Winogradsky columns as a strategy to study typically rare microbial eukaryotes

Winogradsky columns have been widely used to study soil microbial communities, but the vast majority of those investigations have focused on the ecology and diversity of bacteria. In contrast, microbial eukaryotes (ME) have been regularly overlooked in studies based on experimental soil columns. Despite the recognized ecological relevance of ME in soil communities, investigations focused on ME diversity and the abundance of certain groups of interest are still scarce. In the present study, we used DNA metabarcoding (high-throughput sequencing of the V4 region of the 18S rRNA locus) to survey the ME diversity and abundance in an experimental Winogradsky soil column. Consistent with previous surveys in natural soils, our survey identified members of Cercozoa (Rhizaria; 31.2%), Apicomplexa and Ciliophora (Alveolata; 12.5%) as the predominant ME groups, but at particular depths we also detected the abundant presence of ME lineages that are typically rare in natural environments, such as members of the Vampyrellida (Rhizaria) and Breviatea (Amorphea). Our survey demonstrates that experimental soil columns are an efficient enrichment-culture approach that can enhance investigations about the diversity and ecology of ME in soils.

Amplicon-based and metagenomic approaches provide insights into toxigenic potential in understudied Atlantic Canadian lakes

Cyanobacterial blooms and their toxigenic potential threaten freshwater resources worldwide. In Atlantic Canada, despite an increase of cyanobacterial blooms in the last decade, little is known about the toxigenic potential and the taxonomic affiliation of bloom-forming cyanobacteria. In this study, we employed polymerase chain reaction (PCR) and metagenomic approaches to assess the potential for cyanotoxin and other bioactive metabolite production in Harvey Lake (oligotrophic) and Washademoak Lake (mesotrophic) in New Brunswick, Canada, during summer and early fall months. The PCR survey detected the potential for microcystin (hepatotoxin) and anatoxin-a (neurotoxin) production in both lakes, despite a cyanobacterial bloom only being visible in Washademoak. Genus-specific PCR associated microcystin production potential with the presence of Microcystis in both lakes. The metagenomic strategy provided insight into temporal variations in the microbial communities of both lakes. It also permitted the recovery of a near-complete Microcystis aeruginosa genome with the genetic complement to produce microcystin and other bioactive metabolites such as piricyclamide, micropeptin/cyanopeptolin, and aeruginosin. Our approaches demonstrate the potential for production of a diverse complement of bioactive compounds and establish important baseline data for future studies of understudied lakes, which are frequently affected by cyanobacterial blooms.

Seasonality and distribution of cyanobacteria and microcystin toxin genes in an oligotrophic lake of Atlantic Canada

Cyanotoxins are an emerging threat to freshwater resources worldwide. The most frequently reported cyanotoxins are the microcystins, which threaten the health of humans, wildlife, and ecosystems. Determining the potential for microcystin production is hindered by a lack of morphological features that correlate with microcystin production. However, amplicon-based methods permit the detection of microcystin biosynthesis genes and were employed to assess the toxin potential in Lake Utopia, NB, Canada, an oligotrophic lake that occasionally experiences cyanobacteria blooms. Samples collected at 2 week intervals from June 27th to September 27th, 2016, were screened by polymerase chain reaction (PCR) for the microcystin synthetase E gene (mcyE). The mcyE gene was present in some samples every sampling day, despite microcystin not being detected via ELISA, and was most frequently associated with the larger pore size fractions of the serially filtered samples. Further PCR surveys using primer sets to amplify genus-specific (e.g., Microcystis, Anabaena/Dolichospermum, and Planktothrix) mcyE fragments identified Microcystis as the only taxa in Lake Utopia with toxigenic potential. Sequencing of the 16S rRNA V3-V4 region revealed a community dominated by members of the order Synechococcales (from 38 to 96% relative abundance), but with significant presence of taxa from Cyanobacteriales including Microcystaceae and Nostocaceae. A persistent Microcystis population was detected in samples both testing positive and negative for the mcyE gene, highlighting the importance of identifying cyanotoxin production potential by gene presence and not species identity. To our knowledge, this study represents the first application of amplicon-based approaches to studying toxic cyanobacteria in an understudied region-Atlantic Canada.