the-floating-lab-standard-operational-procedure-for-collecting

The Floating Lab: Standard Operational Procedure for Collecting and Filtering Seawater Samples from Operating Ferries for Environmental DNA Analysis

Genetic tools to retrieve information from environmental DNA traces are well-established for both targeted and taxonomically broad biodiversity ...

University of Milano-Bicocca

Marine Research and Higher Education Center (MaRHE Center)

Animal conservation relies on assessing the distribution and habitat use of species, but for endangered/elusive animals this can prove difficult. The Monk Seal, Monachus monachus, is one of the world's most endangered species of pinniped, and the only one endemic to the Mediterranean Sea. During recent decades, direct observations have been few and scattered, making it difficult to determine its distribution away from the Aegean Sea (core distribution area of the post-decline relict population). This study relies on environmental DNA (eDNA) analysis to detect the presence of the Monk Seal in 135 samples collected in 120 locations of the central/western Mediterranean Sea, spanning about 1500 km longitudinally and 1000 km latitudinally. A recently described species-specific qPCR assay was used on marine-water samples, mostly collected during 2021 by a Citizen Science (CS) project. Positive detections occurred throughout the longitudinal range, including the westernmost surveyed area (Balearic archipelago). The distribution of the positive detections indicated six "hotspots", mostly overlapping with historical Monk Seal sites, suggesting that habitat-specific characteristics play a fundamental role. We applied single-season occupancy models to correct for detection probability and to assess the importance of site-specific characteristics. The distance from small islets and protected (or access-restricted) areas was correlated negatively with the detection probability. This novel molecular approach, applied here for the first time in an extensive CS study, proved its potential as a tool for monitoring the distribution of this endangered/elusive species.

Playing "hide and seek" with the Mediterranean monk seal: a citizen science dataset reveals its distribution from molecular traces (eDNA).

Collecting fine-scale occurrence data for marine species across large spatial scales is logistically challenging but is important to determine species distributions and for conservation planning. Inaccurate descriptions of species ranges could result in designating protected areas with inappropriate locations or boundaries. Optimizing sampling strategies therefore is a priority for scaling up survey approaches using tools such as environmental DNA (eDNA) to capture species distributions. In a marine context, commercial vessels, such as ferries, could provide sampling platforms allowing access to undersampled areas and repeatable sampling over time to track community changes. However, sample collection from commercial vessels could be biased and may not represent biological and environmental variability. Here, we evaluate whether sampling along Mediterranean ferry routes can yield unbiased biodiversity survey outcomes, based on perfect knowledge from a stacked species distribution model (SSDM) of marine megafauna derived from online data repositories. Simulations to allocate sampling point locations were carried out representing different sampling strategies (random vs regular), frames (ferry routes vs unconstrained), and number of sampling points. SSDMs were remade from different sampling simulations and compared with the "perfect knowledge" SSDM to quantify the bias associated with different sampling strategies. Ferry routes detected more species and were able to recover known patterns in species richness at smaller sample sizes better than unconstrained sampling points. However, to minimize potential bias, ferry routes should be chosen to cover the variability in species composition and its environmental predictors in the SSDMs. The workflow presented here can be used to design effective sampling strategies using commercial vessel routes globally for eDNA and other biodiversity survey techniques. This approach has potential to provide a cost-effective method to access remote oceanic areas on a regular basis and can recover meaningful data on spatiotemporal biodiversity patterns.

Sampling from commercial vessel routes can capture marine biodiversity distributions effectively.

Author Correction: Playing "hide and seek" with the Mediterranean monk seal: a citizen science dataset reveals its distribution from molecular traces (eDNA).

The monk seal is the most endangered pinniped in the world and the only one found in the Mediterranean, where its distribution and abundance have suffered a drastic decline in the last few decades. Data on its status are scattered due to both its rarity and evasiveness and records are biased towards occasional, mostly coastal encounters. Nowadays, molecular techniques allow us to detect and quantify minute amounts of DNA traces released into the environment (eDNA) by any organism. A species-specific molecular assay is now available for detecting the recent presence of the monk seal in the water column through the analysis of sea-water samples collected from the sea surface. The project "Spot the Monk" uses this non-invasive detection tool to monitor monk seal occurrence in Mediterranean waters by means of eDNA analysis. The simplicity in the acquisition of samples together with the need to collect samples in multiple points simultaneously made the project well suited to the involvement of the general public. Up to today, about 350 samples have been collected and analysed in the central-western Mediterranean by researchers and a multifarious range of citizen scientists - from recreational sailing organisations, both amateur and competitive sportsmen, to fishermen. This work announces the launch of an open-source Observatory (https://www.spot-the-monk-observatory.com/) where the project outcomes are publicly accessible as soon as they are produced. Embracing the principles of Open Science, we believe that such an approach can contribute to filling the knowledge gap about the distribution of this charismatic species in our seas, providing, at the same time, a proof of concept on how data collected by a variety of actors can be returned to the scientific and non-scientific communities in an innovative format for immediate consultation.

An Observatory to monitor range extension of the Mediterranean monk seal based on its eDNA traces: collecting data and delivering results in the "Open Science" era.

Marine mammals play a fundamental role in the functioning of healthy marine ecosystems and are important indicator species. Studying their biology, distributions, behaviour and health are still technically and logistically demanding for researchers. However, the efforts and commitment have not been in vain, since we are witnessing constant and exponential advancement in the study of these animals, thanks to technological progress in numerous fields. These include miniaturization and performance of biologger tags, which are equipped with sensors for measuring physiological parameters, hydrophones, accelerometers, time-depth records and spatial locations; the use of high throughput 'Next Generation' Sequencing to gain genetic information about communities and individual species from nucleic acids in environmental samples at miniscule concentrations; through, to the possibility of monitoring species with autonomous aerial and underwater vehicles. In parallel advances in computing and statistical modelling frameworks support the analysis of increasingly large and complex data sets. In this issue, O'Mahony et al. (2024) draw from at least two of these innovations: (a) the collection of biological material retrieved from large whales' blows using a modified drone and (b) the use of the samples to infer a wide spectrum of genetic information (both nuclear and mitochondrial) about the target animal/population. The methodology is not completely novel, but the study shows an impressive advancement in the amount of data obtained compared to preceding studies using the same approach. In the wake of these promising results, future perspectives are evaluated in relation to alternative sampling methodologies currently in use. It is possible to speculate that, in the next few years, the combination of non-invasive molecular profiling and enhanced drone technology (e.g. assembling increasingly smaller components, thus expanding capacity for autonomous operation) will open up perspectives that were unimaginable at the beginning of this millennium.

The answer, my friend, is blowin' in the wind: Blow sampling provides a new dimension to whale population monitoring.

Citizen Science (CS) offers a promising approach to enhance data collection and engage communities in conservation efforts. This study evaluates the use of CS in environmental DNA (eDNA) monitoring for Mediterranean monk seal conservation. We validated CS by assessing the effectiveness of a newly developed CS-friendly filtration system called "WET" (Water eDNA Trap) in eDNA detection, addressing technical challenges, and analysing volunteer faults. The WET is a 4-litre, manual pump-based filtering system using positive pressure to force water through the filter. We also assessed the use of a retrospective questionnaire as a tool to measure CS's social impact on participants' perceived knowledge, attitudes, and conservation behaviours.

Citizen science in eDNA monitoring for mediterranean monk seal conservation.

Correction: Citizen science in eDNA monitoring for Mediterranean monk seal conservation.

A good understanding of biotic interactions is necessary to accurately predict the vulnerability of ecosystems to climate change. Recently, co-occurrence networks built from environmental DNA (eDNA) metabarcoding data have arisen as a tool to explore interspecific interactions in ecological communities exposed to different human and environmental pressures. Such networks can identify environmentally driven relationships in microbial and eukaryotic communities, but whether inferred co-occurrences robustly represent biotic interactions remains unclear. Here, we tackle this challenge and compare spatio-temporal variability in the structure and complexity of inferred co-occurrence networks and food webs, using 60 eDNA samples covering vertebrates and other eukaryotes in a North Sea coastal ecosystem. We compare topological characteristics and identify highly connected species across spatial and temporal subsets to evaluate variance in community composition and structure. We find consistent trends in topological characteristics across eDNA-derived co-occurrence networks and food webs that support some ability for the co-occurrence networks to detect real ecological processes, despite trophic interactions forming a minority of significant co-occurrences. The lack of significant trophic interactions detected in co-occurrence networks may result from ecological complexities, such as generalist predators having flexible interactions or behavioural partitioning, the inability to distinguish age class with eDNA or co-occurrences being driven by non-trophic or abiotic interactions. We find support for using eDNA-derived co-occurrence networks to infer ecological interactions, but further work is needed to assess their power to reliably detect and differentiate different interaction types and overcome methodological limitations, such as species detection uncertainties, which could influence inferred ecosystem complexity.

Article	Year
Playing "hide and seek" with the Mediterranean monk seal: a citizen science dataset reveals its distribution from molecular traces (eDNA). Scientific reports\| PubMed ID: 36788241	2023
Sampling from commercial vessel routes can capture marine biodiversity distributions effectively. Ecology and evolution\| PubMed ID: 36789340	2023
Author Correction: Playing "hide and seek" with the Mediterranean monk seal: a citizen science dataset reveals its distribution from molecular traces (eDNA). Scientific reports\| PubMed ID: 37046021	2023
An Observatory to monitor range extension of the Mediterranean monk seal based on its eDNA traces: collecting data and delivering results in the "Open Science" era. Biodiversity data journal\| PubMed ID: 38883207	2024
The answer, my friend, is blowin' in the wind: Blow sampling provides a new dimension to whale population monitoring. Molecular ecology resources\| PubMed ID: 39188115	2024
Citizen science in eDNA monitoring for mediterranean monk seal conservation. BMC ecology and evolution\| PubMed ID: 39716069	2024
Correction: Citizen science in eDNA monitoring for Mediterranean monk seal conservation. BMC ecology and evolution\| PubMed ID: 39773447	2025
Inferring Species Interactions From Co-occurrence Networks With Environmental DNA Metabarcoding Data in a Coastal Marine Food Web. Molecular ecology\| PubMed ID: 40035351	2025

Elena Valsecchi

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