.02595-0

Mesbah, 1989, Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography, Int J Syst Bacteriol, 39, 159, 10.1099/00207713-39-2-159

Mincer, 2002, Widespread and persistent populations of a major new marine actinomycete taxon in ocean sediments, Appl Environ Microbiol, 68, 5005, 10.1128/AEM.68.10.5005-5011.2002

Moran, 1995, Evidence for indigenous Streptomyces populations in a marine environment determined with a 16S rRNA probe, Appl Environ Microbiol, 61, 3695, 10.1128/AEM.61.10.3695-3700.1995

Nam, 2003, Tsukamurella spumae sp. nov., a novel actinomycete associated with foaming in activated sludge plants, Syst Appl Microbiol, 26, 367, 10.1078/072320203322497392

Nesterenko, 1982, Rhodococcus luteus nom. nov. and Rhodococcus maris nom. nov, Int J Syst Bacteriol, 32, 1, 10.1099/00207713-32-1-1

Pitcher, 1989, Rapid extraction of bacterial genomic DNA with guanidium thiocyanate, Lett Appl Microbiol, 8, 151, 10.1111/j.1472-765X.1989.tb00262.x

Piza, 2004, Investigation of bacterial diversity in Brazilian tropical estuarine sediments reveals high actinobacterial diversity, Antonie van Leeuwenhoek, 86, 317, 10.1007/s10482-004-0162-5

Pridham, 1948, The utilization of carbon compounds by some Actinomycetales as an aid for species determination, J Bacteriol, 56, 107, 10.1128/JB.56.1.107-114.1948

Rainey, 1995, Dietzia , a new genus including Dietzia maris comb. nov., formerly Rhodococcus maris, Int J Syst Bacteriol, 45, 32, 10.1099/00207713-45-1-32

Rheims, 1998, Verrucosispora gifhornensis gen. nov., sp. nov., a new member of the actinobacterial family Micromonosporaceae, Int J Syst Bacteriol, 48, 1119, 10.1099/00207713-48-4-1119

Riedlinger, 2004, Abyssomicins, inhibitors of the para -aminobenzoic acid pathway produced by the marine Verrucosispora strain AB-18-032, J Antibiot, 57, 271, 10.7164/antibiotics.57.271

Saitou, 1987, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol Biol Evol, 4, 406

Schaal, 1985, Identification of clinically significant actinomycetes and related bacteria using chemical techniques, In Chemical Methods in Bacterial Systematics, 359

Shirling, 1966, Methods for characterization of Streptomyces species, Int J Syst Bacteriol, 16, 313, 10.1099/00207713-16-3-313

1957, Manual of Microbiological Methods

Stach, 2003a, New primers for the class Actinobacteria : application to marine and terrestrial environments, Environ Microbiol, 5, 828, 10.1046/j.1462-2920.2003.00483.x

Stach, 2003b, Statistical approaches to estimating actinobacterial diversity in marine sediments, Appl Environ Microbiol, 69, 6189, 10.1128/AEM.69.10.6189-6200.2003

Stach, 2004, Williamsia maris sp. nov., a novel actinomycete isolated from the Sea of Japan, Int J Syst Evol Microbiol, 54, 191, 10.1099/ijs.0.02767-0

Stackebrandt, 1997, Proposal for a new hierarchic classification system, Actinobacteria classis nov, Int J Syst Bacteriol, 47, 479, 10.1099/00207713-47-2-479

Staneck, 1974, Simplified approach to the identification of aerobic actinomycetes by thin-layer chromatography, Appl Microbiol, 28, 226, 10.1128/AEM.28.2.226-231.1974

Takami, 1999, Biodiversity in deep-sea sites located near the south part of Japan, Extremophiles, 3, 97, 10.1007/s007920050104

Takizawa, 1993, Isolation and diversity of actinomycetes in the Chesapeake Bay, Appl Environ Microbiol, 59, 997, 10.1128/AEM.59.4.997-1002.1993

Tamaoka, 1994, Determination of DNA base composition, In Chemical Methods in Prokaryotic Systematics, 463

Tamura, 1994, A new genus of the order Actinomycetales , Couchioplanes gen. nov., with descriptions of Couchioplanes caeruleus (Horan and Brodsky 1986) comb. nov., and Couchioplanes caeruleus subsp. azureus subsp. nov., Int J Syst Bacteriol, 44, 193, 10.1099/00207713-44-2-193

Tamura, 1995, Five new species of the genus Catenuloplanes : Catenuloplanes niger sp.nov., Catenuloplanes indicus sp. nov.,Catenuloplanes atrovinosus sp. nov., Catenuloplanes castaneus sp.nov., and Catenuloplanes nepalensis sp. nov, Int J Syst Bacteriol, 45, 858, 10.1099/00207713-45-4-858

Tamura, 1997, A new genus of the order Actinomycetales , Spirilliplanes gen. nov., with description of Spirilliplanes yamanashiensis sp. nov, Int J Syst Bacteriol, 47, 97, 10.1099/00207713-47-1-97

Tamura, 2001, A new genus of the order Actinomycetales , Virgosporangium gen. nov., with descriptions of Virgosporangium ochraceum sp.nov. and Virgosporangium aurantiacum sp. nov, Int J Syst Evol Microbiol, 51, 1809, 10.1099/00207713-51-5-1809

Uchida, 1999, A new rapid method of glycolate test by diethyl ether extraction, which is applicable to a small amount of bacterial cells of less than one milligram, J Gen Appl Microbiol, 45, 49, 10.2323/jgam.45.49

Wayne, 1987, Report of the ad hoc committee on reconciliation of approaches to bacterial systematics, Int J Syst Bacteriol, 37, 463, 10.1099/00207713-37-4-463

Williams, 1983, Numerical classification of Streptomyces and related genera, J Gen Microbiol, 129, 1743

Yokota, 1993, Catenuloplanes japonicus gen. nov., sp. nov., nom. rev. a new genus of the order Actinomycetales, Int J Syst Bacteriol, 43, 805

Zhang, 2001, Clarification of the relationship between the members of the family Thermomonosporaceae on the basis of 16S rDNA, 16S–23S rRNA internal transcribed spacer and 23S rDNA sequences and chemotaxonomic analyses, Int J Syst Evol Microbiol, 51, 373, 10.1099/00207713-51-2-373