Lineage-specific molecular probing reveals novel diversity and ecological partitioning of haplosporidians

Abstract

Haplosporidians are rhizarian parasites of mostly marine invertebrates. They include the causative agents of diseases of commercially important molluscs, including MSX disease in oysters. Despite their importance for food security, their diversity and distributions are poorly known. We used a combination of group-specific PCR primers to probe environmental DNA samples from planktonic and benthic environments in Europe, South Africa and Panama. This revealed several highly distinct novel clades, novel lineages within known clades and seasonal (spring vs autumn) and habitatrelated (brackish vs littoral) variation in assemblage composition. High frequencies of haplosporidian lineages in the water column provide the first evidence for life cycles involving planktonic hosts, host-free stages or both. The general absence of haplosporidian lineages from all large online sequence data sets emphasises the importance of lineage-specific approaches for studying these highly divergent and diverse lineages. Combined with host-based field surveys, environmental sampling for pathogens will enhance future detection of known and novel pathogens and the assessment of disease risk.

Assessing myxozoan presence and diversity using environmental DNA

“…Our results suggest that even within pooled DNA extractions from very large volume samples, myxosporean diversity is limited when compared to other parasites (e.g. Hartikainen et al 2014a). For example, the large volume freshwater samples contained on average only 16 OTUs (max 28, min 4) and the species accumulation curves (see Supplementary Fig.…”

“…Filtrands were subsequently dried in a freeze-drier at -56°C for approx. 12h to 115 remove residual moisture and DNA was extracted using the MoBio UltraSoil kit (MoBio Laboratories, Carlsbad, CA, USA) (Hartikainen et al 2014a, as described for the WEY sample set).…”

“…These samples represented a total of 386 DNA extractions of filtrands collected variously as 135 follows (1) South Africa (SA): 80 water samples (~2-10L) collected in December 2011 from freshwater and marine sites (Hartikainen et al, 2014a), (2) Weymouth, southwest England (WEY ENV): 20 DNA extractions incorporating material from six 150L marine water samples filtered serially through >55µ, 20µm and 0.45µm (Hartikainen et al, 2014a) …”

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“…After the identification of novel variants of OTUs and amplicons, the next step in the discovery of novel diversity is normally the design of specific primers and probes for the targeted recovery of organisms from environmental samples (Edgcomb et al, 2011b;Gimmler and Stoeck, 2015;Hartikainen et al, 2014;Orsi et al, 2012;Seenivasan et al, 2013). However, this process is time-, cost-, and labor-…”

“…The detection of novel diversity, in specific, uses a strategy that detects reads distantly related to previously sequenced species (e.g. Berney et al, 2013;Dunthorn et al, 2014b;Edgcomb et al, 2011b;Filker et al, 2014;Hartikainen et al, 2014;Gimmler and Stoeck 2015). While the detection and description of novel protists is a central task since our understanding of their diversity is far from complete , our ability to detect novel diversity in molecular environmental studies is affected by the way in which we cluster reads into operational taxonomic units (OTUs).…”