Genomic copy number variability at the genus, species and population levels impacts in situ ecological analyses of dinoflagellates and harmful algal blooms

Abstract

The application of meta-barcoding, qPCR, and metagenomics to aquatic eukaryotic microbial communities requires knowledge of genomic copy number variability (CNV). CNV may be particularly relevant to functional genes, impacting dosage and expression, yet little is known of the scale and role of CNV in microbial eukaryotes. Here, we quantify CNV of rRNA and a gene involved in Paralytic Shellfish Toxin (PST) synthesis (sxtA4), in 51 strains of 4 Alexandrium (Dinophyceae) species. Genomes varied up to threefold within species and ~7-fold amongst species, with the largest (A. pacificum, 130 ± 1.3 pg cell−1 /~127 Gbp) in the largest size category of any eukaryote. Genomic copy numbers (GCN) of rRNA varied by 6 orders of magnitude amongst Alexandrium (102– 108 copies cell−1) and were significantly related to genome size. Within the population CNV of rRNA was 2 orders of magnitude (105 – 107 cell−1) in 15 isolates from one population, demonstrating that quantitative data based on rRNA genes needs considerable caution in interpretation, even if validated against locally isolated strains. Despite up to 30 years in laboratory culture, rRNA CNV and genome size variability were not correlated with time in culture. Cell volume was only weakly associated with rRNA GCN (20–22% variance explained across dinoflagellates, 4% in Gonyaulacales). GCN of sxtA4 varied from 0–102 copies cell−1, was significantly related to PSTs (ng cell−1), displaying a gene dosage effect modulating PST production. Our data indicate that in dinoflagellates, a major marine eukaryotic group, low-copy functional genes are more reliable and informative targets for quantification of ecological processes than unstable rRNA genes.

Potential Role of Sugars in the Hyphosphere of Arbuscular Mycorrhizal Fungi to Enhance Organic Phosphorus Mobilization

“…This represents the proportion of bacteria that possess these functional genes or have a large copy number of these genes in the bacterial community. Bacteria with larger gene copy numbers may potentially exhibit stronger functionality for that gene [ 56 ].…”

A comparison of two gene regions for assessing community composition of eukaryotic marine microalgae from coastal ecosystems

“…Higher taxonomic resolution achieved using the V4 marker for dinoflagellates may be a consequence of high sequence variation of dinoflagellates within the V4 region 41 , or the greater length of this region increasing the chances of species level nucleotide variation being captured. Dinoflagellates have been shown to have very high rDNA copy number with a lot of variation even within a strain 47 , 48 . This bias to dinoflagellates may also influence the higher levels of diversity indicated by the Shannon and inverse Simpson indices for the V4 region compared to the Chao1.…”

Mapping Selected Emergent Marine Toxin-Producing Organisms Using Historical Samples with Two Methods (Biosensors and Real-Time PCR): A Comparison of Resolution

“…Several of these HAB taxa were associated with ocean temperature or salinity changes [4,29] The biosensor detection was applied to DNA limited quantification of taxa by signal strength. There is much variation in ribosomal rDNA copy numbers between harmful algal genera/species, and it can vary up to six-fold within the Alexandrium genus [48]. Without relating DNA copies to species-specific cell numbers, there is no indication of cell numbers.…”