Biogeography and phylogeny of the NOR5/OM60 clade of Gammaproteobacteria

Shi, Yan; Fuchs, Bernhard M.; Lenk, Sabine; Harder, Jens; Wulf, Jörg; Jiao, Nianzhi; Amann, Rudolf

doi:10.1016/j.syapm.2008.12.001

Cited by 73 publications

(70 citation statements)

References 63 publications

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“…Our sequences fall into the NOR5/OM60 clade also well represented in a metagenomic library from the eastern Mediterranean Sea waters (Feingersch et al, 2010). This clade was recently shown to have a cosmopolitan occurrence in the marine environment, with a clear preference for coastal waters (Yutin et al, 2007;Yan et al, 2009). We did not clearly observed this habitat preference in the Mediterranean Sea since equivalent proportions of pufM gammaproteobacterial sequences were detected in coastal and off shore regions (Lehours et al, 2010).…”

Section: Dominance Of Gammaproteobacteria In the Metabolically Activesupporting

confidence: 56%

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 Gammaproteobacteria In the Metabolically Activesupporting

confidence: 56%

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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“…These belonged mainly to families of psychrophilic microorganisms including Enterobacteriaceae, Alteromonadaceae, Oceanospirillaceae and Legionellaceae (Figure 3a). Among Diversity and biogeography in deep-sea sediments R Schauer et al these phylotypes 11 OTUs (12 sequences) clustered with the NOR5/OM60 clade that includes 'Congregibacter litoralis' strain KT71, the first marine aerobic anoxygenic phototrophic Gammaproteobacteria in culture (Fuchs et al, 2007;Yan et al, 2009 (Figures 3a and b) and to Cret-1F, BD1-1, PWP and South Ionian groups (11 OUT, 27 sequences). These groups included only 16S rRNA gene sequences that originated from other deep-sea or permanent cold marine habitats Li et al, 1999;Ravenschlag et al, 1999;Urakawa et al, 1999;Bowman and McCuaig, 2003;Polymenakou et al, 2005;Xu et al, 2005;Zhao and Zeng, 2005).…”

Section: Bacterial Diversity Of the 16s Ribosomal Rna Genesmentioning

confidence: 99%

Bacterial diversity and biogeography in deep-sea surface sediments of the South Atlantic Ocean

et al. 2009

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Microbial biogeographic patterns in the deep sea depend on the ability of microorganisms to disperse. One possible limitation to microbial dispersal may be the Walvis Ridge that separates the Antarctic Lower Circumpolar Deep Water from the North Atlantic Deep Water. We examined bacterial communities in three basins of the eastern South Atlantic Ocean to determine diversity and biogeography of bacterial communities in deep-sea surface sediments. The analysis of 16S ribosomal RNA (rRNA) gene clone libraries in each basin revealed a high diversity, representing 521 phylotypes with 98% identity in 1051 sequences. Phylotypes affiliated with Gammaproteobacteria, Deltaproteobacteria and Acidobacteria were present in all three basins. The distribution of these shared phylotypes seemed to be influenced neither by the Walvis Ridge nor by different deep water masses, suggesting a high dispersal capability, as also indicated by low distance–decay relationships. However, the total bacterial diversity showed significant differences between the basins, based on 16S rRNA gene sequences as well as on terminal restriction fragment length polymorphism fingerprints. Noticeably, both geographic distance and environmental heterogeneity influenced bacterial diversity at intermediate (10–3000 km) and large scales (>3000 km), indicating a complex interplay of local contemporary environmental effects and dispersal limitation.

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“…Depth does not exceed 50-100 m, except close to the Norwegian coast where it reaches 4200 m (Eisma, 1987). The composition of the bacterioplankton of the North Sea has been studied mainly in the southern part, addressing richness, evenness, seasonal and interannual variations and controls by various biological and environmental factors (Eilers et al, 2000(Eilers et al, , 2001Gerdts et al, 2004;Reinthaler et al, 2005;Alderkamp et al, 2006;Rink et al, 2007;Sapp et al, 2007;Yan et al, 2009). These studies showed that the bacterioplankton is composed of phylogenetic lineages, which are also found in other marine pelagic ecosystems (see above).…”

Section: Introductionmentioning

confidence: 99%

Distribution of Roseobacter RCA and SAR11 lineages in the North Sea and characteristics of an abundant RCA isolate

et al. 2010

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The Roseobacter group and SAR11 clade constitute high proportions of the marine bacterioplankton, but only scarce information exists on the abundance of distinct populations of either lineage. Therefore, we quantified the abundance of the largest cluster of the Roseobacter group, the RCA (Roseobacter clade affiliated) cluster together with the SAR11 clade by quantitative PCR in the southern and eastern North Sea. The RCA cluster constituted up to 15 and 21% of total bacterial 16S ribosomal RNA (rRNA) genes in September 2005 and May 2006, respectively. At a few stations, the RCA cluster exceeded the SAR11 clade, whereas at most stations, SAR11 constituted higher fractions with maxima of 37%. In most samples, only one RCA ribotype was detected. RCA abundance was positively correlated with phaeopigments, chlorophyll, dissolved and particulate organic carbon (POC), turnover rates of dissolved free amino acids (DFAAs), temperature, and negatively correlated with salinity. The SAR11 clade was only correlated with POC (negatively, May) and with DFAA turnover rates (positively, September). An abundant RCA strain, 'Candidatus Planktomarina temperata', was isolated from the southern North Sea. This strain has an identical 16S rRNA gene sequence to the dominant RCA ribotype. Detection of the pufM gene, coding for a subunit of the reaction center of bacteriochlorophyll a, indicates the potential of the isolate for aerobic anoxygenic photosynthesis. Our study shows that a distinct population of the RCA cluster constitutes an abundant bacterioplankton group in a neritic sea of the temperate zone and indicates that this population has an important role during decaying phytoplankton blooms.

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Biogeography and phylogeny of the NOR5/OM60 clade of Gammaproteobacteria

Cited by 73 publications

References 63 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

Bacterial diversity and biogeography in deep-sea surface sediments of the South Atlantic Ocean

Distribution of Roseobacter RCA and SAR11 lineages in the North Sea and characteristics of an abundant RCA isolate

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