Ciliates (Alveolata, Ciliophora) as bioindicators of environmental pressure: A karstic river case

Kulaš, Antonija; Gulin, Vesna; Kepčija, Renata Matoničkin; Žutinić, Petar; Perić, Mirela Sertić; Orlić, Sandi; Kajan, Katarina; Stoeck, Thorsten; Lentendu, Guillaume; Čanjevac, Ivan; Martinić, Ivan; Udovič, Marija Gligora

doi:10.1016/j.ecolind.2021.107430

“…They are united by their unique cortex arrangement, nuclear dualism, and conjugation as a sexual process (Dunthorn and Katz 2008;Lynn 2008). As ciliates populate most of the aquatic and terrestrial ecosystems on Earth, they are often used to evaluate microbial biodiversity and biogeography (Finlay 2002;Foissner et al 2009;Dunthorn et al 2014a;Lentendu et al 2018;Venter et al 2018) and for biomonitoring of stressed environments (Stoeck 2018;Dias et al 2021;Kulaš et al 2021). The latest classification system of the ciliates recognized eleven main ciliate taxa (Armophorea, Colpodea, Heterotrichea, Karyorelictea, Litostomatea, Nassophorea, Oligohymenophorea, Phyllopharyngea, Plagiopylea, Prostomatea, and Spirotrichea), which are grouped into several higher taxa (Adl et al 2019) (Fig.…”

Section: Introductionmentioning

confidence: 99%

Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data

Rajter¹,

Dunthorn²

2021

MBMG

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Although ciliates are one of the most dominant microbial eukaryotic groups in many environments, there is a lack of updated global ciliate alignments and reference trees that can be used for phylogenetic placement methods to analyze environmental metabarcoding data. Here we fill this gap by providing reference alignments and trees for those ciliates taxa with available SSU-rDNA sequences derived from identified species. Each alignment contains 478 ciliate and six outgroup taxa, and they were made using different masking strategies for alignment positions (unmasked, masked and masked except the hypervariable V4 region). We constrained the monophyly of the major ciliate groups based on the recently updated classification of protists and based on phylogenomic data. Taxa of uncertain phylogenetic position were kept unconstrained, except for Mesodinium species that we constrained to form a clade with the Litostomatea. These ciliate reference alignments and trees can be used to perform taxonomic assignments of metabarcoding data, discover novel ciliate clades, estimate species richness, and overlay measured ecological parameters onto the phylogenetic placements.

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“…In this study, we have samples from 5 stations from inner harbour centre that represent a clear gradient of increasing metal concentrations, decreasing macroinvertebrate and eukaryote richness detected using COI and 18S metabarcoding. Ciliates, despite their ubiquity in freshwater systems, the key position they play in trophic webs (feed on bacteria, algae, other protists while also being consumed by other meiofauna) and known sensitivity to a range of water quality types (low to highly polluted), are often a neglected in water quality assessments 49 .…”

Section: Discussionmentioning

confidence: 99%

Multi-marker DNA metabarcoding detects suites of environmental gradients from an urban harbour

Robinson

¹

,

Porter

²

,

McGee

³

et al. 2022

Sci Rep

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There is increasing need for biodiversity monitoring, especially in places where potential anthropogenic disturbance may significantly impact ecosystem health. We employed a combination of traditional morphological and bulk macroinvertebrate metabarcoding analyses to benthic samples collected from Toronto Harbour (Ontario, Canada) to compare taxonomic and functional diversity of macroinvertebrates and their responses to environmental gradients. At the species rank, sites assessed using COI metabarcoding showed more variation than sites assessed using morphological methods. Depending on the assessment method, we detected gradients in magnesium (morphological taxa), ammonia (morphological taxa, COI sequence variants), pH (18S sequence variants) as well as gradients in contaminants such as metals (COI & 18S sequence variants) and organochlorines (COI sequence variants). Observed responses to contaminants such as aromatic hydrocarbons and metals align with known patchy distributions in harbour sediments. We determined that the morphological approach may limit the detection of macroinvertebrate responses to lake environmental conditions due to the effort needed to obtain fine level taxonomic assignments necessary to investigate responses. DNA metabarcoding, however, need not be limited to macroinvertebrates, can be automated, and taxonomic assignments are associated with a certain level of accuracy from sequence variants to named taxonomic groups. The capacity to detect change using a scalable approach such as metabarcoding is critical for addressing challenges associated with biodiversity monitoring and ecological investigations.

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“…In this study, we have samples from 5 stations from inner harbour centre that represent a clear gradient of increasing metal concentrations, decreasing macroinvertebrate richness detected using COI metabarcoding, and increasing relative read abundance of the ciliate group Haptoria using 18S metabarcoding. Ciliates, despite their ubiquity in freshwater systems, the key position they play in trophic webs (feed on bacteria, algae, other protists while also being consumed by other meiofauna) and known sensitivity to a range of water quality types (low to highly polluted), they are often a neglected in water quality assessments 49 .…”

Section: Discussionmentioning

confidence: 99%

Multi-marker DNA metabarcoding detects suites of environmental gradients from an urban harbour

Robinson

¹

,

Porter

²

,

McGee

³

et al. 2022

Preprint

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There is increasing need for biodiversity monitoring, especially in places where potential anthropogenic disturbance may significantly impact ecosystem health. We employed a combination of traditional morphological and bulk macroinvertebrate metabarcoding analyses to benthic samples collected from Toronto Harbour (Ontario, Canada) to compare taxonomic and functional diversity of macroinvertebrates and their responses to environmental gradients. At the species rank, sites assessed using COI metabarcoding showed more variation than sites assessed using morphological methods. Depending on the assessment method, we detected gradients in magnesium (morphological taxa), ammonia (morphological taxa, COI sequence variants), pH (18S sequence variants) as well as gradients in contaminants such as metals (COI & 18S sequence variants) and organochlorines (COI sequence variants). Observed responses to contaminants such as aromatic hydrocarbons and metals align with known patchy distributions in harbour sediments. We determined that the morphological approach may limit the detection of macroinvertebrate responses to lake environmental conditions due to the effort needed to obtain fine level taxonomic assignments necessary to investigate responses. DNA metabarcoding, however, need not be limited to macroinvertebrates, can be automated, and taxonomic assignments are associated with a certain level of accuracy from sequence variants to named taxonomic groups. The capacity to detect change using a scalable approach such as metabarcoding is critical for addressing challenges associated with biodiversity monitoring and ecological investigations.

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Ciliates (Alveolata, Ciliophora) as bioindicators of environmental pressure: A karstic river case

Cited by 28 publications

References 68 publications

Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data

Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data

Multi-marker DNA metabarcoding detects suites of environmental gradients from an urban harbour

Multi-marker DNA metabarcoding detects suites of environmental gradients from an urban harbour

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