Spatial variation in RNA:DNA ratios of Diporeia spp. in the Great Lakes region

Abstract

Over the past two decades, Diporeia in all of the Laurentian Great Lakes, except Superior, have declined dramatically. These declines have seemingly coincided with expansion of invasive Dreissena polymorpha and D. bugensis, however the exact mechanisms underlying decreasing Diporeia densities are obscure. We explored the use of RNA:DNA (R/D) ratios as a conditional index for Diporeia by experimentally demonstrating that Diporeia R/D responds to periods of starvation. Moreover, during 2008-2009 we collected Diporeia from throughout the Great Lakes and Cayuga Lake (New York, USA), and used R/D ratios to index condition of these in situ collected animals. We evaluated spatial and temporal variation of nucleic acid indices using classification and regression tree (CART) analysis with a suite of environmental variables included as potential predictors. Diporeia R/D of in situ collected specimens exhibited pronounced spatial and temporal variation, but multiple CART models described only a small amount of this variation. While we observed some variation in Diporeia R/D among lakes, nucleic acid ratios appeared to respond weakly to Diporeia population characteristics and local environmental conditions. Specifically, CART analyses revealed that Diporeia R/D was particularly low at extreme depths, and interestingly, Diporeia nucleic acids were not strongly associated with the presence of dreissenids. In summary, while a limited amount of variation in Diporeia R/D was attributable to environmental conditions, the majority of Diporeia R/D variation was unaccounted for. Hence, the causative factors underlying spatio-temporal variation of Diporeia R/D and the mechanistic reasons for Diporeia declines in the Great Lakes remain largely unknown.

An eDNA/eRNA‐based approach to investigate the life cycle of non‐cultivable shellfish micro‐parasites: the case of Bonamia ostreae, a parasite of the European flat oyster Ostrea edulis

“…Bonamia ostreae RNA detection limit appeared 10 times lower than DNA one, indicating a higher sensitivity of the RNA‐based approach. While the gene encoding 18S RNA might be present in several copies in the parasite genome, RNA and more particularly ribosomal RNA are expected to be much more abundant, depending notably on the metabolism of the cells (Roberts et al , 2011; Ryan et al , 2012).…”

Distribution of circular single‐stranded DNA viruses associated with benthic amphipods of genus Diporeia in the Laurentian Great Lakes

“…Finger Lakes benthic communities in central New York; Watkins et al., ). Hypotheses attributing changes in Diporeia abundance to niche displacement and bivalve‐imposed food limitation (either through the interception of detrital deposits or mitigation of calcite‐dependent phytoplankton blooms) have been refuted both in situ and in mesocosm trials (Dermott, Bonnell, & Jarvis, ; Nalepa, Fanslow, & Foley, ; Nalepa et al., ; Ryan, Sepúlveda, Nalepa, & Höök, ; Watkins et al., ). Diporeia population densities are also poorly associated with variation in lake productivity, benthic flux of organic carbon and fish predation (Watkins et al., ).…”

Stable isotope patterns of benthic organisms from the Great Lakes region indicate variable dietary overlap ofDiporeiaspp. and dreissenid mussels

“…At each site, we collected three additional grab samples, which were stored in 10% formalin stained with Rose Bengal until processing. Upon return to the laboratory, we picked organisms from these samples under a dissecting microscope and placed them in 70% ethanol for long-term storage (see Ryan et al 2012 for details). Historic specimens of Diporeia were obtained from samples collected in fall from sites C-5 and H-11 in Lake Michigan in 1986, 1992 (Fig.…”