Peter Shum

Chilomastix spp. are flagellated protists found in the intestines of a broad range of hosts. They are generally non-pathogenic and have been little studied, especially using molecular techniques, and significant taxonomic uncertainty regarding the host specificity of lineages remains. As part of a study of intestinal microbial communities of wild Barbary macaques ( Macaca sylvanus ) from Morocco, we mined 50 faecal metagenomic sequence libraries and found 11 rRNA sequences matching Chilomastix . Compared to published 18S rRNA sequences, the Barbary macaque Chilomastix sequences formed a well-supported clade distinct from human-derived C. mesnili ST1 from Indonesia. The macaque Chilomastix sequences cluster with a single pig-derived isolate and two sequences from Japanese macaques ( Macaca fuscata ). This indicates that M. sylvanus harbours a lineage of Chilomastix distinct from the common human strain of C. mesnili and geographically widespread. We were also able to reconstruct the complete rDNA operon from this lineage.

Conservation management, aimed at mitigating the ongoing biodiversity loss, critically relies on ecosystem monitoring to enable accurate estimates of species distributions and population sizes. Environmental DNA (eDNA) analysis has become increasingly popular for non-invasive and high-throughput species assessment, including fish species diversity. Beyond the established sample collection protocols, natural samplers of eDNA (nsDNA) – organisms that trap environmental genetic material in their tissues – show considerable promise, with recent work especially demonstrating the remarkable effectiveness of sea sponges. Here, the potential of jellyfish (phylum Cnidaria) to serve as motile, marine, pelagic natural samplers of eDNA was investigated through DNA metabarcoding using fish specific primers. Jellyfish are opportunistic marine predators known to consume fish eggs and larvae and their presence has been associated with certain fish species, making them potentially useful for open water fish assessment. Four species, the many-ribbed jellyfish ( Aequorea forskalea , Class Hydrozoa), the moon jelly ( Aurelia solida , Class Scyphozoa, Order Semaeostomeae), the barrel jellyfish ( Rhizostoma pulmo Class Scyphozoa, Order Rhizostomeae) and the fried-egg jellyfish Cotylorhiza tuberculata (Class Scyphozoa, Order Rhizostomeae) were collected from the Italian waters of the Gulf of Trieste (northern Adriatic Sea) and nsDNA isolated, sequenced and analysed. Across all species, 28 fish Molecular Operational Taxonomic Units (MOTUs) were detected including pelagic species, benthic species likely spawning at the time of sampling, and species known to associate with the presence of jellyfish. We highlight the potential of jellyfish as tools for enhancing biodiversity monitoring, particularly in remote and inaccessible areas where conventional surveys may be difficult to employ.

Volunteer‐based biodiversity recording is a powerful source of scalable data yet to be used to its full potential by the scientific community. Coastal ecosystems are varied and diverse, making it difficult for managers to identify flexible methods for monitoring biological components. Emerging technologies such as environmental DNA (eDNA) analysis are promising for measuring aquatic biodiversity, yet most management organizations lack personnel and capacity to collect molecular data. Here we investigate, together as professional and non‐professional (citizen) scientists, the efficacy of a quasi‐passive eDNA capture technique. Volunteer SCUBA divers and snorkelers used low‐cost materials, namely cotton medical gauze, to capture eDNA via swimming. We compared this method to conventional eDNA capture techniques in an aquarium and nature, collectively iterating the field and laboratory procedures to improve feasibility. With a small (<30) network of volunteers, we detected 275 unique teleost and elasmobranch taxa, 180 of which could be identified to species level. These detections were from varied marine habitats spanning 90° of latitude, including Atlantic, Pacific and Indian Ocean waters off European, North American, African and Asiatic coasts. The swimming motion of divers was more effective than stationary soaking and the fish communities sampled by divers were comparable to that of conventional eDNA samples. The ease of this technique, matched by the eagerness and generosity of volunteers, presents an untapped, viable approach for scaling multi‐species marine eDNA monitoring as well as an avenue for improving science literacy.

Tropicalization, the process by which tropical species expand their ranges poleward due to global ocean warming, is a prominent threat to Mediterranean marine ecosystems, challenging their effective management and conservation. The arrival of non-indigenous fish is exacerbated by the Suez Canal that allows Indo-Pacific species to enter the region from the Red Sea. While some non-indigenous species (NIS) have already changed the composition and function of native Mediterranean communities, many others continue to arrive but often go unnoticed without regular surveys or until they are strongly established. We conducted biodiversity surveys using underwater visual census (UVC), aqueous environmental DNA (eDNA) and sponge-derived eDNA (i.e., eDNA accumulated in sea sponge tissue) at two protected locations in Zakynthos, Greece. Seven NIS were detected by eDNA, but only one (dusky spinefoot, Siganus luridus ) was detected with all three methods. The fish assemblages of the two locations could be distinguished based on both UVC and eDNA but not from sponge-derived eDNA data, perhaps given low filtration rates. Of the three methods, aqueous eDNA metabarcoding provided the most comprehensive species list including new NIS detected (with the red-toothed triggerfish, Odonus niger , and the houndfish, Tylosurus crocodilus , being the first and third record in the Mediterranean Sea, respectively). Our findings highlight the potential value of incorporating molecular methods into regular monitoring as early warning tools for detecting NIS in marine protected areas threatened by ocean warming.

1. Volunteer-based biodiversity recording is a powerful source of scalable data yet to be used to its full potential by the scientific community. Coastal ecosystems are varied and diverse, making it difficult for managers to identify flexible methods for monitoring biological components. Emerging technologies such as environmental DNA (eDNA) analysis are promising for measuring aquatic biodiversity, yet most management organizations lack personnel and capacity to collect molecular data. 2. Here we investigate, together as professional and non-professional scientists, the efficacy of a quasi-passive eDNA capture technique. Volunteer SCUBA divers and snorkelers used low-cost materials, namely cotton medical gauze, to capture eDNA via swimming. We compared this method to conventional eDNA capture techniques in an aquarium and nature, collectively iterating the field and laboratory procedures to improve feasibility. 3. With a small (< 30) network of volunteers, we detected 275 unique teleost and elasmobranch species from varied marine habitats spanning 90 degrees of latitude. The swimming motion of divers was more effective than stationary soaking and the fish communities sampled by divers were comparable to that of conventional eDNA samples. 4. The ease of this technique matched by the eagerness and generosity of volunteers presents an untapped, viable approach for scaling multi-species marine eDNA monitoring as well as an avenue for improving science literacy.

Coelacanths are rare, elusive, ancient lobe-finned fish species, residing in poorly accessible tropical marine caves and requiring close monitoring and protection. Environmental DNA (eDNA) approaches are being increasingly applied in the detection of rare and threatened species. Here we devise an eDNA approach to detect the presence of African coelacanths ( Latimeria chalumnae ) off the eastern coast of South Africa. Novel coelacanth-specific primers were designed to avoid cross-amplification with other fish lineages and validated for specificity. These primers were tested on field samples in conjunction with remotely operated vehicle (ROV) visual surveys. Samples were collected from a known coelacanth habitat and two adjacent slope habitats a few kilometres apart. Coelacanth DNA was detected from three of 15 samples collected. Two of these positive eDNA detections occurred in the presence of coelacanths, as evidenced by ROV footage, while the third positive detection was at a station where coelacanths had not been previously observed. eDNA detections are discussed in relation to the species’ metabolic rate, movement patterns and population size, as well as the local oceanographic features. We demonstrate that eDNA can provide a non-invasive method to extend the knowledge of coelacanth distribution ranges and boost research efforts around these iconic fishes.

Marine biodiversity monitoring in the Mediterranean’s increasingly threatened ecosystems is crucial for effective ecosystem conservation and management. Here, we leveraged the Mediterranean International Trawl Survey program (MEDITS) to implement eDNA sampling through the recently tested ‘metaprobe’ procedure and characterize fish assemblages in three separate areas off the Italian coasts: Northern Adriatic Sea (NoAS), Ligurian and Northern Tyrrhenian Sea (LNTS), and Sardinian Sea (SaS). By combining the information from two homologous mitochondrial 12S metabarcodes––i.e., Elas02 and Tele02 targeting elasmobranchs and teleosts, respectively––we identified 108 species, over 60% of which overlapped with those caught by the trawl net. We produced an accurate reconstruction of fish community composition of the examined sites, reflecting differences in species assemblages linked with both geographic area and depth range. Metaprobe eDNA data consistently returned a biodiversity ‘bonus’ mostly consisting of pelagic taxa not captured through bottom trawl surveys, including rare and endangered taxa (e.g., elasmobranchs). Overall, the spatial characterisation of the assemblages across the surveyed areas was better delineated and more robust using eDNA metabarcoding than trawl data. Our results support the operationalisation of the metaprobe as a simple, inexpensive, versatile sampling tool, in association with pre-existing ship surveys, to overcome many of the limitations of marine data collection and strengthen marine management.

Norwegian lobster, Nephrops norvegicus, are a generalist scavenger and predator capable of short foraging excursions but can also suspension feed. Existing knowledge about their diet relies on a combination of methods including morphology-based stomach content analysis and stable isotopes, which often lack the resolution to distinguish prey items to species level particularly in species that thoroughly masticate their prey. DNA metabarcoding overcomes many of the challenges associated with traditional methods and it is an attractive approach to study the dietary profiles of animals. Here, we present the diet of the commercially valuable Nephrops norvegicus using DNA metabarcoding of gut contents. Despite difficulties associated with host amplification, our cytochrome oxidase I (COI) molecular assay successfully achieves higher resolution information than traditional approaches. We detected taxa that were likely consumed during different feeding strategies. Dinoflagellata, Chlorophyta and Bacillariophyta accounted for almost 50% of the prey items consumed, and are associated with suspension feeding, while fish with high fisheries discard rates were detected which are linked to active foraging. In addition, we were able to characterise biodiversity patterns by considering Nephrops as natural samplers, as well as detecting parasitic dinoflagellates (e.g., Hematodinium sp.), which are known to influence burrow related behaviour in infected individuals in over 50% of the samples. The metabarcoding data presented here greatly enhances a better understanding of a species’ ecological role and could be applied as a routine procedure in future studies for proper consideration in the management and decision-making of fisheries.