Fast, accurate error-correction of amplicon pyrosequences using Acacia

Bragg, Lauren M.; Stone, Graham N.; Imelfort, Michael; Hugenholtz, Philip; Tyson, Gene W.

doi:10.1038/nmeth.1990

Cited by 308 publications

(263 citation statements)

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“…Sequences were checked for chimeras using UCHIME ver. 3.0.617 (Edgar et al, 2011), denoised using Acacia (Bragg et al, 2012) and then parsed using the QIIME pipeline with default settings (Caporaso et al, 2010). We tested the hypotheses that: (1) the presence of photosynthetic symbionts influences the diversity of marine invertebrate-associated microbiomes, and (2) that the diversity of marine invertebrate-associated microbiomes differs between host species.…”

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Coral reef invertebrate microbiomes correlate with the presence of photosymbionts

et al. 2013

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Coral reefs provide habitat for an array of marine invertebrates that host symbiotic microbiomes. Photosynthetic symbionts including Symbiodinium dinoflagellates and diatoms potentially influence the diversity of their host-associated microbiomes by releasing carbon-containing photosynthates and other organic compounds that fuel microbial metabolism. Here we used 16S ribosomal RNA (rRNA) gene amplicon pyrosequencing to characterise the microbiomes of 11 common Great Barrier Reef marine invertebrate species that host photosynthetic symbionts and five taxa in which they are absent. The presence of photosynthetic symbionts influenced the composition but not the species richness, evenness and phylogenetic diversity of invertebrateassociated microbiomes. Invertebrates without photosynthetic symbionts were dominated by Alphaproteobacteria, whereas those hosting photosynthetic symbionts were dominated by Gammaproteobacteria. Interestingly, many microbial species from photosymbiont-bearing invertebrates, including Oceanospirillales spp., Alteromonas spp., Pseudomonas spp., Halomonas spp., are implicated in the metabolism of dimethylsulfoniopropionate (DMSP). DMSP is produced in high concentrations by photosynthetic dinoflagellates and is involved in climate regulation by facilitating cloud formation. Microbiomes correlated with host taxa and replicate individuals from most sampled species grouped in distance-based redundancy analysis of retrieved 16S rRNA gene sequences. This study highlights the complex nature of invertebrate holobionts and confirms the importance of photosynthetic symbionts in structuring marine invertebrate bacterial communities.

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Coral reef invertebrate microbiomes correlate with the presence of photosymbionts

et al. 2013

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“…Acacia (version 1.52; Bragg et al, 2012) was used to error-correct the amplicon 454 pyrosequencing reads with an average quality cutoff score of 30. The output from Acacia was then de-multiplexed using QIIME.…”

Section: Discussionmentioning

confidence: 99%

Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies

et al. 2015

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Diverse microbial consortia profoundly influence animal biology, necessitating an understanding of microbiome variation in studies of animal adaptation. Yet, little is known about such variability among fish, in spite of their importance in aquatic ecosystems. The Trinidadian guppy, Poecilia reticulata, is an intriguing candidate to test microbiome-related hypotheses on the drivers and consequences of animal adaptation, given the recent parallel origins of a similar ecotype across streams. To assess the relationships between the microbiome and host adaptation, we used 16S rRNA amplicon sequencing to characterize gut bacteria of two guppy ecotypes with known divergence in diet, life history, physiology and morphology collected from low-predation (LP) and high-predation (HP) habitats in four Trinidadian streams. Guts were populated by several recurring, core bacteria that are related to other fish associates and rarely detected in the environment. Although gut communities of lab-reared guppies differed from those in the wild, microbiome divergence between ecotypes from the same stream was evident under identical rearing conditions, suggesting host genetic divergence can affect associations with gut bacteria. In the field, gut communities varied over time, across streams and between ecotypes in a stream-specific manner. This latter finding, along with PICRUSt predictions of metagenome function, argues against strong parallelism of the gut microbiome in association with LP ecotype evolution. Thus, bacteria cannot be invoked in facilitating the heightened reliance of LP guppies on lower-quality diets. We argue that the macroevolutionary microbiome convergence seen across animals with similar diets may be a signature of secondary microbial shifts arising some time after host-driven adaptation.

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“…Forward and reverse primer sequences were also removed. The program Acacia (Bragg et al 2012) was used to remove pyrosequencing noise. Chimeric sequences were removed using UCHIME (Edgar et al 2011).…”

Section: Pyrosequencing Data Analysismentioning

confidence: 99%

Potentially Active Iron, Sulfur, and Sulfate Reducing Bacteria in Skagerrak and Bothnian Bay Sediments

Reyes

Schneider

Thürmer

et al. 2017

Geomicrobiology Journal

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In many marine surface sediments, the reduction of manganese (Mn) and iron (Fe) oxides is obscured by sulfate reduction, which is regarded as the predominant anaerobic microbial respiration process. However, many dissimilatory sulfate and sulfur reducing microorganisms are known to utilize alternative electron acceptors such as metal oxides. In this study, we tested whether sulfate and sulfur reducing bacteria are linked to metal oxide reduction based on biogeochemical modeling of porewater concentration profiles of Mn 2C and Fe 2C in Bothnian Bay (BB) and Skagerrak (SK) sediments. Steady-state modeling of Fe 2C and Mn 2C porewater profiles revealed zones of net Fe (0-9 cm BB; »10 and 20 cm SK) and Mn (0-5 cm BB; 2-8 cm SK) species transformations. 16S rRNA pyrosequencing analysis of the in-situ community showed that Desulfobacteraceae, Desulfuromonadaceae and Desulfobulbaceae were present in the zone of Fereduction of both sediments. Rhodobacteraceae were also detected at high relative abundance in both sediments. BB sediments appeared to harbor a greater diversity of potential Fe-reducers compared to SK. Additionally, when the upper 10 cm of sediment from the SK was incubated with lepidocrocite and acetate, Desulfuromonas was the dominant bacteria. Real-time quantitative polymerase chain reaction (qPCR) results showed decreasing dsrA gene copy numbers with depth coincided with decreased Fe-reduction activity. Our results support the idea that sulfur and sulfate reducing bacteria contribute to Fe-reduction in the upper centimeters of both sediments.

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Fast, accurate error-correction of amplicon pyrosequences using Acacia

Cited by 308 publications

References 5 publications

Coral reef invertebrate microbiomes correlate with the presence of photosymbionts

Coral reef invertebrate microbiomes correlate with the presence of photosymbionts

Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies

Potentially Active Iron, Sulfur, and Sulfate Reducing Bacteria in Skagerrak and Bothnian Bay Sediments

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