Parvularcula bermudensis gen. nov., sp. nov., a marine bacterium that forms a deep branch in the α-Proteobacteria

Abstract

Parvularcula bermudensis gen. nov., sp. nov., a marine bacterium that forms a deep branch in the a-Proteobacteria Jang-Cheon Cho and Stephen J. Giovannoni CorrespondenceStephen J. Giovannoni steve.giovannoni@orst.edu Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA Two bacterial strains, HTCC2503 T and HTCC2517, were isolated from the Bermuda Atlantic Time Series Station in the western Sargasso Sea, Atlantic Ocean, by new high-throughput culture methods that rely on dilution to extinction in very-low-nutrient media. Characterization of the two strains by polyphasic approaches revealed that they belonged to the same species. These isolates are Gram-negative, strictly aerobic, chemoheterotrophic, slightly motile short rods with a single flagellum. The temperature, pH and NaCl concentration ranges for growth were 10-37˚C, 6?0-9?0 and 0?75-20 % (w/v), respectively. Colonies on marine agar were very small (0?3-0?8 mm in diameter), yellowish-brown and very hard. Carotenoid pigments were synthesized but bacteriochlorophyll a was not. Several kinds of pentose, hexose, sugar alcohol, oligosaccharide and amino acid were utilized as sole carbon sources. Oxidase was produced, but catalase was not. All cellular fatty acids were even-numbered monounsaturated or saturated fatty acids and the major fatty acid was cis-7-octadecenoic acid (73?3 %). The DNA G+C content of strain HTCC2503 T was 60?8 mol%. Phylogenetic analyses of 16S rRNA gene sequences clearly indicated that the strains formed a distinct lineage, allied with activated sludge environmental clone H9, in the a-Proteobacteria. The clade containing strains HTCC2503 T and HTCC2517 and clone H9 could not be phylogenetically associated with any of the six known orders of the a-Proteobacteria. From this polyphasic evidence, it is proposed that the novel strains should be classified as Parvularcula bermudensis gen. nov., sp. nov. The type strain is HTCC2503 T (=ATCC BAA-594 T =KCTC 12087 T ) and the reference strain is HTCC2517. INTRODUCTIONIt is generally accepted that standard plate-count methods on solid-surface media recover <1 % of all microbial cells from marine environments (Kogure et al., 1979;Ferguson et al., 1984). Molecular biological tools, such as 16S rRNA gene cloning and sequencing, have elucidated this issue for a decade (Giovannoni et al., 1990;DeLong, 1992;Suzuki et al., 1997; Béjà et al., 2000), and have led to the conclusion that the most abundant marine microbial groups are as yet uncultivated and probably play a significant role in marine biogeochemical cycling (Giovannoni & Rappé, 2000). Acquisition of pure cultures for the study of their physiology, ecology and taxonomy is an important goal of research in this field. Recently, high-throughput culture (HTC) methods were developed, which allowed large numbers of microbial isolates to be recovered by dilution to extinction in natural sea-water media . The first cultured representative of the SAR11 clade (Rappé et al., 2002) and many novel strains in the Proteobacteria were ...

Amphiplicatus metriothermophilus gen. nov., sp. nov., a thermotolerant alphaproteobacterium isolated from a hot spring

“…At the time of writing, the order comprises one family and the family comprises a single genus, Parvularcula, which was established by Cho & Giovannoni (2003) and consists of three species with validly published names: Parvularcula bermudensis (Cho & Giovannoni, 2003), Parvularcula lutaonensis (Arun et al, 2009) and Parvularcula dongshanensis (Yu et al, 2013). The isolates belonging to the genus Parvularcula were obtained from seawater, a coastal hot spring and a soft coral, respectively, which indicates that the evolutionary cluster had a high similarity of habitat and metabolism pathways.…”

“…At the time of writing, the order comprises one family and the family comprises a single genus, Parvularcula, which was established by Cho & Giovannoni (2003) , 2013). The isolates belonging to the genus Parvularcula were obtained from seawater, a coastal hot spring and a soft coral, respectively, which indicates that the evolutionary cluster had a high similarity of habitat and metabolism pathways.…”

Pelagibaca bermudensis gen. nov., sp. nov., a novel marine bacterium within the Roseobacter clade in the order Rhodobacterales

“…The original liquid culture of strain HTCC2601 T was obtained using previously described high-throughput culturing approaches (Cho & Giovannoni, 2003a). The strain was purified as single colonies on marine agar 2216 (MA; Difco) after incubation for 4 days at 25 u C, and was stored as 10 % (v/v) glycerol suspensions in liquid nitrogen.…”

“…Phenotypic characterizations were been performed as described previously (Cho & Giovannoni, 2003a), using MA as basal medium at 30 u C. Unless otherwise indicated, standard methods were employed for the phenotypic characterization of the strain, as described by Smibert & Krieg (1994). A catalase test was performed by the addition of 3?0 % H 2 O 2 to fresh colonies; oxidase activity was determined using Kovács' oxidase reagent.…”

“…Nearly complete (1460 bp) 16S rRNA gene sequences of strain HTCC2601 T were obtained as described previously (Cho & Giovannoni, 2003a) and used for phylogenetic analyses. Preliminary BLAST network searches in GenBank showed that, for strain HTCC2601 T , the closest relative with a validly published name was Salipiger mucosus A3 T (96?5 % sequence similarity).…”