The Windblown: Possible Explanations for Dinophyte DNA in Forest Soils

Gottschling, Marc; Czech, Lucas; Mahé, Frédéric; Adl, Sina M.; Dunthorn, Micah

doi:10.1111/jeu.12833

Cited by 10 publications

(10 citation statements)

References 65 publications

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“…Many of the colpodean OTUs analyzed here had multiple likely placement locations on the reference tree. These alternative placements were not considered in most published phylogenetic placement studies using EPA‐ng (Aguirre‐von‐Wobeser, 2021; Bass et al, 2018; Fuchsman et al, 2022; Gottschling et al, 2021; Iniesto et al, 2021; Metz et al, 2021; Schoenle et al, 2020). Here, for the first time, we showcased together the features of the program GAPPA tool that can take multiple likely placements when performing taxonomic assignments into account.…”

Section: Discussionmentioning

confidence: 99%

“…Guillou et al, 2013; Ratnasingham & Hebert, 2007) are routinely used for such assignments in numerous metabarcoding studies. However, phylogenetic placement approaches for taxonomic assignments are being increasingly employed (Bass et al, 2018; Czech et al, 2022; Gottschling et al, 2021; Jamy et al, 2020). These two alternative approaches to assigning OTUs are beginning to be compared to each other (Hleap et al, 2021; Jamy et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Interpreting phylogenetic placements for taxonomic assignment of environmental DNA

Ewers

Rajter

Czech

et al. 2023

J Eukaryotic Microbiology

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Taxonomic assignment of operational taxonomic units (OTUs) is an important bioinformatics step in analyzing environmental sequencing data. Pairwise alignment and phylogenetic‐placement methods represent two alternative approaches to taxonomic assignments, but their results can differ. Here we used available colpodean ciliate OTUs from forest soils to compare the taxonomic assignments of VSEARCH (which performs pairwise alignments) and EPA‐ng (which performs phylogenetic placements). We showed that when there are differences in taxonomic assignments between pairwise alignments and phylogenetic placements at the subtaxon level, there is a low pairwise similarity of the OTUs to the reference database. We then showcase how the output of EPA‐ng can be further evaluated using GAPPA to assess the taxonomic assignments when there exist multiple equally likely placements of an OTU, by taking into account the sum over the likelihood weights of the OTU placements within a subtaxon, and the branch distances between equally likely placement locations. We also inferred the evolutionary and ecological characteristics of the colpodean OTUs using their placements within subtaxa. This study demonstrates how to fully analyze the output of EPA‐ng, by using GAPPA in conjunction with knowledge of the taxonomic diversity of the clade of interest.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Interpreting phylogenetic placements for taxonomic assignment of environmental DNA

Ewers

Rajter

Czech

et al. 2023

J Eukaryotic Microbiology

Self Cite

View full text Add to dashboard Cite

show abstract

“…Many of the colpodean OTUs analysed here had multiple likely placement locations on the reference tree. These alternative placements were not considered in most published phylogenetic placement studies using EPA-ng, (Aguirre-von-Wobeser, 2021;Bass et al, 2018;Fuchsman et al, 2022;Gottschling et al, 2021;Iniesto et al, 2021;Metz et al, 2021;Schoenle et al, 2020). Here, for the first time, we showcased together the features of the program GAPPA tool that can take multiple likely placements when performing taxonomic assignments into account.…”

Section: Additive Likelihood Values and Distances Between Placementsmentioning

confidence: 99%

“…Local or global pairwise alignment approaches (e.g., Needleman & Wunsch, 1970;Smith & Waterman, 1981) using a taxonomic reference database (e.g., Guillou et al, 2013;Ratnasingham & Hebert, 2007) are routinely used for such assignments in numerous metabarcoding studies. However, phylogenetic placement approaches for taxonomic assignments are being increasingly employed (Bass et al, 2018;Czech et al, 2022;Gottschling et al, 2021;Jamy et al, 2020). These two alternative approaches to assigning OTUs are beginning to be compared to each other (Hleap et al, 2021;Jamy et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Comparison of phylogenetic placements to pairwise alignments for taxonomic assignment of ciliate OTUs

Ewers

Rajter

Czech

et al. 2022

Preprint

Self Cite

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Taxonomic assignment of OTUs is an important bioinformatics step in analyzing environmental sequencing data. Pairwise-alignment and phylogenetic-placement methods represent two alternative approaches to taxonomic assignments, but their results can differ. Here we used available colpodean ciliate OTUs from forest soils to compare the taxonomic assignments of VSEARCH (which performs pairwise alignments) and EPA-ng (which performs phylogenetic placements). We showed that when there are differences in taxonomic assignments between pairwise alignments and phylogenetic placements at the subtaxon level, there is a low pairwise similarity of the OTUs to the reference database. We then showcase how the output of EPA-ng can be further evaluated using GAPPA to assess the taxonomic assignments when there exist multiple equally likely placements of an OTU, by taking into account the sum over the likelihood weights of the OUT placements within a subtaxon, and the branch distances between equally likely placement locations. We also inferred evolutionary and ecological characteristics of the colpodean OTUs using their placements within subtaxa. This study demonstrates how to fully analyse the output of EPA-ng, by using GAPPA in conjunction with knowledge of the taxonomic diversity of the clade of interest.

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“…Different biomonitoring studies in aquatic environments have used this approach for the survey of metazoans (Mitsi et al 2019 ), protists (Elferink et al 2017 ; Keck et al 2018 ; Gottschling et al 2021 ), and prokaryotes (López-Cortés et al 2020 ; Iniesto et al 2021 ). Recently, a comprehensive and curated cyanobacterial reference database that can be readily used for the phylogenetic placement of these organisms was released ( Cydrasil ; Roush et al 2021 ), widening the biomonitoring potential of this tool.…”

Section: Introductionmentioning

confidence: 99%

Improving environmental monitoring of Vibrionaceae in coastal ecosystems through 16S rRNA gene amplicon sequencing

Banchi

Manna

Fonti

et al. 2022

Environ Sci Pollut Res

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The Vibrionaceae family groups genetically and metabolically diverse bacteria thriving in all marine environments. Despite often representing a minor fraction of bacterial assemblages, members of this family can exploit a wide variety of nutritional sources, which makes them important players in biogeochemical dynamics. Furthermore, several Vibrionaceae species are well-known pathogens, posing a threat to human and animal health. Here, we applied the phylogenetic placement coupled with a consensus-based approach using 16S rRNA gene amplicon sequencing, aiming to reach a reliable and fine-level Vibrionaceae characterization and identify the dynamics of blooming, ecologically important, and potentially pathogenic species in different sites of the northern Adriatic Sea. Water samples were collected monthly at a Long-Term Ecological Research network site from 2018 to 2021, and in spring and summer of 2019 and 2020 at two sites affected by depurated sewage discharge. The 41 identified Vibrionaceae species represented generally below 1% of the sampled communities; blooms (up to ~ 11%) mainly formed by Vibrio chagasii and Vibrio owensii occurred in summer, linked to increasing temperature and particulate matter concentration. Pathogenic species such as Vibrio anguilllarum, Vibrio tapetis, and Photobacterium damselae were found in low abundance. Depuration plant samples were characterized by a lower abundance and diversity of Vibrionaceae species compared to seawater, highlighting that Vibrionaceae dynamics at sea are unlikely to be related to wastewater inputs. Our work represents a further step to improve the molecular approach based on short reads, toward a shared, updated, and curated phylogeny of the Vibrionaceae family.

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The Windblown: Possible Explanations for Dinophyte DNA in Forest Soils

Cited by 10 publications

References 65 publications

Interpreting phylogenetic placements for taxonomic assignment of environmental DNA

Interpreting phylogenetic placements for taxonomic assignment of environmental DNA

Comparison of phylogenetic placements to pairwise alignments for taxonomic assignment of ciliate OTUs

Improving environmental monitoring of Vibrionaceae in coastal ecosystems through 16S rRNA gene amplicon sequencing

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