A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on biodiversity and ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental DNA and RNA to cost-efficiently and accurately monitor biodiversity, technical limitations and conceptual issues still stand in the way of its routine application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception of the methodology as being premature or “in development”, hence restraining regulators from binding these tools into legal frameworks. This review focuses on the strengths and limitations of genomics-based strategies that have emerged over the past ten years and have been classified for this purpose into three broad strategies: (A) Taxonomy-based approaches that focus on known bio-indicators or the diversity of taxonomically described taxa, (B) De novo approaches that do not require well-established taxonomy, and (C) Function-based approaches that rely on community-wide metrics, where taxa are interchangeable, or on functional profiles instead of compositional turnovers. We finally propose a roadmap for the implementation of environmental genomics into routine monitoring programs that leverage recent analytical advancements, upon which some critical limitations are alleviated.

Human impacts have been eroding marine ecosystems in such a way that biodiversity patterns are changing. Therefore, policies and science-based solutions are indispensable for monitoring threats to the most impacted species. In such effort, the analysis of elasmobranchs' environmental traces via eDNA metabarcoding represent a candidate tool for effective monitoring and conservation that is often advocated to be cost-effective and easily replicated. Here, we tested a realistic approach to monitor future changes through elasmobranchs' metabarcoding with published primers, in which, elasmobranch diversity from the coastal waters of the Fernando de Noronha Archipelago (Brazil) was studied here. We detected a total of three elasmobranch species, namely Hypanus berthalutzae, Ginglymostoma cirratum, and Prionace glauca among numerous other fish species. Even though the technique proved to be a useful tool, some practical constraints were identified, and primarily caused by currently published environmental primers. In order to ensure the broad application of the method, we pointed out feasible adjustments to the problematic parameters based on our survey and other elasmobranch metabarcoding studies. The current drawbacks of the approach need to be considered by managers, conservation actors, and researchers, who are considering this methodology in order to avoid unrealistic promises for the cost incurred.

Elasmobranchs are threatened and eDNA metabarcoding is a powerful tool that can help efforts to better understand and conserve them. Nevertheless, the inter‐calibration between optimal methodological practices and its implementation in resource‐limited situations is still an issue. Based on promising results from recent studies, the authors applied a cost‐effective protocol with parameters that could be easily replicated by any conservationist. Nonetheless, the results with fewer elasmobranchs detected than expected reveal that endorsed primers and sampling strategies still require further optimization, especially for applications in resource‐limited conservation programmes.

Coastal areas provide important ecological services to populations accessing, for example, tourism services, fisheries, minerals and petroleum. Coastal zones worldwide are exposed to multiple stressors that threaten the sustainability of receiving environments. Assessing the health of these valuable ecosystems remains a top priority for environmental managers to ensure the key stressor sources are identified and their impacts minimized. The objective of this review was to provide an overview of current coastal environmental monitoring frameworks in the Asia-Pacific region. This large geographical area includes many countries with a range of climate types, population densities and land uses. Traditionally, environmental monitoring frameworks have been based on chemical criteria set against guideline threshold levels. However, regulatory organizations are increasingly promoting the incorporation of biological effects-based data in their decision-making processes. Using a range of examples drawn from across the region, we provide a synthesis of the major approaches currently being applied to examine coastal health in China, Japan, Australia and New Zealand. In addition, we discuss some of the challenges and investigate potential solutions for improving traditional lines of evidence, including the coordination of regional monitoring programs, the implementation of ecosystem-based management and the inclusion of indigenous knowledge and participatory processes in decision-making.

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The removal of groundwater results in the lowering of water tables, which, for groundwater organisms, translates to reduced habitat availability and changed environmental conditions in the habitat that remains. While changes in groundwater levels may be well modelled and predicted, the impacts on groundwater ecosystems remain poorly known. There are three key processes associated with groundwater drawdown in shallow alluvial aquifers that may threaten groundwater ecosystems. These processes are 1. the physical decline of water levels, from which fauna can be stranded in isolated or unsaturated sediments; 2. the loss of or change to habitat, particularly as water levels move through different geological strata and 3. changes in hydrological connectivity, that may influence water quality as a result of increasing distance or disconnection from the surface and other water sources. Results from laboratory studies show the variable capacity for stygobiotic invertebrates to move with declining water tables, dependent on both drawdown rate and sediment attributes. Once isolated in unsaturated habitats, our tests show that survival of fauna is limited beyond 48 h. Invertebrates are constrained by sediment size and unable to use those with relatively small pore spaces and may not be able to use all available saturated habitats. This talk will present a framework that identifies the key threats of groundwater drawdown to groundwater ecosystems and will highlight the current state of knowledge of each of these threatening processes. We present the results of empirical studies on the response of stygobiotic invertebrates to specific elements of the framework.

Distribution of biota within groundwater is often patchy, and attributed to the heterogeneity of the aquifer environment. Geology and hydrological connectivity are often the factors that most influence water chemistry and habitat availability thus biota, however phreatophytic trees, other sources of carbon and nutrients may also influence biotic distribution. Critically, limited knowledge on the relative importance of such factors on the distribution of groundwater biota makes it difficult to distinguish natural variation from human impacts on groundwater ecosystems, thus inpact our ability to undertake biomonitoring of ecosystem health. This study uses complementary field surveys and laboratory studies to unravel the relative influence of water quality, climate, and sediment size on biotic communities. Field surveys combined traditional pumping and net collections with eDNA community profiling (metabarcoding) of 16S rDNA to characterise groundwater microbes in shallow alluvial aquifers within the Murray-Darling Basin, Australia. Laboratory studies examined the influence of sediment size on stygobiotic amphipods, syncarids and copepods. For stygofauna, sediment size, and thus size of interstitial voids, is a key limiting factor. For microbes, water chemistry influences microbial activity and functional processes, which may in turn influence biogeochemical cycling and ecosystem services provided by groundwater ecosystems.

Diversity indices are commonly used to measure changes in marine benthic communities. Although diversity indices give a good understanding of how biological communities respond to changes in sediment, responses of these indices can vary because of small sample sizes, and insensitive responses can result from an inappropriate choice of test community. This study focused on species density and two indices of community structure and explored how they respond to variations in sediment characteristics in our target region, Japan, and in two local areas within this region. Our analysis of the Japanese regional dataset showed a decrease in species density and the dominance of a few species as sediment conditions degraded. Local case studies showed that species density responded to sediment degradation at sites where the community was variable. However, the indices for community structure sometimes became misleading because of inaccurate estimates with small sample sizes, and could become insensitive because of masking by community variability. We conclude that species density is a sensitive indicator of change for marine benthic communities, but that indices of community structure should only be used when there is a sufficient sample size and a test community is distinguishable from other coexisting communities.