Biology subjects

von Ammon, U.

Publications and source records attributed to von Ammon, U..

3 recordsLinked to original sources

bioRxiv2024

CRISPR-based environmental biosurveillance assisted via artificial intelligence design of guide-RNAs

Environmental biosecurity challenges are worsening for aquatic ecosystems as climate change and increased anthropogenic pressures facilitate the spread of invasive species, thereby broadly impacting ecosystem composition, functioning, and services. Environmental DNA (eDNA) has transformed traditional biomonitoring through detection of trace DNA fragments left by organisms in their surroundings, primarily by application of the quantitative polymerase chain reaction (qPCR). However, qPCR presents challenges, including limited portability, reliance on precise thermal cycling, and susceptibility to inhibitors. To address these challenges and enable field-deployable monitoring, isothermal amplification techniques such as Recombinase Polymerase Amplification (RPA) paired with Clustered Regularly Interspaced Short Palindromic Repeats and associated proteins (CRISPR-Cas) have been proposed as alternatives. We report here the development of CORSAIR (CRISPR-based envirOnmental biosuRveillance aSsisted via Artificial Intelligence guide-RNAs), that harnesses the programmability of the CRISPR-Cas technology, RPA and the artificial intelligence (AI)-based tool Activity-informed Design with All-inclusive Patrolling of Targets (ADAPT) to deploy a swift RPA-CRISPR-Cas13a-based method that detects eDNA from two invasive species as proof of concept: Sabella spallanzanii and Undaria pinnatifida. CORSAIR showcased a robust, streamlined method augmented by ADAPT, reaching a high specificity when tested against co-occurring species and a 100% agreement with 12 PCR-benchmarked eDNA samples, reaching a sensitivity of 0.34 copies uL-1 in 1 hour with a cost of 3.5 USD per sample; thus highlighting CORSAIR as a powerful environmental biosurveillance platform for environmental nucleic acid detection. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/627849v1_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@b60942org.highwire.dtl.DTLVardef@119e924org.highwire.dtl.DTLVardef@1956bforg.highwire.dtl.DTLVardef@18e18b9_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG

molecular biology↗

bioRxiv2024

Experimental challenge of Chinook salmon with Tenacibaculum maritimum and Tenacibaculum dicentrarchi fulfils Kochs postulates

The bacterial skin disease tenacibaculosis, caused by Tenacibaculum species, can compromise numerous species of economically important marine fish, including salmonids. While tenacibaculosis is a known threat to Atlantic salmon (Salmo salar) aquaculture, the pathogenesis of Tenacibaculum maritimum and Tenacibaculum dicentrarchi on Chinook salmon (Oncorhynchus tshawytscha) has not yet been investigated. In this study, three molecular O-AGC types of T. maritimum (O-AGC Type 3-0, Type 2-1 and Type 3-2) and T. dicentrarchi isolated during a disease outbreak of farmed Chinook salmon in Aotearoa New Zealand were assessed for their ability to induce tenacibaculosis in salmon smolts under controlled conditions. Naive Chinook salmon were exposed to T. maritimum or T. dicentrarchi by immersion. Clinical signs of tenacibaculosis were apparent post-exposure and observed in 100% of all three molecular O-AGC types of T.-maritimum-challenged fish, with 100% morbidity in O-AGC Type 2-1 and Type 3-2 and 60% in O-AGC Type 3-0. Chinook salmon exposed to T. dicentrarchi showed characteristic clinical signs of disease in 51% of the challenged population, with 28% morbidity. Common gross pathological signs observed for both Tenacibaculum species were congruent with observations on farmed fish in the field, including scale loss, erythematous skin lesion, skin ulcers, fin necrosis, mouth erosion and gill ulceration. Exophthalmia was observed only in T. maritimum-challenged fish, while skin ulcers appeared grossly more severe with exposed musculature in T. dicentrarchi-challenged fish. Pure T. maritimum and T. dicentrarchi cultures were reisolated from the skin and gills of the challenged fish and their identity was confirmed by species-specific PCR and molecular O-AGC typing. Challenge experiments and associated field surveillance (for T. maritimum) did not show the presence of culturable T. maritimum cells in the anterior kidney. This provides compelling evidence that tenacibaculosis in farmed Chinook salmon is an external infectious disease, and that Tenacibaculum is a marine obligate organism that is unable to survive in fish body fluids and does not cause septicaemia. This has repercussions for approaches to experimental challenges with Tenacibaculum species, which must occur by immersion rather than intraperitoneal or intramuscular inoculation, to replicate the natural transmission pathway and to ensure a successful challenge model. This study fulfilled modernised Kochs postulates for the three molecular O-AGC types of T. maritimum and single strain of T. dicentrarchi as aetiological agents of tenacibaculosis in Chinook salmon that cause mortalities with considerable external abnormalities. Author summaryChinook salmon, Oncorhynchus tshawytscha, is the most significant species of Pacific salmon for its large size and nutritional content which makes it a premium choice for aquaculture. In Aotearoa|New Zealand, Chinook salmon is the only marine salmon species farmed. For a decade, the industry was impacted by an undiagnosed skin disease resulting in high mortalities. Disease susceptibility in Chinook salmon is scarcely studied and added to the challenge for a timely diagnosis. This novel research provides insight on disease susceptibility of Chinook salmon and confirms Tenacibaculum species identified in New Zealand pose a high threat to the aquaculture industry. This research has global implications and contributes valuable insights and approaches to disease management that can be applied in British Columbia and Canada where Chinook salmon populations are in decline.

microbiology↗

bioRxiv2021

Assessing the utility of marine filter feeders for environmental DNA (eDNA) biodiversity monitoring

Aquatic environmental DNA (eDNA) surveys are transforming how we monitor marine ecosystems. The time-consuming pre-processing step of active filtration, however, remains a bottleneck. Hence, new approaches omitting active filtration are in great demand. One exciting prospect is to use the filtering power of invertebrates to collect eDNA. While proof-of-concept has been achieved, comparative studies between aquatic and filter feeder eDNA signals are lacking. Here, we investigated the differences among four eDNA sources (water; bivalves; sponges; and ethanol in which filter-feeding organisms were stored) along a vertical transect in Doubtful Sound, New Zealand using three metabarcoding primers (fish (16S); MiFish-E/U). While concurrent SCUBA diver observations validated eDNA results, laboratory trials corroborated in-field bivalve eDNA detection results. Combined, eDNA sources detected 59 vertebrates, while divers observed eight fish species. There were no significant differences in alpha and beta diversity between water and sponge eDNA and both sources were highly correlated. Vertebrate eDNA was detected in ethanol, although only a reduced number of species were detected. Bivalves failed to reliably detect eDNA in both field and mesocosm experiments. While additional research into filter feeder eDNA accumulation efficiency is essential, our results provide strong evidence for the potential of incorporating sponges into eDNA surveys.

molecular biology↗