Sharks frequently sustain cutaneous injuries throughout their lifetimes, yet subsequent infections are surprisingly rare, and wounds appear to heal rapidly. This has led scientists to explore the potential mechanisms behind shark skin’s putative ‘superior’ capacity for fending off infection. Interestingly, research has turned to the skin-associated microbiome for the answer. Although exploration of the bacterial microbiome has led to its proposal as a potential key factor in wound healing, the role of the fungal microbiome (or mycobiome) remains significantly overlooked. Here, we endeavoured to characterise the fungal communities colonising the skin of 46 blacktip reef sharks (Carcharhinus melanopterus) and one sicklefin lemon shark (Negaprion acutidens) in order to determine whether the presence of wounds corresponded to shifts within their fungal communities. We found that there were no significant differences between the fungal consortia harboured by insulted and intact skin, mirroring findings related to their bacterial counterparts. Further, we demonstrated fluctuating taxonomic profiles and the lack of a substantial ‘core’ community of fungal members shared across individuals, highlighting the need to disentangle the role of stochastic versus deterministic processes in shaping fungal communities in the shark skin microbiome. Finally, exploring co-occurrence patterns highlighted 21 positive associations between 13 fungal genera. We encourage future research to uncover the role of rare fungal amplicon sequence variants (ASVs) and investigate the ecological consequences of co-occurrence networks in order to elucidate the role of the skin mycobiome in shark health.

Seagrass meadows are vital ecosystems, yet methods to monitor their health lack standardization, which makes data comparison challenging. To identify key approaches and evaluate alignment with expert opinion, we compared the most used health monitoring methods across 500 studies with a survey of 34 experts. The most reported methods in studies were environmental parameters (44%), percent cover (41%), biomass (40%), distribution/extent (39%), and species composition (37%). Expert importance ratings closely matched: distribution/extent and species composition (100/100), percent cover (99/100), and environmental parameters (92/100). Notably, few studies used physiological-level (10.4%) methods. Experts also anticipated growing roles for remote sensing, eDNA, and AI-assisted image analysis. Together, this study shows a consensus around core, cost-effective methods despite limited integration across biological scales. To address this gap, we propose a multi-level monitoring framework that pairs traditional indicators with early-warning metrics to strengthen seagrass conservation and restoration at broader scales.

Intensive agriculture with high reliance on pesticides and fertilizers constitutes a major strategy for ‘feeding the world’. However, such conventional intensification is linked to diminishing returns and can result in ‘intensification traps’—production declines triggered by the negative feedback of biodiversity loss at high input levels. Here we developed a novel framework that accounts for biodiversity feedback on crop yields to evaluate the risk and magnitude of intensification traps. Simulations grounded in systematic literature reviews showed that intensification traps emerge in most landscape types, but to a lesser extent in major cereal production systems. Furthermore, small reductions in maximal production (5–10%) could be frequently transmitted into substantial biodiversity gains, resulting in small-loss large-gain trade-offs prevailing across landscape types. However, sensitivity analyses revealed a strong context dependence of trap emergence, inducing substantial uncertainty in the identification of optimal management at the field scale. Hence, we recommend the development of case-specific safety margins for intensification preventing double losses in biodiversity and food security associated with intensification traps.

Bumblebees (genus Bombus ) have received increased academic and conservation attention with the recognition of a global pollinator crisis. However, the Bombus subgenus Psithyrus (cuckoo bumblebees), has been overlooked. Psithyrus species parasitise social Bombus species and are frequently viewed as being detrimental to their hosts. This lack of attention, combined with the taxon’s relatively low abundances and enhanced vulnerability to climate change due to its phenological dependence on Bombus , means there is an urgent conservation challenge facing Psithyrus . We found that academic literature focused on Psithyrus comprised less than 2% of the total works on Bombus , despite forming approximately 11% of Bombus species. We argue that species of the Psithyrus subgenus have key roles in the ecosystem and have been potentially overlooked bioindicator of Bombus diversity. We present evidence suggesting that the close phenological ties between Psithyrus and its hosts are being impacted by climate change. Going forward, research on Psithyrus distributions and phenology will be essential for conserving this subgenus. Additionally, addressing these areas provides broader opportunities to improve our understanding of ecosystem dynamics under climate change and their associated links with ecosystem services.

Corals are facing a range of threats, including rises in sea surface temperature and ocean acidification. Some now argue that keeping corals ex situ (in aquaria), may be not only important but necessary to prevent local extinction, for example in the Florida Reef Tract. Such collections or are already becoming common place, especially in the Caribbean, and may act as an ark, preserving and growing rare or endangered species in years to come. However, corals housed in aquaria face their own unique set of threats. For example, hobbyists (who have housed corals for decades) have noticed seasonal mortality is commonplace, incidentally following months of peak pollen production. So, could corals suffer from hay fever? If so, what does the future hold? In short, the answer to the first question is simple, and it is no, corals cannot suffer from hay fever, primarily because corals lack an adaptive immune system, which is necessary for the diagnosis of such an allergy. However, the threat from pollen could still be real. In this review, we explore how such seasonal mortality could play out. We explore increases in reactive oxygen species, the role of additional nutrients and how the microbiome of the pollen may introduce disease or cause dysbiosis in the holobiont.

(A; master-data file of the Arthrospira project)

Ratios between viruses, heterotrophic prokaryotes and chlorophyll a are key indicators of microbial food structure and both virus–prokaryote and prokaryote–chlorophyll ratios have been proposed to decrease with system productivity. However, the mechanisms underlying these responses are still insufficiently resolved and their consistency across aquatic ecosystem types requires critical evaluation. We assessed microbial community ratios in highly productive African soda-lakes and used our data from naturally hypereutrophic systems which are largely underrepresented in literature, to complement earlier across-system meta-analyses. In contrast to marine and freshwater systems, prokaryote–chlorophyll ratios in African soda-lakes did not decrease along productivity gradients. High-resolution time series from two soda-lakes indicated that this lack of response could be driven by a weakened top–down control of heterotrophic prokaryotes. Our analysis of virus–prokaryote relationships, revealed a reduction of virus–prokaryote ratios by high suspended particle concentrations in soda-lakes. This effect, likely driven by the adsorption of free-living viruses, was also found in three out of four additionally analysed marine datasets. However, the decrease of virus–prokaryote ratios previously reported in highly productive marine systems, was neither detectable in soda-lakes nor freshwaters. Hence, our study demonstrates that system-specific analyses can reveal the diversity of mechanisms that structure microbial food-webs and shape their response to productivity increases.

(B, data file used for the analysis)

1. Cost-effective strategies to increase biodiversity are a fundamental requirement to reconcile conservation and food production in agricultural landscapes. Key for the implementation of such strategies is an accurate quantification of both their benefits and potential associated trade-offs.2. We therefore assessed, in a commercially managed grassland, biodiversity responses to two low-cost management interventions and their mediating effects on ecosystem services.3. In a 6-year experiment, we showed that a one-time seed bank activation treatment had strong initial impacts on biodiversity, increasing plant richness in year 1 by 61%. Long-term effects, which were also driven by the second management intervention, the propagation of the keystone species yellow rattle, were weaker but nonetheless substantial. These positive biodiversity responses improved ecosystem multifunctionality through additive positive effects of richness, evenness and phylogenetic distinctiveness on nectar production and structural habitat complexity.4. In contrast, hay biomass production was negatively affected by both management interventions, resulting in a multilevel trade-off between biomass production competing with biodiversity conservation and the provisioning of other ecosystem services.5. Synthesis and applications. In this study, we demonstrate that the maximisation of either biodiversity or biomass production requires largely different land management practices. The evaluation of this trade-off, however, is strongly dependent on its social, economic and ecological context and requires clearly defined land management priorities for both food production and biodiversity conservation.

Global declines in biodiversity highlight the need to effectively monitor the density and distribution of threatened species. In recent years, molecular survey methods detecting DNA released by target-species into their environment (eDNA) have been rapidly on the rise. Despite providing new, cost-effective tools for conservation, eDNA-based methods are prone to errors. Best field and laboratory practices can mitigate some, but the risks of errors cannot be eliminated and need to be accounted for. Here, we synthesize recent advances in data processing tools that increase the reliability of interpretations drawn from eDNA data. We review advances in occupancy models to consider spatial data-structures and simultaneously assess rates of false positive and negative results. Further, we introduce process-based models and the integration of metabarcoding data as complementing approaches to increase the reliability of target-species assessments. These tools will be most effective when capitalizing on multi-source data sets collating eDNA with classical survey and citizen-science approaches, paving the way for more robust decision-making processes in conservation planning.

ABSTRACT Using time-lapse photography in a laboratory setting, we exposed Anodonta anatina and Unio pictorum for 4 h to algal (Chlorella vulgaris) concentrations ranging from 0.5 to 20.0 mg ash-free dry mass l−1 and to three different temperatures (11 ± 1, 15 ± 1 and 19 ± 1 °C). We analysed the proportion of mussels in locomotion, duration of locomotory activities, posterior tip movement and valve opening behaviour. The proportion of mussels in locomotion was significantly higher for A. anatina and for A. anatina was significantly lower at 11 °C. For both species, the proportion of mussels in locomotion, the duration of locomotion and movement of the posterior tip decreased with increasing algal concentration. The locomotory duration was significantly shorter in U. pictorum. In both species, valve opening peaked at intermediate algal concentrations, with the deviation from the peak being more prominent in A. anatina. Finally, we recorded a contrasting locomotory strategy for the two species (A. anatina crawled on the sediment surface, whereas U. pictorum moved through the sediment) and identified potential density dependence in behavioural adaptation.

Societal Impact Statement Large areas of tropical forest are degraded. While global tree cover is being mapped with increasing accuracy from space, much less is known about the quality of that tree cover. Here we present a field protocol for rapid assessments of forest condition. Using extensive field data from Tanzania, we show that a focus on remotely‐sensed deforestation would not detect significant reductions in forest quality. Radar‐based remote sensing of degradation had good agreement with the ground data, but the ground surveys provided more insights into the nature and drivers of degradation. We recommend the combined use of rapid field assessments and remote sensing to provide an early warning, and to allow timely and appropriately targeted conservation and policy responses. Summary Tropical forest degradation is widely recognised as a driver of biodiversity loss and a major source of carbon emissions. However, in contrast to deforestation, more gradual changes from degradation are challenging to detect, quantify and monitor. Here, we present a field protocol for rapid, area‐standardised quantifications of forest condition, which can also be implemented by non‐specialists. Using the example of threatened high‐biodiversity forests in Tanzania, we analyse and predict degradation based on this method. We also compare the field data to optical and radar remote‐sensing datasets, thereby conducting a large‐scale, independent test of the ability of these products to map degradation in East Africa from space. Our field data consist of 551 ‘degradation’ transects collected between 1996 and 2010, covering >600 ha across 86 forests in the Eastern Arc Mountains and coastal forests. Degradation was widespread, with over one‐third of the study forests—mostly protected areas—having more than 10% of their trees cut. Commonly used optical remote‐sensing maps of complete tree cover loss only detected severe impacts (≥25% of trees cut), that is, a focus on remotely‐sensed deforestation would have significantly underestimated carbon emissions and declines in forest quality. Radar‐based maps detected even low impacts (<5% of trees cut) in ~90% of cases. The field data additionally differentiated types and drivers of harvesting, with spatial patterns suggesting that logging and charcoal production were mainly driven by demand from major cities. Rapid degradation surveys and radar remote sensing can provide an early warning and guide appropriate conservation and policy responses. This is particularly important in areas where forest degradation is more widespread than deforestation, such as in eastern and southern Africa.

Protozoan predators form an essential component of activated sludge communities that is tightly linked to wastewater treatment efficiency. Nonetheless, very little is known how protozoan predation is channelled via bacterial communities to affect ecosystem functioning. Therefore, we experimentally manipulated protozoan predation pressure in activated-sludge communities to determine its impacts on microbial diversity, composition and putative functionality. Different components of bacterial diversity such as taxa richness, evenness, genetic diversity and beta diversity all responded strongly and positively to high protozoan predation pressure. These responses were non-linear and levelled off at higher levels of predation pressure, supporting predictions of hump-shaped relationships between predation pressure and prey diversity. In contrast to predation intensity, the impact of predator diversity had both positive (taxa richness) and negative (evenness and phylogenetic distinctiveness) effects on bacterial diversity. Furthermore, predation shaped the structure of bacterial communities. Reduction in top-down control negatively affected the majority of taxa that are generally associated with increased treatment efficiency, compromising particularly the potential for nitrogen removal. Consequently, our findings highlight responses of bacterial diversity and community composition as two distinct mechanisms linking protozoan predation with ecosystem functioning in activated sludge communities.

Coral reefs are suffering unprecedented declines in health state on a global scale. Some have suggested that human assisted evolution or assisted gene flow may now be necessary to effectively restore reefs and pre-condition them for future climate change. An understanding of the key metabolic processes in corals, including under stressed conditions, would greatly facilitate the effective application of such interventions. To date, however, there has been little research on corals at this level, particularly regarding studies of the metabolome of Scleractinian corals. Here, the metabolomic profiles [measured using 1H nuclear magnetic resonance spectroscopy (1H NMR) and ultra-high-performance liquid chromatography-mass spectrometry (LC-MS)] of two dominant reef building corals, Acropora hyacinthus and A. millepora, from two distinct geographical locations (Australia and Singapore) were characterized. We assessed how an acute temperature stress (an increase of 3.25°C ± 0.28 from ambient control levels over 8 days), shifted the corals’ baseline metabolomic profiles. Regardless of the profiling method utilized, metabolomic signatures of coral colonies were significantly distinct between coral species, a result supporting previous work. However, this strong species-specific metabolomic signature appeared to mask any changes resulting from the acute heat stress. On closer examination, we were able to discriminate between control and temperature stressed groups using a partial least squares discriminant analysis classification model (PLSDA). However, in all cases “late” components needed to be selected (i.e., 7 and 8 instead of 1 and 2), suggesting any treatment effect was small, relative to other sources of variation. This highlights the importance of pre-characterizing the coral colony metabolomes, and of factoring that knowledge into any experimental design that seeks to understand the apparently subtle metabolic effects of acute heat stress on adult corals. Further research is therefore needed to decouple these apparent individual and species-level metabolomic responses to climate change in corals.

AbstractEcosystems are currently changing at unprecedented rates due to anthropogenic influences. Application of appropriate management regimes and mitigation measures requires knowledge of ecological community composition and monitoring of any changes that occur. Environmental DNA‐based monitoring is becoming increasingly common and offers substantial potential as a noninvasive method associated with highly repeatable and reliable results. In this study, we monitored river systems in Western Greece that have been strongly impacted by anthropogenic activities and the spread of an alien invasive fish species, the Eastern mosquitofish (Gambusia holbrooki). This invasive species has been credited as the major cause for the drastic decline of two endemic killifish species (Valencia letourneuxi and Valencia robertae). Here, we investigated the efficacy of an environmental DNA (eDNA‐based) method of detection for all three species, as an alternative to conventional monitoring methods. Initially, a mesocosm experiment provided material for the design and validation of the sampling protocol. This was followed by two sampling periods in the field conducted in autumn 2017 and 2018, comparing the novel eDNA assays with the conventional surveying methods in six and 20 systems, respectively. eDNA detection consistently outperformed the traditional monitoring methods for both V. letourneuxi and V. robertae and was comparable for the invasive G. holbrooki. This supports the now increasing body of literature, highlighting the benefits of species‐specific, targeted eDNA assays for the assessment of threatened and/or invasive species, one which can be utilized by conservation organizations and government bodies alike. However, we note that care should always be taken when designing such tools and strict validation steps should be adhered to, particularly with respect to minimizing the probability of false positives and negatives.

eDNA-based methods represent non-invasive and cost-effective approaches for species monitoring and their application as a conservation tool has rapidly increased within the last decade. Currently, they are primarily used to determine the presence/absence of invasive, endangered or commercially important species, but they also hold potential to contribute to an improved understanding of the ecological interactions that drive species distributions. However, this next step of eDNA-based applications requires a thorough method development. We developed an eDNA assay for the white-clawed crayfish (Austropotamobius pallipes), a flagship species of conservation in the UK and Western Europe. Multiple subsequent in-situ and ex-situ validation tests aimed at improving method performance allowed us to apply eDNA-based surveys to evaluate interactions between white-clawed crayfish, crayfish plague and invasive signal crayfish. The assay performed well in terms of specificity (no detection of non-target DNA) and sensitivity, which was higher compared to traditional methods (in this case torching). The eDNA-based quantification of species biomass was, however, less reliable. Comparison of eDNA sampling methods (precipitation vs. various filtration approaches) revealed that optimal sampling method differed across environments and might depend on inhibitor concentrations. Finally, we applied our methodology together with established assays for crayfish plague and the invasive signal crayfish, demonstrating their significant interactions in a UK river system. Our analysis highlights the importance of thorough methodological development of eDNA-based assays. Only a critical evaluation of methodological strengths and weaknesses will allow us to capitalise on the full potential of eDNA-based methods and use them as decision support tools in environmental monitoring and conservation practice.

Increasing temperatures on a global scale and locally deteriorating water quality affect coral distribution and health. Mechanisms that convey environmental robustness are poorly understood and have been attributed to the coral host, algal symbionts, and prokaryotic associates. Flexibility of the host’s (bacterial) microbiome has been suggested to contribute to environmental robustness, but the underlying mechanisms are unclear. We therefore utilised the vastly contrasting water quality gradient present along Hong Kong’s highly urbanised coastline to explore whether flexibility in the microbiome of Oulastrea crispata relates to spatial variations in temperature, salinity, dissolved oxygen, pH, nitrate, nitrite, ammonia, total nitrogen, phosphorus, turbidity, and chlorophyll a. We identified differences in the coral microbiomes between sites, but the measured environmental variables only explained ~ 23% of the variation suggesting other factors are contributing substantially. The observed structural complexity of the microbiome (based on alpha diversity indices) appears to be relatively conserved across the environmental gradient even at sites where no other hard coral can survive. Therefore, we conclude that, at least in O. crispata , flexibility in the microbiome does not appear to underpin the robustness of this broadly distributed coral.

'One World - One Health' is a developing concept which aims to explicitly incorporate linkages between the environment and human society into wildlife and human health care. Past work in the field has concentrated on aspects of disease, particularly emerging zoonoses, and focused on terrestrial systems. Here, we argue that marine environments are crucial components of the 'One World - One Health' framework, and that coral reefs are the epitome of its underlying philosophy. That is, they provide vast contributions to a wide range of ecosystem services with strong and direct links to human well-being. Further, the sensitivity of corals to climate change, and the current emergence of a wide range of diseases, make coral reefs ideal study systems to assess links, impacts, and feedback mechanisms that can affect human and ecosystem health. There are well established protocols for monitoring corals, as well as global networks of coral researchers, but there remain substantial challenges to understanding these complex systems, their health and links to provisioning of ecosystem services. We explore these challenges and conclude with a look at how developing technology offers potential ways of addressing them. We argue that a greater integration of coral reef research into the 'One World - One Health' framework will enrich our understanding of the many links within, and between, ecosystems and human society. This will ultimately support the development of measures for improving the health of both humans and the environment.

Isogenus nubecula is a critically endangered Plecoptera species. Considered extinct in the UK, the species was recently rediscovered in one location of the river Dee in Wales after 22 years of absence. As many species belonging to the Perlodidae, this species can be a bio-indicator, utilised for assessing water quality and health status of a given freshwater system. However, conventional monitoring of invertebrates via kick-sampling for example, is an invasive and expensive (time consuming). Further, such methods require a high level of taxonomic expertise. Here, we compared the traditional kick-sampling method with the use of eDNA detection using qPCR and ddPCR-analyses. In spring 2018, we sampled eDNA from twelve locations on the river Dee. I. nubecula was detected using kick-sampling in five of these locations, three locations using both eDNA detection and kick-sampling and one location using eDNA detection alone – resulting in a total of six known and distinct populations of this critically endangered species. Interestingly, despite the eDNA assay being validated in vitro and in silico, and results indicating high sensitivity, qPCR analysis of the eDNA samples proved to be ineffective. In contrast, ddPCR analyses resulted in a clear detection of I. nubecula at four locations suggesting that inhibition most likely explains the big discrepancy between the obtained qPCR and ddPCR results. It is therefore important to explore inhibition effects on any new eDNA assay. We also highlight that ddPCR may well be the best option for the detection of aquatic organisms which are either rare or likely to shed low levels of eDNA into their environment.

There is little documentation available on the impact of abandoned, lost or discarded fishing nets ('ghost nets') on turtle populations. Here, we utilise data collected over a 5 year period to assess (1) if a particular net type or characteristic was identifiable as entangling more turtles and (2) if particular fishing practices (i.e. types of nets) could be managed to reduce turtle entanglement in the Maldivian archipelago. A total of 131 turtles were entangled in the 752 reported ghost nets, and olive ridley turtles Lepidochelys olivacea appeared to be the most vulnerable (making up 97% of entangled turtles). However, we estimate that the 752 nets in this study, reported over a 51 month period, could have entangled between 3400 and 12200 turtles across the Indian Ocean prior to being detected in the Maldives. Mesh size, seasonality (i.e. north east monsoon), and the presence of floats were all identified as variables significantly affecting the likelihood of turtle entanglement. The probability of entanglement increased as the mesh size increased but decreased when floats were present. Additionally, turtles were more likely to be entangled during the north east monsoon when currents flow from east to west. Cluster analysis indicated that there were at least 11 broadly assigned net types found floating in the study area, and these were dominated by trawl and gill nets. Our analyses highlight the need for a detailed database of existing gear types coupled with gear marking to improve traceability of ghost nets in the Indian Ocean.