Biology subjects

Deeg, C. M.

Publications and source records attributed to Deeg, C. M..

7 recordsLinked to original sources

bioRxiv2024

eDNA sampling systems for salmon ecosystem monitoring

Environmental DNA (eDNA) is transforming the way aquatic ecosystems are monitored and managed by scientists, resource managers, ENGOs, First Nations communities, and citizen scientists alike. However, the lack of sampling systems enabling high filtration volumes and rapid sample collection in the field have thus far hindered broad scale eDNA studies in the ocean specifically for small and medium scale organizations. To overcome these challenges, several modular water sampling systems that utilize hollow-membrane filtration cartridges were developed by RKS laboratories and tested by the Fisheries and Oceans, Canada, Molecular Genetics Laboratory. Compared to Sterivex filters, an industry standard for eDNA filtration, the hollow-membrane filtration cartridges allowed for a six-fold increase in filtration volume and threefold increase in filtration speed. The field sampling systems, which combine pumps, a programmable controller, an air pump, an ozone generator, and up to eight filters at once, enabled efficient direct eDNA filtration from diverse aquatic environments, from creeks to the open ocean. To evaluate ease of deployment, we present the results of a three day workshop where technical staff of an Indigenous resource management organization, without any prior knowledge in eDNA sampling, were trained and performed independent eDNA sample collection. The samples were analyzed by metabarcoding and qPCR to reveal the distributions of salmon and other species co-occurring in salmon ecosystems, from large ephemeral predators, to the planktonic prey of salmon, even including their pathogens. In this example study, we further observed a substantial shift in community composition in the vicinity of aquaculture facilities where marine species associated with aquaculture feed were detected in freshwater at high relative abundance. This study demonstrates how these sampling systems provide an efficient entry point for small and medium scale organizations to utilize eDNA to fulfill their research and monitoring objectives.

genomics↗

bioRxiv2023

Tenacibaculosis in wild-caught, captive Chinook salmon (Oncorhynchus tshawytscha) in British Columbia, Canada

Substantial, acute mortality was observed in wild-caught Chinook salmon (Oncorhynchus tshawytscha) of various ages and sizes, from sub-adults to returning adults, held in tanks during two holding studies carried out in August and September 2022 at the Bamfield Marine Sciences Centre (BMSC), in Bamfield, British Columbia, Canada. Within days of capture, a substantial number of fish began presenting lethargy, loss of balance, abnormal swimming behavior, and skin ulcers involving the caudal peduncle, fins, belly, trunk and mouth. Molecular testing revealed high levels of Tenacibaculum dicentrarchi in skin swabs and gills, without appreciable consistent detections of other infectious agents. T. dicentrarchi was also isolated from the skin ulcers. Histological analysis confirmed the presence of ulcerative dermatitis and myositis, associated with mats of filamentous, rod-shaped bacteria. In two individuals, the infection became systemic, with a bacterial colony (identified as T. dicentrarchi) observed in the liver of one individual. In-situ hybridization against T. dicentrarchi and T. maritimum confirmed the presence of only the former agent in the gills and skin ulcers of the affected fish. This clinical report represents the first diagnosed case of tenacibaculosis in wild-caught (captive) Chinook salmon in British Columbia. CONFLICT OF INTERESTThe authors have no conflicts of interest to report. DATA AVAILABILITY STATEMENTThe data that support the findings of this study are available from the corresponding author upon reasonable request.

pathology↗

bioRxiv2021

In-field genetic stock identification of overwintering coho salmon in the Gulf of Alaska: Evaluation of Nanopore sequencing for remote real-time deployment

Genetic stock identification (GSI) by single nucleotide polymorphism (SNP) sequencing has become the gold standard for stock identification in Pacific salmon, which are found in mixed-stocks during the oceanic phase of their lifecycle. Sequencing platforms currently applied require large batch sizes and multi-day processing in specialized facilities to perform genotyping by the thousands. However, recent advances in third-generation single-molecule sequencing platforms, like the Oxford Nanopore minION, provide base calling on portable, pocket-sized sequencers and hold promise for the application of real-time, in-field stock identification on variable batch sizes. Here we report and evaluate utility and comparability of at-sea stock identification of coho salmon Oncorhynchus kisutch based on targeted SNP amplicon sequencing on the minION platform during the International Year of the Salmon Signature Expedition to the Gulf of Alaska in the winter of 2019. Long read sequencers are not optimized for short amplicons, therefore we concatenate amplicons to increase coverage and throughput. Nanopore sequencing at-sea yielded stock assignment for 50 of the 80 assessed individuals. Nanopore-based SNP calls agreed with Ion Torrent based genotypes in 83.25%, but assignment of individuals to stock of origin only agreed in 61.5% of individuals highlighting inherent challenges of Nanopore sequencing, such as resolution of homopolymer tracts and indels. However, poor representation of assayed coho salmon in the queried baseline dataset contributed to poor assignment confidence on both platforms. Future improvements will focus on lowering turnaround time, accuracy, throughput, and cost, as well as augmentation of the existing baselines, specifically in stocks from coastal northern BC and Alaska. If successfully implemented, Nanopore sequencing will provide an alternative method to the large-scale laboratory approach. Genotyping by amplicon sequencing in the hands of diverse stakeholders could inform management decisions over a broad expanse of the coast by allowing the analysis of small batches in remote areas in near real-time.

genetics↗

bioRxiv2020

The use of CRISPR-Cas Selective Amplicon Sequencing (CCSAS) to reveal the eukaryotic microbiome of metazoans

Characterization of the eukaryotic microbiome is required to understand the role of microbial communities in health and disease. Such investigation relies on sequencing 18S ribosomal RNA genes (rDNA), which serve as taxonomic markers; however, this is compromised by contaminating host rDNA sequences. To overcome this problem, we developed CRISPR-Cas Selective Amplicon Sequencing (CCSAS), a high-resolution and efficient approach for characterizing eukaryotic microbiomes. CCSAS uses taxon-specific single-guide RNA (sgRNA) to direct Cas9 to cut 18S rDNA sequences of the host. Validation shows that >96.5% of rDNA amplicons from ten model organisms were cleaved, while rDNA from protists and fungi were unaffected. In oyster spat, CCSAS resolved [~]8.5-fold more taxa, and several additional major phylogenetic groups when compared to the best available alternative approach. We designed taxon-specific sgRNA for [~]16,000 metazoan and plant taxa, making CCSAS widely available for characterizing eukaryotic microbiomes that have largely been neglected because of methodological challenges.

microbiology↗

bioRxiv2018

From the inside out: An epibiotic Bdellovibrio predator with an expanded genomic complement

Bdellovibrio and like organisms are abundant environmental predators of prokaryotes that show a diversity of predation strategies, ranging from intra-periplasmic to epibiotic predation. The novel epibiotic predator Bdellovibrio qaytius was isolated from a eutrophic freshwater pond in British Columbia, where it was a continual part of the microbial community. Bdellovibrio qaytius was found to preferentially prey on the beta-proteobacterium Paraburkholderia fungorum. Despite its epibiotic replication strategy, B. qaytius encodes a complex genomic complement more similar to periplasmic predators as well as several biosynthesis pathways not previously found in epibiotic predators. Bdellovibrio qaytius is representative of a widely distributed basal cluster within the genus Bdellovibrio, suggesting that epibiotic predation might be a common predation type in nature and ancestral to the genus.

microbiology↗

bioRxiv2018

Chromulinavorax destructans, a pathogenic TM6 bacterium with an unusual replication strategy targeting protist mitochondrion

Most of the diversity of microbial life is not available in culture, and as such we lack even a fundamental understanding of the biological diversity of several branches on the tree of life. One branch that is highly underrepresented is the candidate phylum TM6, also known as the Dependentiae. Their biology is known only from reduced genomes recovered from metagenomes around the world and two isolates infecting amoebae, all suggest that they live highly host-associated lifestyles as parasites or symbionts. Chromulinavorax destructans is an isolate from the TM6/Dependentiae that infects and lyses the abundant heterotrophic flagellate, Spumella elongata. Chromulinavorax destructans is characterized by a high degree of reduction and specialization for infection, so much so it was discovered in a screen for giant viruses. Its 1.2 Mb genome shows no metabolic potential and C. destructans instead relies on extensive transporter system to import nutrients, and even energy in the form of ATP from the host. Accordingly, it replicates in a viral-like fashion, while extensively reorganizing and expanding the host mitochondrion. 44% of proteins contain signal sequences for secretion, which includes many proteins of unknown function as well as 98 copies of ankyrin-repeat domain proteins, known effectors of host modulation, suggesting the presence of an extensive host-manipulation apparatus.

microbiology↗

bioRxiv2017

The kinetoplastid-infecting Bodo saltans virus (BsV), a window into the most abundant giant viruses in the sea

Giant viruses are ecologically important players in aquatic ecosystems that have challenged concepts of what constitutes a virus. Herein, we present the giant Bodo saltans virus (BsV), the first characterized representative of the most abundant giant viruses in the oceans, and the first klosneuvirus isolate, a subgroup of the Mimiviridae proposed from metagenomic data. BsV infects an ecologically important microzooplankton, the kinetoplastid Bodo saltans. Its 1.39 Mb genome is the largest described for the Mimiviridae and encodes 1227 predicted ORFs, including pathways for host-independent replication. Yet, much of its translational machinery has been lost, including all tRNAs. Essential genes are invaded by homing endonuclease-encoding self-splicing introns that may defend against competing viruses. Putative anti-host factors show extensive gene duplication via a genomic accordion indicating an ongoing evolutionary arms race and highlighting the rapid evolution and genomic plasticity that has led to genome gigantism and the enigma that is giant viruses.

genomics↗