The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

Yilmaz, Pelin; Parfrey, Laura Wegener; Yarza, Pablo; Gerken, Jan; Pruesse, Elmar; Quast, Christian; Schweer, Timmy; Peplies, Jörg; Ludwig, Wolfgang; Glöckner, Frank Oliver

doi:10.1093/nar/gkt1209

Cited by 2,855 publications

(2,060 citation statements)

References 33 publications

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“…Next, phylogenetic assignment and statistical analyses for the tag sequences were conducted. Sequencing tags were aligned using the partial order algorithm (SINA; www.arb-silva.de/aligner/) with the reference multiple alignment SILVA SSU Ref NR (56). All of the aligned sequences were then clustered into operational taxonomic units (OTUs) by 97% sequence identity using MOTHUR 1.31.1, with default parameters according to the average-clustering algorithm.…”

Section: Methodsmentioning

confidence: 99%

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Hadal biosphere: Insight into the microbial ecosystem in the deepest ocean on Earth

Nunoura

Takaki

Hirai

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

251

314

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Hadal oceans at water depths below 6,000 m are the least-explored aquatic biosphere. The Challenger Deep, located in the western equatorial Pacific, with a water depth of ∼11 km, is the deepest ocean on Earth. Microbial communities associated with waters from the sea surface to the trench bottom (0 ∼10,257 m) in the Challenger Deep were analyzed, and unprecedented trench microbial communities were identified in the hadal waters (6,000 ∼10,257 m) that were distinct from the abyssal microbial communities. The potentially chemolithotrophic populations were less abundant in the hadal water than those in the upper abyssal waters. The emerging members of chemolithotrophic nitrifiers in the hadal water that likely adapt to the higher flux of electron donors were also different from those in the abyssal waters that adapt to the lower flux of electron donors. Species-level niche separation in most of the dominant taxa was also found between the hadal and abyssal microbial communities. Considering the geomorphology and the isolated hydrotopographical nature of the Mariana Trench, we hypothesized that the distinct hadal microbial ecosystem was driven by the endogenous recycling of organic matter in the hadal waters associated with the trench geomorphology.hadal | trench | niche separation | nitrification | Challenger Deep

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Section: Methodsmentioning

confidence: 99%

“…org), and the principal component analysis was carried out using the tree by UniFrac. Representative SSU rRNA gene sequences were aligned and phylogenetically classified into certain taxonomic units using ARB (56). The phylogenetic tree of thaumarchaeal SSU rRNA genes was constructed by Clustal X based on the unambiguous residues.…”

Section: Methodsmentioning

confidence: 99%

Hadal biosphere: Insight into the microbial ecosystem in the deepest ocean on Earth

Nunoura

Takaki

Hirai

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

251

314

View full text Add to dashboard Cite

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“…We used the Greengenes database for 16S rRNA sequence analysis (DeSantis et al., 2006) and SILVA taxonomy sequence database for 18S rRNA analysis (Yilmaz et al., 2013). Note that although 16S primers were designed to amplify both bacteria and archaea, no archaea were recovered.…”

Section: Methodsmentioning

confidence: 99%

Mosquito vector‐associated microbiota: Metabarcoding bacteria and eukaryotic symbionts across habitat types in Thailand endemic for dengue and other arthropod‐borne diseases

Thongsripong

Chandler

Green

et al. 2017

Ecology and Evolution

118

112

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Vector‐borne diseases are a major health burden, yet factors affecting their spread are only partially understood. For example, microbial symbionts can impact mosquito reproduction, survival, and vectorial capacity, and hence affect disease transmission. Nonetheless, current knowledge of mosquito‐associated microbial communities is limited. To characterize the bacterial and eukaryotic microbial communities of multiple vector species collected from different habitat types in disease endemic areas, we employed next‐generation 454 pyrosequencing of 16S and 18S rRNA amplicon libraries, also known as metabarcoding. We investigated pooled whole adult mosquitoes of three medically important vectors, Aedes aegypti, Ae. albopictus, and Culex quinquefasciatus, collected from different habitats across central Thailand where we previously characterized mosquito diversity. Our results indicate that diversity within the mosquito microbiota is low, with the majority of microbes assigned to one or a few taxa. Two of the most common eukaryotic and bacterial genera recovered (Ascogregarina and Wolbachia, respectively) are known mosquito endosymbionts with potentially parasitic and long evolutionary relationships with their hosts. Patterns of microbial composition and diversity appeared to differ by both vector species and habitat for a given species, although high variability between samples suggests a strong stochastic element to microbiota assembly. In general, our findings suggest that multiple factors, such as habitat condition and mosquito species identity, may influence overall microbial community composition, and thus provide a basis for further investigations into the interactions between vectors, their microbial communities, and human‐impacted landscapes that may ultimately affect vector‐borne disease risk.

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“…Operational taxonomic units (OTUs) were clustered and denoised with UPARSE (Edgar, 2013) while chimeric OTUs were removed against the RDP reference database (http://drive5.com/uchime/ rdp_gold.fa) with the UCHIME algorithm (Edgar et al, 2011). Finally, reads were merged with FLASH (Magoč and Salzberg, 2011) and a taxonomy assigned against the SILVA 123 rRNA database (Yilmaz et al, 2014) with Lambda (Hauswedell et al, 2014), using the following optional LotuS command line options: "-p miSeq -id 0.97 -doBlast lambda -amplicon_type SSU -tax_group bacteria -derepMin 6:1,3:2 -CL uparse -thr 14." OTUs were summed to genus, family, class and phylum level per sample, according to their taxonomic classification.…”

Section: Bioinformatic Analysismentioning

confidence: 99%

Pole-to-Pole Connections: Similarities between Arctic and Antarctic Microbiomes and Their Vulnerability to Environmental Change

et al. 2017

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The global biogeography of microorganisms remains poorly resolved, which limits the current understanding of microbial resilience toward environmental changes. Using high-throughput 16S rRNA gene amplicon sequencing, we characterized the microbial diversity of terrestrial and lacustrine biofilms from the Arctic, Antarctic and temperate regions. Our analyses suggest that bacterial community compositions at the poles are more similar to each other than they are to geographically closer temperate habitats, with 32% of all operational taxonomic units (OTUs) co-occurring in both polar regions. While specific microbial taxa were confined to distinct regions, representing potentially endemic populations, the percentage of cosmopolitan taxa was higher in Arctic (43%) than in Antarctic samples (36%). The overlap in polar microbial OTUs may be explained by natural or anthropogenically-mediated dispersal in combination with environmental filtering. Current and future changing environmental conditions may enhance microbial invasion, establishment of cosmopolitan genotypes and loss of endemic taxa.

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The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

Cited by 2,855 publications

References 33 publications

Hadal biosphere: Insight into the microbial ecosystem in the deepest ocean on Earth

Hadal biosphere: Insight into the microbial ecosystem in the deepest ocean on Earth

Mosquito vector‐associated microbiota: Metabarcoding bacteria and eukaryotic symbionts across habitat types in Thailand endemic for dengue and other arthropod‐borne diseases

Pole-to-Pole Connections: Similarities between Arctic and Antarctic Microbiomes and Their Vulnerability to Environmental Change

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