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

Abstract

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.

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

“…We hypothesized that ciliate communities will be the similar in samples taken close together and that beyond some minimum distance, the community membership changes. We also expected to find strong assemblage changes related to the distance from shore as previously observed [16, 17, 19] such that communities are more diverse offshore. To evaluate these hypotheses, we contrasted the biogeographies of individual taxa (operational taxonomic units, or OTUs) with those of whole assemblages and evaluated patterns associated with physical and biological features of the environment.…”

“…Analyses of oligotrich and choreotrich ciliates, the main focus of the current study, have found complex patterns of diversity on a large spatial scale (transect of 130 km with samples every 6 km) [16, 17]. These studies reveal that the patterns of variation in ciliate communities are related to distance from shore and to the degree of water column stratification, as evidenced both by analyses of DGGE and HTS [16, 17, 19]. …”

“…The raw reads are available under the BioProject PRJNA339757 and Sequence Read Archive SRP082687. We analyzed the data following recommendations from previous studies [16, 19, 33, 34]. In summary, OTU libraries were built in QIIME version 1.9.1 [35], clustering with Uclust 1.2.22q at 99% similarity [36].…”

“…phylotypes) and all common phylotypes were excised from the gels, amplified by 10 cycles of PCR, and sequenced by the Sanger method (GenBank accession numbers KX714479-KX714518). The resulting phylotypes from DGGE and the OTUs from HTS were compared to our curated list of morphospecies sequences from GenBank and DGGE phylotypes from previous studies [16, 17, 19]. We used two approaches to assign taxonomy: a BLAST approach and a phylogenetic approach.…”

Ciliate micrograzer dynamics of the New England Shelf

“…DNA sequencing has contributed to the study of protist communities, providing new insight into diversity (Pawlowski et al, 2016), predator-prey interactions (Martinez-Garcia et al, 2012), and discrepancies between morphologically defined species and genotypes (Stoupin et al, 2012;Santoferrara et al, 2016) .…”