Utility of Genetic Markers and Morphology for Species Discrimination within the Order Tintinnida (Ciliophora, Spirotrichea)

Santoferrara, Luciana F.; McManus, George B.; Alder, V.A.

doi:10.1016/j.protis.2011.12.002

Cited by 69 publications

(130 citation statements)

References 57 publications

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“…The lorica is the main character used to delimit tintinnid morphospecies, which agree partially with OTUs defined by ribosomal DNA sequences (Santoferrara et al, 2013). Tintinnids are major consumers of phytoplankton, and their feeding ecology relates to morphology given that prey size is determined by the diameter of the lorica aperture (Dolan et al, 2013a, b).…”

Section: Introductionmentioning

confidence: 76%

“…Each dominant OTU (generally correlated to the distribution of their corresponding morphospecies, if known) was associated with multiple, closely-related OTUs (that is, same cluster in RAxML tree and similarity 499%) that usually occurred in the same samples but with many fewer reads (Figures 3a-e). These variants may result from the known intraindividual and intra-specific variability in tintinnid SSU rDNA (Gong et al, 2013;Santoferrara et al, 2013) or from HTS errors (Reeder and Knight, 2009), in part retained in the data due to our OTU clustering at 100% similarity. A lower cutoff is not adequate for our amplicon because that can cause sequences of separate known species to be clustered into the same OTU Santoferrara et al, 2014).…”

Section: Comparison Of Tintinnid Morphospecies and Otusmentioning

confidence: 99%

“…Loricae containing their cell were counted, measured and identified following original descriptions and the work of Alder (1999). Morphospecies found in non-acid Lugol's samples were isolated and sequenced using the method by Santoferrara et al (2013). The small subunit ribosomal DNA (SSU rDNA) sequences from 10 morphospecies, 5 of them newly sequenced, were deposited in NCBI GenBank (accession codes KT792924 to KT792933; Supplementary Results).…”

Section: Samplingmentioning

confidence: 99%

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Patterns and processes in microbial biogeography: do molecules and morphologies give the same answers?

et al. 2016

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Our knowledge on microbial biogeography depends on the way we define and study diversity. In contrast to most microbes, some protist lineages have conspicuous structures that allow comparisons of diversity concepts and measures-those based on molecules and those based on morphology. We analyzed a group of shell-bearing planktonic ciliates, the tintinnids, in a coast-to-ocean gradient using highthroughput sequencing and microscopy. First, we compared molecular operational taxonomic units (OTUs) and morphospecies in terms of assemblage composition, distribution and relationships with the environment. OTUs revealed potentially novel and rare taxa, while morphospecies showed clearer correlations with environmental factors, and both approaches coincided in supporting a coastal versus oceanic pattern. Second, we explored which processes influence assembly across the environmental gradient examined. Assemblage fluctuations were associated with significant distance-decay and changes in morphospecies size and prey proxies, thus suggesting niche partitioning as a key structuring mechanism. Our conclusion is that molecules and morphologies generally agreed, but they provided complementary data, the first revealing hidden diversity, and the latter making better connections between distribution patterns and ecological processes. This highlights the importance of linking genotypes and phenotypes (using multidisciplinary analyses and/or reliable databases of barcoded species), to understand the diversity, biogeography and ecological roles of microbes.

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Section: Introductionmentioning

confidence: 76%

Section: Comparison Of Tintinnid Morphospecies and Otusmentioning

confidence: 99%

Section: Samplingmentioning

confidence: 99%

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Patterns and processes in microbial biogeography: do molecules and morphologies give the same answers?

et al. 2016

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“…Tintinnids, in particular, because of their distinct, but diverse morphology, are a model group for these 'hybrid' studies (Santoferrara et al, 2012. Mesodinium spp., the autotrophic ciliate, presents cryptic diversity (Garcia-Cuetos et al, 2012a;Johnson et al, 2016) through a species complex of 8 different subclades, but contrastingly also presents various morphologies.…”

Section: Modern Advancements In Ciliate Methodsmentioning

confidence: 99%

Ciliate micrograzer dynamics of the New England Shelf

Brownlee¹

2017

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Protists play important roles in grazing and nutrient recycling, but quantifying these roles has been hindered by difficulties in collecting, culturing, and observing these often-delicate cells. During long-term deployments at the Martha's Vineyard Coastal Observatory (MVCO) (Massachusetts, USA), Imaging FlowCytobot (IFCB) made it possible to study live cells in situ without the need to culture or preserve. IFCB records images of cells with chlorophyll fluorescence above a trigger threshold, so taxonomically resolved analysis of protists is limited to mixotrophs and herbivores, which have eaten recently. To overcome this limitation, I coupled a broad-application 'live cell' fluorescent stain with a modified IFCB so that protists which do not contain chlorophyll (such as consumers of unpigmented bacteria and other heterotrophs) can also be recorded. Staining IFCB (IFCB-S) revealed higher abundances of grazers than the original IFCB, as well as some cell types not previously detected. To analyze a 10-year time series of herbivorous ciliates at MVCO and address broad patterns of seasonality of major ciliate classes and their components, I employed a statistical model that estimates a seasonal density pattern and simultaneously accounts for and separates any annual-scale effects. I describe the seasonality of three functional groups: a phototrophic ciliate, a mixotroph, and a group of strict heterotrophs, and comment on potential drivers of these patterns. DNA sequencing has also contributed to the study of protist communities, providing new insight into diversity, predator-prey interactions, and discrepancies between morphologically defined species and genotype. To explore how well IFCB images can be used to detect seasonal community change of the class Spirotrichea, an important and numerous group, I used high-throughput sequencing (HTS), which does not discriminate between chlorophyll-containing cells and the rest of the community. I report on species and genera of ciliates for which morphotype and genotype displayed high congruency. In comparing how well temporal aspects of genotypes and morphotypes correspond, I found that HTS was critical to detect and identify certain ciliates occupying a niche associated with warmer temperatures. I further showed that when these types of analyses are combined with IFCB results, they can provide hypotheses about food preferences. These last six and a half years have been full of scientific and self-discovery. I could not have pursued this adventure without a village of support. I'd like to thank all of these people.To my advisor, Heidi, your guidance, patience, and belief in me is something I will always cherish and never forget. Apart from being an amazing advisor in a academic way (opening my eyes to diverse questions, guiding my writing, etc.), you also helped me with many life obstacles and stimulated me during my difficult moments. I am forever grateful I had you as role model throughout these years and for that I am a better scientist.To Rob, thank you for takin...

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“…Although the LSU rDNA has not been utilized to analyze Oligotrichia, its utility has been demonstrated in an investigation of a related group, the Tintinnida (Spirotrichea: Choreotrichia) (Santoferrara et al, 2013). …”

Section: Introductionmentioning

confidence: 99%

Multi-gene-based phylogenetic analysis of oligotrich ciliates with emphasis on two dominant groups: Cyrtostrombidiids and strombidiids (Protozoa, Ciliophora)

Gao

Song

et al. 2016

Molecular Phylogenetics and Evolution

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-based phylogenetic analysis of oligotrich ciliates with emphasis on two dominant groups: cyrtostrombidiids and strombidiids (Protozoa, Ciliophora), Molecular Phylogenetics and Evolution (2016), doi: http://dx.doi.org/10. 1016/j.ympev.2016.08.019 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. ABSTRACTPhylogenetic analyses of ciliated protists are frequently based on single molecular markers, usually the small subunit ribosomal RNA gene (SSU rDNA), despite the well-known limitations of this approach.Here, 78 new sequences of three linked genes (SSU rDNA, ITS1-5.8S rDNA-ITS2, LSU rDNA) were characterized and applied to phylogenetic analyses of oligotrichs (s. str.). It was found that: (1) and Apostrombidium is confirmed, which updates the evolutionary hypothesis for oligotrichs based on ciliary patterns; and (5) two relatively stable clades were found in the family Strombidiidae.

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Utility of Genetic Markers and Morphology for Species Discrimination within the Order Tintinnida (Ciliophora, Spirotrichea)

Cited by 69 publications

References 57 publications

Patterns and processes in microbial biogeography: do molecules and morphologies give the same answers?

Patterns and processes in microbial biogeography: do molecules and morphologies give the same answers?

Ciliate micrograzer dynamics of the New England Shelf

Multi-gene-based phylogenetic analysis of oligotrich ciliates with emphasis on two dominant groups: Cyrtostrombidiids and strombidiids (Protozoa, Ciliophora)

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