Roseateles depolymerans gen. nov., sp. nov., a new bacteriochlorophyll a-containing obligate aerobe belonging to the β-subclass of the Proteobacteria

Suyama, Tetsushi; Shigematsu, Toru; Takaichi, Shinichi; Nodasaka, Yoshinobu; Fujikawa, Seizo; Hosoya, Hiroyuki; Tokiwa, Yutaka; Kanagawa, Takahiro; Hanada, Satoshi

doi:10.1099/00207713-49-2-449

Cited by 95 publications

(61 citation statements)

References 41 publications

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“…All our isolates belonged to the Alphaproteobacteria. This finding is not very surprising because AAP bacteria are dispersed throughout the Alphaproteobacteria, with one known betaproteobacterial representative, Roseateles depolymerans (Suyama et al, 1999), one described gammaproteobacterial species, Congregibacter litoralis (Eilers et al, 2001;Fuchs et al, 2007) and three unassigned gammaproteobacterial isolates (Cho and Giovannoni, 2004;Cho et al, 2007;Thrash et al, 2010). The distribution of our isolates within at least 9 different genera reflects a high cultivable diversity for this functional group in the Mediterranean Sea.…”

Section: Dominance Of Alphaproteobacteria In the Cultivable Communitymentioning

confidence: 74%

Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea

et al. 2011

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Abstract. Aerobic anoxygenic phototrophic (AAP) bacteria play significant roles in the bacterioplankton productivity and biogeochemical cycles of the surface ocean. In this study, we applied both cultivation and mRNA-based molecular methods to explore the diversity of AAP bacteria along an oligotrophic gradient in the Mediterranean Sea in early summer 2008. Colony-forming units obtained on three different agar media were screened for the production of bacteriochlorophyll-a (BChl-a), the light-harvesting pigment of AAP bacteria. BChl-a-containing colonies represented a low part of the cultivable fraction. In total, 54 AAP strains were isolated and the phylogenetic analyses based on their 16S rRNA and pufM genes showed that they were all affiliated to the Alphaproteobacteria. The most frequently isolated strains belonged to Citromicrobium bathyomarinum, and Erythrobacter and Roseovarius species. Most other isolates were related to species not reported to produce BChl-a and/or may represent novel taxa. Direct extraction of RNA from seawater samples enabled the analysis of the expression of pufM, the gene coding for the M subunit of the reaction centre complex of aerobic anoxygenic photosynthesis. Clone libraries of pufM gene transcripts revealed that most phylotypes were highly similar to sequences previously recovered from the Mediterranean Sea and a large majority (∼94 %) was affiliated to the Gammaproteobacteria. The most abundantly detected phylotypes occurred in the western and eastern Mediterranean basins. However, some were exclusivelyCorrespondence to: C. Jeanthon (jeanthon@sb-roscoff.fr) detected in the eastern basin, reflecting the highest diversity of pufM transcripts observed in this ultra-oligotrophic region. To our knowledge, this is the first study to document extensively the diversity of AAP isolates and to unveil the active AAP community in an oligotrophic marine environment. By pointing out the discrepancies between culture-based and molecular methods, this study highlights the existing gaps in the understanding of the AAP bacteria ecology, especially in the Mediterranean Sea and likely globally.

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Section: Dominance Of Alphaproteobacteria In the Cultivable Communitymentioning

confidence: 74%

Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea

et al. 2011

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“…Some aerobic methylotrophic bacteria and Rhizobia spp. as well as the beta-proteobacterium Roseateles depolymerans (29) are capable of BChl a synthesis (10,30,36). However, Rhizobia spp.…”

Section: Discussionmentioning

confidence: 99%

Aerobic Anoxygenic Phototrophic Bacteria in the Mid-Atlantic Bight and the North Pacific Gyre

Cottrell

Mannino

Kirchman

2006

Appl Environ Microbiol

147

156

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The abundance of aerobic anoxygenic phototrophic (AAP) bacteria, cyanobacteria, and heterotrophs was examined in the Mid-Atlantic Bight and the central North Pacific Gyre using infrared fluorescence microscopy coupled with image analysis and flow cytometry. AAP bacteria comprised 5% to 16% of total prokaryotes in the Atlantic Ocean but only 5% or less in the Pacific Ocean. In the Atlantic, AAP bacterial abundance was as much as 2-fold higher than that of Prochlorococcus spp. and 10-fold higher than that of Synechococcus spp. In contrast, Prochlorococcus spp. outnumbered AAP bacteria 5-to 50-fold in the Pacific. In both oceans, subsurface abundance maxima occurred within the photic zone, and AAP bacteria were least abundant below the 1% light depth. The abundance of AAP bacteria rivaled some groups of strictly heterotrophic bacteria and was often higher than the abundance of known AAP bacterial genera (Erythrobacter and Roseobacter spp.). Concentrations of bacteriochlorophyll a (BChl a) were low (ϳ1%) compared to those of chlorophyll a in the North Atlantic. Although the BChl a content of AAP bacteria per cell was typically 20-to 250-fold lower than the divinyl-chlorophyll a content of Prochlorococcus, the pigment content of AAP bacteria approached that of Prochlorococcus in shelf break water. Our results suggest that AAP bacteria can be quite abundant in some oceanic regimes and that their distribution in the water column is consistent with phototrophy.Prokaryotic microbes play a central role in carbon cycling and food web dynamics in the ocean. Much has been learned about the contribution to primary production by autotrophic prokaryotes (15,20) and the central role of heterotrophic prokaryotes in the consumption of dissolved organic materials (DOM) (35) and degradation of sinking particles in the ocean (25). However, less is known about photoheterotrophic bacteria, such as the aerobic anoxygenic phototrophic (AAP) bacteria and proteorhodopsin-containing bacteria (1), which probably have phototrophic as well as heterotrophic metabolisms. These bacteria may have unique impacts on carbon cycling. Kolber et al. (19) obtained the first evidence that AAP bacteria may be more abundant in the ocean than implied by the low concentrations of bacteriochlorophyll a (BChl a) measured in seawater (14). Direct counts of infrared (IR) fluorescing bacteria suggested that AAP bacteria could comprise as much as 10% of the total microbial community (19). However, Schwalbach and Fuhrman (27) pointed out that this estimate may be too high because of problems in distinguishing cyanobacteria from AAP bacteria. Their direct-count and quantitative-PCR data indicate that AAP bacteria were usually a small fraction of total prokaryotic abundance in surface waters of several marine environments, but surface waters of the Chesapeake Bay and Long Island Sound did have relatively high proportions of AAP bacteria (10% to 18%). In addition to uncertainty about surface waters, it is not clear how AAP bacteria vary with depth in the oceans, exce...

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“…Red-like cbbL genes were amplified with primer pair cbbLR1F (59-AAGGAYGACGAGAACATC-39) and cbbLR1R (59-TCG-GTCGGSGTGTAGTTGAA-39). Amplification of greenlike cbbL gene primers cbbLG1F (59-GGCAACGTGTTC-GGSTTCAA-39) and cbbLG1R (59-TTGATCTCTTT CC-ACGTTTCC-39) were used, where S represents G or C. The cycle conditions for cbbL-specific primers were as follows: initial denaturation at 95 u C for 4 min, followed by 32 Suyama et al (1999).…”

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confidence: 99%

Description of Pelomonas aquatica sp. nov. and Pelomonas puraquae sp. nov., isolated from industrial and haemodialysis water

Gomila

Bowien

Falsen

et al. 2007

International Journal of Systematic and Evolutionary Microbiology

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Three Gram-negative, rod-shaped, non-spore-forming bacteria (strains CCUG 52769T, CCUG 52770 and CCUG 52771) isolated from haemodialysis water were characterized taxonomically, together with five strains isolated from industrial waters (CCUG 52428, CCUG 52507, CCUG 52575T, CCUG 52590 and CCUG 52631). Phylogenetic analysis based on 16S rRNA gene sequences indicated that these isolates belonged to the class Betaproteobacteria and were related to the genus Pelomonas, with 16S rRNA gene sequence similarities higher than 99 % with the only species of the genus, Pelomonas saccharophila and to Pseudomonas sp. DSM 2583. The type strains of Mitsuaria chitosanitabida and Roseateles depolymerans were their closest neighbours (97.9 and 97.3 % 16S rRNA gene sequence similarity, respectively). Phylogenetic analysis was also performed for the internally transcribed spacer region and for three genes [hoxG (hydrogenase), cbbL/cbbM (Rubisco) and nifH (nitrogenase)] relevant for the metabolism of the genus Pelomonas. DNA–DNA hybridization, major fatty acid composition and phenotypical analyses were carried out, which included the type strain of Pelomonas saccharophila obtained from different culture collections (ATCC 15946T, CCUG 32988T, DSM 654T, IAM 14368T and LMG 2256T), as well as M. chitosanitabida IAM 14711T and R. depolymerans CCUG 52219T. Results of DNA–DNA hybridization, physiological and biochemical tests supported the conclusion that strains CCUG 52769, CCUG 52770 and CCUG 52771 represent a homogeneous phylogenetic and genomic group, including strain DSM 2583, clearly differentiated from the industrial water isolates and from the Pelomonas saccharophila type strain. On the basis of phenotypic and genotypic characteristics, these strains belong to two novel species within the genus Pelomonas, for which the names Pelomonas puraquae sp. nov. and Pelomonas aquatica sp. nov. are proposed. The type strains of Pelomonas puraquae sp. nov. and Pelomonas aquatica sp. nov. are CCUG 52769T (=CECT 7234T) and CCUG 52575T (=CECT 7233T), respectively.

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Roseateles depolymerans gen. nov., sp. nov., a new bacteriochlorophyll a-containing obligate aerobe belonging to the β-subclass of the Proteobacteria

Cited by 95 publications

References 41 publications

Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea

Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea

Aerobic Anoxygenic Phototrophic Bacteria in the Mid-Atlantic Bight and the North Pacific Gyre

Description of Pelomonas aquatica sp. nov. and Pelomonas puraquae sp. nov., isolated from industrial and haemodialysis water

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