Comparison of prokaryotic diversity at offshore oceanic locations reveals a different microbiota in the Mediterranean Sea

Zaballos, Milagros; López‐López, Arantxa; Øvreås, Lise; Bartual, S.G.; D’Auria, Giuseppe; Alba, Jose Carlos; Legault, Boris A; Pushker, Ravindra; Daae, Frida Lise; Rodrı́guez-Valera, Francisco

doi:10.1111/j.1574-6941.2006.00060.x

Cited by 1,212 publications

(73 citation statements)

References 60 publications

(122 reference statements)

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“…Group 1A appears scarce in open oceanic libraries (DeLong et al, 2006; Figure 1). However, in a previous study of the Ionian sampling site (Zaballos et al, 2006) several 16S rRNA sequences (clusters Arch 1, 2, 3 and 4) that can be ascribed to the 1A group were detected, although none was found in samples of similar depth from the Greenland Sea, indicating that this group might be more abundant in the bathypelagic Mediterranean. Along these lines, we identified and sequenced three clones in our Mediterranean libraries, but failed to detect any in the South Atlantic or Polar Front samples.…”

Section: Genome Fragments From Group 1a Crenarchaeotamentioning

confidence: 99%

Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions

et al. 2008

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Marine planktonic archaea are widespread and abundant in deep oceanic waters but, despite their obvious ecological importance, little is known about them. Metagenomic analyses of large genome fragments allow access to both gene content and genome structure from single individuals of these cultivation-reluctant organisms. We present the comparative analysis of 22 archaeal genomic clones containing 16S rRNA genes that were selected from four metagenomic libraries constructed from meso- and bathypelagic plankton of different oceanic regions (South Atlantic, Antarctic Polar Front, Adriatic and Ionian Sea; depths from 500 to 3000 m). We sequenced clones of the divergent archaeal lineages Group 1A (Crenarchaeota) and Group III (Euryarchaeota) as well as clones from the more frequent Group I Crenarchaeota and Group II Euryarchaeota. Whenever possible, we analysed clones that had identical or nearly identical 16S rRNA genes and that were retrieved from distant geographical locations, that is, that defined pan-oceanic operational taxonomic units (OTUs). We detected genes involved in nitrogen fixation in Group 1A Crenarchaeota, and genes involved in carbon fixation pathways and oligopeptide importers in Group I Crenarchaeota, which could confirm the idea that these are mixotrophic. A two-component system resembling that found in ammonia-oxidizing bacteria was found in Group III Euryarchaeota, while genes for anaerobic respiratory chains were detected in Group II Euryarchaeota. Whereas gene sequence conservation was high, and recombination and gene shuffling extensive within and between OTUs in Group I Crenarchaeota, gene sequence conservation was low and global synteny maintained in Group II Euryarchaeota. This implies remarkable differences in genome dynamics in Group I Crenarchaeota and Group II Euryarchaeota with recombination and mutation being, respectively, the dominant genome-shaping forces. These observations, along with variations in GC content, led us to hypothesize that the two groups of organisms have fundamentally different lifestyles.

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Section: Genome Fragments From Group 1a Crenarchaeotamentioning

confidence: 99%

Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions

et al. 2008

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“…The 16S-ITS operon was amplified using the primers B1055F and PitsEcyanR (Ernst et al, 2003;Zaballos et al, 2006), whereas in a separate reaction the cpcBA operon was amplified using the primers cpcBF (UFP)/ cpcAR (URP) (Robertson et al, 2001). For each PCR reaction, the mixture contained 0.625 units of HotStarTaq (Qiagen, Venlo, The Netherlands), 0.2 mM of each dNTP (Roche, Woerden, The Netherlands), 1 Â PCR buffer (Qiagen), 5 pmol of the forward and reverse primers were used per reaction and purified Milli-Q-Grade (MQ-grade) water (Millipore purification unit, 18 MO Á cm (Millipore, Billerica, MA, USA)) was added to a final volume of 25 ml.…”

Section: Pcr Reactionsmentioning

confidence: 99%

Colorful microdiversity of Synechococcus strains (picocyanobacteria) isolated from the Baltic Sea

et al. 2008

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Synechococcus is a cosmopolitan genus of picocyanobacteria living in the photic zone of freshwater and marine ecosystems. Here, we describe the isolation of 46 closely related picocyanobacterial strains from the Baltic Sea. The isolates showed considerable variation in their cell size and pigmentation phenotypes, yielding a colorful variety of red, pink and blue-green strains. These pigmentation phenotypes could not be differentiated on the basis of their 16S rRNA-internal transcribed spacer (ITS) sequences. Thirty-nine strains, designated BSea, possessed 16S rRNA-ITS sequences almost identical with Synechococcus strain WH5701. Despite their similar 16S rRNA-ITS sequences, the BSea strains separated into several different clusters when comparing the phycocyanin (cpcBA) operon. This separation was largely consistent with the phycobiliprotein composition of the different BSea strains. The majority of phycocyanin (PC)-rich Bsea strains clustered with WH5701. Remarkably, the phycoerythrin (PE)-rich strains of BSea formed an as yet unidentified cluster within the cpcBA phylogeny, distantly related to other PE-rich groups. Detailed analysis of the cpcBA operon using neighbour-net analysis indicated that the PE-rich BSea strains are probably endemic for the Baltic Sea. Comparison of the phylogenies obtained by the 16S rRNA-ITS, the cpcBA, and the concatenated 16S rRNA-ITS and cpcBA operon sequences revealed possible events of horizontal gene transfer among different Synechococcus lineages. Our results show that microdiversity is important in Synechococcus populations and that it can reflect extensive diversification of different pigmentation phenotypes into different ecological niches.

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“…The remaining phylotypes, which formed more than 65% of total clones analysed in 16S rDNA and rRNA libraries, belonged to MGI-related phylotypes of Thaumarchaeota and were found both in the intermediate LIW layer and the deeper TDW layer. For this cluster of marine mesophilic archaea, the lifestyle adapted to deep-sea habitats has already been demonstrated previously [20,[52][53][54][55].…”

Section: Phylogenetic Analysis Of 16s Rdna and 16s Rrna Archaeal Clonmentioning

confidence: 94%

“…In the aphotic layers, the abiotic factors that could potentially influence microbial populations are weaker, with temperature and nutrient concentration presenting a more homogeneous trend. The majority of clones recovered from the Station Vector deep layers (LIW and TDW masses, respectively) was related to deep-sea microbiota detected at different bathypelagic depths (up to 3500 m), in deep-sea marine sediments, microbial mats, abyssal plain in the Northeast Atlantic and deep-sea ridge flank crustal fluid in the Northeast Pacific oceans (Figures S1-S4) [53,59,60]. Archaeal communities in the Station Vector water column were found to be depth specific in both types of clone libraries.…”

Section: Discussionmentioning

confidence: 99%

Variations in Microbial Community Structure through the Stratified Water Column in the Tyrrhenian Sea (Central Mediterranean)

Smedile

Scarfi

Domenico

et al. 2015

JMSE

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Abstract:The central Mediterranean Sea is among the most oligotrophic habitats in the marine environment. In this study, we investigated the abundance, diversity and activity of prokaryoplankton in the water column (25-3000-m depth) at Station Vector (Tyrrhenian Sea, 39°32.050′ N; 13°22.280′ E). This specific water column consists of three different water masses (Modified Atlantic Water (MAW), Levantine Intermediate Water (LIW) and Tyrrhenian Deep Water (TDW), possessing a typical stratification of the Central Mediterranean basin. CARD-FISH showed that the metabolically-active fraction of bacterial populations exceeded the archaeal fraction along the whole water column, except OPEN ACCESS J. Mar. Sci. Eng. 2015, 3 846 at the deepest water masses. 16S rDNA and 16S rRNA clone libraries obtained from each type of water mass were used to analyse the prokaryoplankton community structure and to distinguish between active and "less active" microbial fractions. Our results showed that the rRNA-derived bacterial libraries seemed to be more depth specific compared to 16S rDNA-derived counterparts. Major differences were detected between the active fractions of bacterioplankton thriving in photic (25 m, MAW) and aphotic layers (500-3000 m, LIW and TDW respectively), whereas no statistically-significant differences were detected within the deep, aphotic layers (500-3000 m, LIW and TDW). Archaeal communities possessed more depth-specific distribution patterns with both total and active fractions showing depth stratification. Cyanobacteria and Marine Group II MAGII of Euryarchaea dominated the MAW prokaryoplankton. A notable fraction of Geitlerinema-related cyanobacteria was detected among the metabolically-active bacterial population recovered from the mesopelagic (500 m, LIW) aphotic layer, which is indicative of their mixotrophic behaviour. Heterotrophic Gammaproteobacteria and members of Marine Group 1.1a and the PSL12-related ALOHA group of Thaumarchaeota were both abundant in the aphotic layers (both LIW and TDW). Discrepancies observed between 16S rDNA-and 16S rRNA-based libraries are most likely linked to different physiological states of the prokaryoplankton community members recovered from different layers. Taking into account the relative homogeneity of the main physicochemical parameters throughout the whole water column, light and energy source are likely the most relevant environmental variables shaping microbial biodiversity through the Station Vector water column.

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Comparison of prokaryotic diversity at offshore oceanic locations reveals a different microbiota in the Mediterranean Sea

Cited by 1,212 publications

References 60 publications

Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions

Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions

Colorful microdiversity of Synechococcus strains (picocyanobacteria) isolated from the Baltic Sea

Variations in Microbial Community Structure through the Stratified Water Column in the Tyrrhenian Sea (Central Mediterranean)

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