Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms

Marine microbial eukaryotes play critical roles in planktonic food webs and have been described as most diverse in the photic zone where productivity is high. We used high-throughput sequencing (HTS) to analyse the spatial distribution of planktonic ciliate diversity from shallow waters (<30 m depth) to beyond the continental shelf (>800 m depth) along a 163 km transect off the coast of New England, USA. We focus on ciliates in the subclasses Oligotrichia and Choreotrichia (class Spirotrichea), as these taxa are major components of marine food webs. We did not observe the decrease of diversity below the photic zone expected based on productivity and previous analyses. Instead, we saw an increase of diversity with depth. We also observed that the ciliate communities assessed by HTS cluster by depth layer and degree of water column stratification, suggesting that community assembly is driven by environmental factors. Across our samples, abundant OTUs tend to match previously characterized morphospecies while rare OTUs are more often undescribed, consistent with the idea that species in the rare biosphere remain to be characterized by microscopy. Finally, samples taken below the photic zone also reveal the prevalence of two uncharacterized (i.e. lacking sequenced morphospecies) clades - clusters X1 and X2 - that are enriched within the nano-sized fraction (2-10 μm) and are defined by deletions within the region of the SSU-rDNA analysed here. Together, these data reinforce that we still have much to learn about microbial diversity in marine ecosystems, especially in deep-waters that may be a reservoir for rare species and uncharacterized taxa.

show abstract

“…For example, analyses of a marine coastal environment found more than 8000 OTUs (Forster et al . ). However, Forster et al .…”

Section: Discussionmentioning

confidence: 97%

Unexpected biodiversity of ciliates in marine samples from below the photic zone

et al. 2016

View full text Add to dashboard Cite

show abstract

“…In particular, lineages in the class Spirotrichea often dominate ciliate communities in open ocean waters. They have a pivotal position in marine food webs as these largely heterotrophic lineages are predators of both phytoplankton and bacteria [8–10]. Members of the class Spirotrichea have been observed in a wide range of locations: from surface to the deep ocean [10, 11], and from polar to tropical waters [9, 12].…”

Section: Introductionmentioning

confidence: 99%

“…They have a pivotal position in marine food webs as these largely heterotrophic lineages are predators of both phytoplankton and bacteria [8–10]. Members of the class Spirotrichea have been observed in a wide range of locations: from surface to the deep ocean [10, 11], and from polar to tropical waters [9, 12]. Previous studies by morphological analysis [12–15] or by molecular approaches (e.g.…”

Section: Introductionmentioning

confidence: 99%

Patchiness of Ciliate Communities Sampled at Varying Spatial Scales along the New England Shelf

2016

View full text Add to dashboard Cite

Although protists (microbial eukaryotes) provide an important link between bacteria and Metazoa in food webs, we do not yet have a clear understanding of the spatial scales on which protist diversity varies. Here, we use a combination of DNA fingerprinting (denaturant gradient gel electrophoresis or DGGE) and high-throughput sequencing (HTS) to assess the ciliate community in the class Spirotrichea at varying scales of 1–3 km sampled in three locations separated by at least 25 km—offshore, midshelf and inshore—along the New England shelf. Analyses of both abundant community (DGGE) and the total community (HTS) members reveal that: 1) ciliate communities are patchily distributed inshore (i.e. the middle station of a transect is distinct from its two neighboring stations), whereas communities are more homogeneous among samples within the midshelf and offshore stations; 2) a ciliate closely related to Pelagostrobilidium paraepacrum ‘blooms’ inshore and; 3) environmental factors may differentially impact the distributions of individual ciliates (i.e. OTUs) rather than the community as a whole as OTUs tend to show distinct biogeographies (e.g. some OTUs are restricted to the offshore locations, some to the surface, etc.). Together, these data show the complexity underlying the spatial distributions of marine protists, and suggest that biogeography may be a property of ciliate species rather than communities.

show abstract

“…Indeed, the number and nature of polymorphisms and of true subpopulations included within a single, similarity-based OTU cluster can vary greatly across OTUs 23 . A number of recently introduced algorithms aim to account for such variation using graph-based clustering approaches and grouping sequences based on local base differences between reads rather than by overall percent similarity 24,25 . These algorithms have proved successful in identifying higher-resolution sequence clusters and more accurately describing the population structure in each sample.…”

Section: High-resolution Characterization Of the Microbiome's Taxonommentioning

confidence: 99%

High-resolution characterization of the human microbiome

Noecker

McNally

Eng

et al. 2017

Translational Research

View full text Add to dashboard Cite

The human microbiome plays an important and increasingly recognized role in human health. Studies of the microbiome typically employ targeted sequencing of the 16S rRNA gene, whole metagenome shotgun sequencing, or other meta-omic technologies to characterize the microbiome's composition, activity, and dynamics. Processing, analyzing, and interpreting these data involve numerous computational tools that aim to filter, cluster, annotate, and quantify the obtained data and ultimately provide an accurate and interpretable profile of the microbiome's taxonomy, functional capacity, and behavior. These tools, however, are often limited in resolution and accuracy and may fail to capture many biologically- and clinically-relevant microbiome features, such as strain-level variation or nuanced functional response to perturbation. Over the past few years, extensive efforts have been invested toward addressing these challenges and developing novel computational methods for accurate and high-resolution characterization of microbiome data. These methods aim to quantify strain-level composition and variation, detect and characterize rare microbiome species, link specific genes to individual taxa, and more accurately characterize the functional capacity and dynamics of the microbiome. These methods and the ability to produce detailed and precise microbiome information are clearly essential for informing microbiome-based personalized therapies. In this review, we survey these methods, highlighting the challenges each method sets out to address and briefly describing methodological approaches.

show abstract

Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms

Cited by 48 publications

References 72 publications

Unexpected biodiversity of ciliates in marine samples from below the photic zone

Unexpected biodiversity of ciliates in marine samples from below the photic zone

Patchiness of Ciliate Communities Sampled at Varying Spatial Scales along the New England Shelf

High-resolution characterization of the human microbiome

Contact Info

Product

Resources

About