Archaeal Diversity in Deep-Sea Sediments Estimated by Means of Different Terminal-Restriction Fragment Length Polymorphisms (T-RFLP) Protocols

Luna, Gian Marco; Stumm, K.; Pusceddu, Antonio; Danovaro, Roberto

doi:10.1007/s00284-009-9445-4

Cited by 20 publications

(14 citation statements)

References 27 publications

(39 reference statements)

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“…Recently, Mediterranean-specific archaeal “ecotypes” were identified in bathypelagic waters [99], while fingerprinting analyses to determine benthic archaeal OTU richness reported a diversity roughly 10 times lower than that for Bacteria (range 3–35 OTUs per gram of sediment; [100]). As in the case of bacterial assemblages, the composition of Mediterranean archaeal assemblages is significantly different from that of deep Atlantic sediments [100]. Interestingly, significant longitudinal differences could be observed between the Western, Central, and Eastern Mediterranean, with a turnover diversity reaching 99%, indicating high regional variability [95].…”

Section: Resultsmentioning

confidence: 99%

“…Prokaryotic diversity has been investigated using molecular approaches that include a wide range of techniques, among them fingerprinting methods such as ARISA or T-RFLP, which reflect the richness and community composition of the dominant components of the assemblage in large sets of samples [88], [100], [265] and the cloning and sequencing of 16S rRNA genes, which also provide information on the phylogenetic identity of dominant members [96], [193]. ARISA and T-RFLP analyses were carried out as described, respectively, by Danovaro et al [97] and Luna et al [88], [100].…”

Section: Methodsmentioning

confidence: 99%

“…ARISA and T-RFLP analyses were carried out as described, respectively, by Danovaro et al [97] and Luna et al [88], [100]. Clone libraries were created from bacterial 16S ribosomal RNA genes amplified by PCR (polymerase chain reaction) with the universal bacterial primers 27f (modified to match also Planctomycetales; 5′-AGRGTTTGATCMTGGCTCAG-3′) and 1492r (5′-GGYTACCTTGTTACGACTT-3′); details are provided in [89], [95], [96].…”

Section: Methodsmentioning

confidence: 99%

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Deep-Sea Biodiversity in the Mediterranean Sea: The Known, the Unknown, and the Unknowable

et al. 2010

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Deep-sea ecosystems represent the largest biome of the global biosphere, but knowledge of their biodiversity is still scant. The Mediterranean basin has been proposed as a hot spot of terrestrial and coastal marine biodiversity but has been supposed to be impoverished of deep-sea species richness. We summarized all available information on benthic biodiversity (Prokaryotes, Foraminifera, Meiofauna, Macrofauna, and Megafauna) in different deep-sea ecosystems of the Mediterranean Sea (200 to more than 4,000 m depth), including open slopes, deep basins, canyons, cold seeps, seamounts, deep-water corals and deep-hypersaline anoxic basins and analyzed overall longitudinal and bathymetric patterns. We show that in contrast to what was expected from the sharp decrease in organic carbon fluxes and reduced faunal abundance, the deep-sea biodiversity of both the eastern and the western basins of the Mediterranean Sea is similarly high. All of the biodiversity components, except Bacteria and Archaea, displayed a decreasing pattern with increasing water depth, but to a different extent for each component. Unlike patterns observed for faunal abundance, highest negative values of the slopes of the biodiversity patterns were observed for Meiofauna, followed by Macrofauna and Megafauna. Comparison of the biodiversity associated with open slopes, deep basins, canyons, and deep-water corals showed that the deep basins were the least diverse. Rarefaction curves allowed us to estimate the expected number of species for each benthic component in different bathymetric ranges. A large fraction of exclusive species was associated with each specific habitat or ecosystem. Thus, each deep-sea ecosystem contributes significantly to overall biodiversity. From theoretical extrapolations we estimate that the overall deep-sea Mediterranean biodiversity (excluding prokaryotes) reaches approximately 2805 species of which about 66% is still undiscovered. Among the biotic components investigated (Prokaryotes excluded), most of the unknown species are within the phylum Nematoda, followed by Foraminifera, but an important fraction of macrofaunal and megafaunal species also remains unknown. Data reported here provide new insights into the patterns of biodiversity in the deep-sea Mediterranean and new clues for future investigations aimed at identifying the factors controlling and threatening deep-sea biodiversity.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Deep-Sea Biodiversity in the Mediterranean Sea: The Known, the Unknown, and the Unknowable

et al. 2010

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“…Comparison of clone sequences with T-RFLP (Table S1, supplementary material) indicate that not all T-RFLP OTUs are represented in the library. A bias of the Archaea-specific primer pair used against the documented methanogenic Archaea is unlikely, as amplification of a wide range of methanogens is generally achieved with this primer set [21,32,33,63], and e.g., Methanosarcina was readily amplified as a positive control by the PCR reaction.…”

Section: Environmental Euryarchaeotamentioning

confidence: 99%

Local Conditions Structure Unique Archaeal Communities in the Anoxic Sediments of Meromictic Lake Kivu

et al. 2012

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“…Among these, bacteria and archaea have been studied in detail (Stackebrandt et al 1993;Urakawa et al 1999;Li et al 1999;Takai and Horikoshi 1999;DeLong and Pace. 2001;Sogin et al 2006;Hongxiang et al 2008;Luna et al 2009). A few recent studies have reported eukaryotic diversity from extreme environments such as hydrothermal vents (López-García et al 2003, anoxic environments Jebaraj et al 2010) and deep-sea sediments (Bass et al 2007;Edgcomb et al 2011).…”

Section: Introductionmentioning

confidence: 97%

Assessment of fungal diversity in deep-sea sediments by multiple primer approach

Singh

Raghukumar

Verma

et al. 2011

World J Microbiol Biotechnol

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Increasing evidence of the fungal diversity in deep-sea sediments has come from amplification of environmental DNA with fungal specific or eukaryote primer sets. In order to assess the fungal diversity in deep-sea sediments of the Central Indian Basin (CIB) at ~5,000 m depth, we amplified sediment DNA with four different primer sets. These were fungal-specific primer pair ITS1F/ITS4 (internal transcribed spacers), universal 18S rDNA primers NS1/NS2, Euk18S-42F/Euk18S-1492R and Euk18S-555F/Euk18S-1269R. One environmental library was constructed with each of the primer pairs, and 48 clones were sequenced per library. These sequences resulted in 8 fungal Operational Taxonomic Units (OTUs) with ITS and 19 OTUs with 18S rDNA primer sets respectively by taking into account the 2% sequence divergence cut-off for species delineation. These OTUs belonged to 20 distinct fungal genera of the phyla Ascomycota and Basidiomycota. Seven sequences were found to be divergent by 79-97% from the known sequences of the existing database and may be novel. A majority of the sequences clustered with known sequences of the existing taxa. The phylogenetic affiliation of a few fungal sequences with known environmental sequences from marine and hypersaline habitat suggests their autochthonous nature or adaptation to marine habitat. The amplification of sequences belonging to Exobasidiomycetes and Cystobasidiomycetes from deep-sea is being reported for the first time in this study. Amplification of fungal sequences with eukaryotic as well as fungal specific primers indicates that among eukaryotes, fungi appear to be a dominant group in the sampling site of the CIB.

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Archaeal Diversity in Deep-Sea Sediments Estimated by Means of Different Terminal-Restriction Fragment Length Polymorphisms (T-RFLP) Protocols

Cited by 20 publications

References 27 publications

Deep-Sea Biodiversity in the Mediterranean Sea: The Known, the Unknown, and the Unknowable

Deep-Sea Biodiversity in the Mediterranean Sea: The Known, the Unknown, and the Unknowable

Local Conditions Structure Unique Archaeal Communities in the Anoxic Sediments of Meromictic Lake Kivu

Assessment of fungal diversity in deep-sea sediments by multiple primer approach

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