Analysis of the community structure of abyssal kinetoplastids revealed similar communities at larger spatial scales

Abstract

Knowledge of the spatial scales of diversity is necessary to evaluate the mechanisms driving biodiversity and biogeography in the vast but poorly understood deep sea. The community structure of kinetoplastids, an important group of microbial eukaryotes belonging to the Euglenozoa, from all abyssal plains of the South Atlantic and two areas of the eastern Mediterranean was studied using partial small subunit ribosomal DNA gene clone libraries. A total of 1364 clones from 10 different regions were retrieved. The analysis revealed statistically not distinguishable communities from both the South-East Atlantic (Angola and Guinea Basin) and the South-West Atlantic (Angola and Brazil Basin) at spatial scales of 1000-3000 km, whereas all other communities were significantly differentiated from one another. It seems likely that multiple processes operate at the same time to shape communities of deep-sea kinetoplastids. Nevertheless, constant and homogenous environmental conditions over large spatial scales at abyssal depths, together with high dispersal capabilities of microbial eukaryotes, maintain best the results of statistically indistinguishable communities at larger spatial scales.

Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans

“…Geographic distance explained only a small part (10%) of the genetic variability among samples (Figure 3b), and in fact only a few geographically close stations had a very similar community composition (for example, 17 and 19; 112 and 121). Similarity among nearby samples has been found in other studies of marine microbial eukaryotes at spatial scales of thousands of kilometers (Scheckenbach et al, 2010;Salani et al, 2012) and it is likely caused by similar environmental conditions in nearby sites. In our study, the most important factor explaining microbial eukaryotic composition was the water mass type, which explained 26% of the variability observed, and a similar effect has been reported for marine prokaryotes (Agogué et al, 2008;Varela et al, 2008;Galand et al, 2009;Kirchman et al, 2010).…”

“…Most of these studies focused on the water column, always in a regional scale, either by using universal eukaryotic primers (López-García et al, 2001;Stoeck et al, 2003;Countway et al, 2007;Not et al, 2007;Edgcomb et al, 2011b) or group-specific primers (Bass et al, 2007;Lara et al, 2009). Other diversity studies were done in benthic environments, such as deep-sea subsurface and surface sediments (Edgcomb et al, 2011a;Salani et al, 2012) or in hydrothermal vents (Edgcomb et al, 2002;Sauvadet et al, 2010). The bathypelagic microbial eukaryotic diversity has also been studied by fluorescence in situ hybridization staining (Morgan-Smith et al, 2011;Morgan-Smith et al, 2013).…”

Diversity, Ecology and Biogeochemistry of Cyst-Forming Acantharia (Radiolaria) in the Oceans

“…Cloning and sequencing analyses suggest that the diversity of protists, as it is the case for bacteria [46], appears to decline in deep layers, where Radiolaria (including Acantharia), Alveolata and Euglenozoa have been reported to be the most abundant eukaryotic taxa [16], [18], [47]. Our study confirms that Acantharia, and more specifically clades I, A, B and C, can represent an important component of deep-sea protists worldwide, up to 11% of the environmental tag sequences.…”

Methodological Studies on Estimates of Abundance and Diversity of Heterotrophic Flagellates from the Deep-Sea Floor

“…Molecular environmental diversity studies of the deep-sea floor have mainly been focusing on assumed "hot spots" of activity (e.g., hydrothermal vents, methane seeps) mostly from the bathyal zone carried out on a local scale [26][27][28]. Our previous studies of deep-sea nanofauna [29][30][31][32][33] indicated the existence of a specific abyssal nanofauna which contains a large number of endemic taxa [31,33].Recent comprehensive studies [34] indicated protists as the most diverse eukaryotic organisms. The diversity of phyla ( Figure 1) with their specific differences (e.g., ultrastructure) makes it necessary to consider specifically designed fixatives or molecular techniques.…”

“…The methodological spectrum of next-generation sequencing (NGS) and DNA-barcoding for HF has increased significantly in the last years [17,34]. Conserved samples for bulk analysis of RNA (active organisms, metatranscriptomics) and DNA (whole metagenome studies) can be used to analyze the presence of protist genotypes in the deep sea [31,33]. However, there are still some unsolved problems like specific instead of general primers, different rRNA copy numbers for protists, PCR biases, the difficulty of differentiating active from inactive forms (e.g., cysts), and incomplete databases containing incorrect labeled species [45,55,56].…”