Lake Erie field trials to advance autonomous monitoring of cyanobacterial harmful algal blooms

Abstract

Biomolecular analyses are used to investigate the dynamics of cyanobacterial harmful algal blooms (cyanoHABs), with samples collected during monitoring often analyzed by qPCR and sometimes amplicon and metagenomic sequencing. However, cyanoHAB research and monitoring programs face operational constraints due to the reliance on human resources for sample collections. To address this impediment, a third-generation Environmental Sample Processor (3G ESP) integrated with a long-range autonomous underwater vehicle (LRAUV) was tested during seasonal blooms of Microcystis in western Lake Erie (WLE) in 2018 and 2019. The LRAUV-3G ESP successfully performed flexible, autonomous sampling across a wide range of cyanoHAB conditions, and results indicated equivalency between autonomous and manual methods. No significant differences were found between LRAUV-3G ESP and manual sample collection and handling methods in the 12 parameters tested. Analyzed parameters included concentrations of total cyanobacteria and microcystin toxin gene via qPCR; relative abundances of bacterial amplicon sequence variants (ASVs) from 16S rRNA gene amplicon sequencing; and community diversity measures from both 16S amplicon and metagenomic sequencing. The LRAUV-3G ESP provided additional sampling capacity and revealed differences between field seasons for bacterial taxa and concentrations of total cyanobacteria and microcystin toxin gene. Metagenomic analysis of multiple microcystin toxin genes corroborated the use of the mcyE gene as a proxy for the genomic potential of WLE cyanoHABs to produce microcystin. Overall, this study provides support for the use of autonomous ‘omics capability in WLE to help expand the spatial and temporal coverage of cyanoHAB monitoring operations.

Compact and automated eDNA sampler for in situ monitoring of marine environments

“…This is despite differences in the protocol such as volume filtered and temporal resolution, aligning with prior studies, which have shown similar results 42,43 . A recent study performed using the 3G ESP also demonstrated that results were equivalent between autonomous and manual sampling 44 . Interestingly, sample volumes in the ESP study were reversed where the autonomous sampler filtered a higher volume (1 L), and the manual sampling filtered a lower volume (36-100 mL) 44 .…”

“…A recent study performed using the 3G ESP also demonstrated that results were equivalent between autonomous and manual sampling 44 . Interestingly, sample volumes in the ESP study were reversed where the autonomous sampler filtered a higher volume (1 L), and the manual sampling filtered a lower volume (36-100 mL) 44 . Our protocol generated comparable results with a lower autonomous sampler volume, which allows sampling time to be kept to a minimum.…”

The Western Lake Erie Culture Collection: A promising resource for evaluating the physiological and genetic diversity ofMicrocystisand its associated microbiome

“…Although isolation and cultivation methods were largely the same from year to year, we isolated a diverse collection of Microcystis strains with variable accessory genomes and associated bacterial communities that represent the extensive diversity of Microcystis strains (Dick et al, 2021) and colony-associated bacteria (Smith et al 2021) observed in the field. Whereas the 159 publicly available genomes of cultured Microcystis are dominated by genotypes with the complete set of mcy genes (Dick et al 2021), with only one partial genotype (Yancey et al 2022), the majority of WLECC strains lack mcy genes altogether, and two strains contain the partial genotype. Further, the WLECC includes a diverse array Microcystis traits (secondary metabolism, CCM, nutrient metabolism) that may be critical in strain succession and community function in natural environments (Dick et al, 2021).…”

“…Xenic, unialgal cultures that contained Microcystis were collected for isolation and cultivation during weekly cyanoHAB cruises from various NOAA Great Lakes Environmental Research Laboratory (GLERL) sampling stations within western Lake Erie (Cooperative Institute for Great Lakes Research, n.d.) during September 2017, June and August of 2018, and July and August of 2019 at stations WE2, WE4, WE6, WE8, and WE12 (Cooperative Institute for Great Lakes Research, n.d.; Den Uyl et al, 2022). Further information regarding collection date, location, and isolation technique is outlined in Table 1.…”

Autonomous eDNA collection using an uncrewed surface vessel over a 4200‐km transect of the eastern Pacific Ocean

“…For example, we have coupled the Environmental Sample Processor (ESP) with a long-range autonomous underwater vehicle (LRAUV) to collect eDNA samples in coastal, open ocean, and freshwater lake environments (Den Uyl et al, 2022;Truelove et al, 2022;Yamahara et al, 2019). Similarly, Govindarajan et al (2022)…”