Low level of anthropization linked to harsh vertebrate biodiversity declines in Amazonia

No attenuation of fish and mammal biodiversity declines in the Guiana Shield

Real-time biodiversity monitoring should provide more resolved data to quantify shifts in ecological communities progressively altered by anthropogenic disturbances. Identifying biodiversity trends requires a rapid and efficient inventory method that enables the collection and delivery of high-resolution data within short intervals. Using aquatic environmental DNA (eDNA), we investigated spatiotemporal changes in fish and mammal communities along the Maroni River in French Guiana. We compared spatial biodiversity trends between two years, separated by a four-year interval, during which an increase in anthropogenic disturbances was observed. To evaluate biodiversity changes, we examined the impact of these disturbances on both taxonomic and functional diversity. Our findings revealed that, while the increase in disturbances did not result in major biodiversity decline, it continued to drive alterations in community taxonomic and functional richness. Communities underwent changes in their functional structure, with mammal communities experiencing a decline in extreme functional traits, while fish communities lost functional redundancy in generalist functions and experienced a reduction in extreme functional strategies. In a context of small-scale anthropogenic disturbances, these changes highlight the necessity of long-term, short-interval monitoring to capture rapid reorganisation of ecological communities under stress.

Environmental DNA integrity index is sensitive for species biomass estimation in freshwater

Environmental DNA (eDNA) derived from aquatic vertebrates has recently been employed to estimate species presence. However, the accuracy of these estimations is contingent upon the degradation rate of eDNA. In this study, we introduced the eDNA Integrity Index (eDI) to adjust eDNA concentration for the purpose of estimating carp biomass. The adjusted eDNA concentration is designated as the Biomass Index (BI). We investigated the degradation rate of eDNA through a series of simulation experiments, followed by experiments conducted in tanks and ponds. In all experimental setups, eDNA concentration exhibited a gradual decline, while eDI demonstrated rapid fluctuations following the removal of fish species. Notably, the eDI decreased to nearly zero within two days, whereas eDNA remained detectable for over a month. In experiments involving multiple species raised in conjunction, we observed no significant mutual interference among different species concerning eDI. Furthermore, temperature was determined to have a minimal impact on eDI. Although both eDNA concentration and BI were positively correlated with carp biomass across all experiments, BI exhibited a stronger correlation (R2 > 0.95), was more sensitive to variations in biomass, and provided a more accurate estimate of carp biomass. We successfully applied this methodology to estimate the biomass of carp in a fishpond, demonstrating that precise biomass data can reflect the potential distribution of common carp in natural environments. We present a non-invasive, straightforward, rapid, and accurate method for biomass estimation. SYNOPSIS: We developed an environmental DNA integrity-based method which can estimate species biomass sensitively for species distribution and resource investigations.

Describing functional diversity of communities from environmental DNA

Comprehensive assessments of functional diversity are needed to understand ecosystem alterations under global changes. The 'Fun-eDNA' approach characterises functional diversity by assigning traits to taxonomic units obtained through environmental DNA (eDNA) sampling. By simultaneously analysing an unprecedented number of taxa over broad spatial scales, the approach provides a whole-ecosystem perspective of functional diversity. Fun-eDNA is increasingly used to tackle multiple questions, but aligning eDNA with traits poses several conceptual and technical challenges. Enhancing trait databases, improving the annotation of eDNA-based taxonomic inventories, interdisciplinary collaboration, and conceptual harmonisation of traits are key steps to achieve a comprehensive assessment of diverse taxa. Overcoming these challenges can unlock the full potential of eDNA in leveraging measures of ecosystem functions from multi-taxa assessments.

The socioeconomic and environmental niche of protected areas reveals global conservation gaps and opportunities

The global network of protected areas has rapidly expanded in the past decade and is expected to cover at least 30% of land and sea by 2030 to halt biodiversity erosion. Yet, the distribution of protected areas is highly heterogeneous on Earth and the social-environmental preconditions enabling or hindering protected area establishment remain poorly understood. Here, using fourteen socioeconomic and environmental factors, we characterize the multidimensional niche of terrestrial and marine protected areas, which we use to accurately establish, at the global scale, whether a particular location has preconditions favourable for paestablishment. We reveal that protected areas, particularly the most restrictive ones, over-aggregate where human development and the number of non-governmental organizations are high. Based on the spatial distribution of vertebrates and the likelihood to convert non-protected areas into strictly protected areas, we identify 'potential' versus 'unrealistic' conservation gains on land and sea, which we define as areas of high vertebrate diversity that are, respectively, favourable and unfavourable to protected area establishment. Where protected areas are unrealistic, alternative strategies such as other effective area-based conservation measures or privately protected areas, could deliver conservation outcomes.

Effects of trade and poaching pressure on extinction risk for cacti in the Atacama Desert

In this era of a global biodiversity crisis, vascular plants are facing unprecedented extinction rates. We conducted an assessment of the extinction risk of 32 species and 7 subspecies of Copiapoa, a genus endemic to Chile's fog-dependent coastal Atacama Desert. We applied the International Union for Conservation of Nature Red List Categories and Criteria enhanced by expert insights and knowledge. Our primary aim was to analyze the impact of trade and poaching on their extinction risk. We employed machine learning models, including multinomial logistic regression (MLR), decision tree (DT), and random forest (RF), to analyze the relationships between conservation status and various factors. These factors encompassed trade and poaching activities, landscape condition, human footprint, monthly cloud frequency, and biological traits such as evolutionary distinctiveness and maximum diameter. Seven taxa had an area of occupancy (AOO) of <10 km2, 10 additional taxa had an AOO of <20 km2, and 16 taxa had an AOO of ≤100 km2. This reassessment exposed a critical level of extinction risk for the genus; 92% of the taxa were classified as threatened, 41% as critically endangered, 41% as endangered, and 10% as vulnerable. MLR, DT, and RF exhibited accuracies of 0.784, 0.730, and 0.598, respectively, and identified trade and poaching pressure and landscape condition as the primary drivers of extinction risk. Our assessment of Copiapoa showed trade, poaching, habitat degradation, and their synergic impacts as the main drivers of the genus' extinction risk. Our results highlight the urgent need for nations to develop and enforce strategies to monitor and control trade and poaching pressure because these factors are crucial for the long-term persistence of desert plants.

Application of Synchronous Evaluation-Diagnosis Model with Quantitative Stressor-Response Analysis (SED-QSR) to Urban Lake Ecological Status: A Proposed Multiple-Level System

Ecological integrity assessment and degradation diagnosis are used globally to evaluate the health of water bodies and pinpoint critical stressors. However, current studies mainly focus on separate evaluation or diagnosis, leading to an inadequate exploration of the relationship between stressors and responses. Here, based on multiple data sets in an urban lake system, a synchronous evaluation-diagnosis model with quantitative stressor-response analysis was advanced, aiming to improve the accuracy of evaluation and diagnosis. The weights for key physicochemical stressors were quantitatively determined in the sequence of NDAVIadj > CODMn > TP > NH4+-N by the combination of generalized additive model and structural equation modeling, clarifying the most significant effects of aquatic vegetation on the degradation of fish assemblages. Then, sensitive biological metrics were screened by considering the distinct contributions of four key stressors to alleviate the possible deviation caused by common methods. Finally, ecological integrity was evaluated by summing the key physicochemical stressors and sensitive biological metrics according to the model-deduced weights instead of empirical weights. Our system's diagnosis and evaluation results achieved an accuracy of over 80% when predicting anthropogenic stress and biological status, which highlights the great potential of our multiple-level system for ecosystem management.

Stochastic process is main factor to affect plateau river fish community assembly

Plateau river ecosystems are often highly vulnerable and responsive to environmental change. The driving mechanism of fish diversity and community assembly in plateau rivers under changing environments presents a significant complexity to the interdisciplinary study of ecology and environment. This study integrated molecular biological techniques and mathematical models to identify the mechanisms influencing spatial heterogeneity of freshwater fish diversity and driving fish community assembly in plateau rivers. By utilizing environmental-DNA metabarcoding and the null model, this study revealed the impact of the stochastic process on fish diversity variations and community assembly in the Huangshui Plateau River of the Yellow River Basin (YRB) in China. This research identified 30 operational taxonomic units (OTUs), which correspond to 20 different fish species. The findings of this study revealed that the fish α-diversity in the upstream region of Xining is significantly higher than in the middle-lower reach (Shannon index: P = 0.017 and Simpson: P = 0.035). This pattern was not found to be related to any other environmental factors besides altitude (P = 0.023) that we measured. Further, the study indicated that the assembly of fish communities in the Huangshui River primarily depends on stochastic ecological processes. These findings suggested that elevation was not the primary factor impacting the biodiversity patterns of fish in plateau rivers. In plateau rivers, spatial heterogeneity of fish community on elevation is mainly determined by stochastic processes under habitat fragmentation, rather than any other physicochemical environmental factors. The limitations of connectivity in the downstream channel of the river could be taken the mainly responsibility for stochastic processes of fish community in Huangshui River. Incorporating ecological processes in the eDNA approach holds great potential for future monitoring and evaluation of fish biodiversity and community assembly in plateau rivers.

Revealing human impact on natural ecosystems through soil bacterial DNA sampled from an archaeological site

Human activities have affected the surrounding natural ecosystems, including belowground microorganisms, for millennia. Their short- and medium-term effects on the diversity and the composition of soil microbial communities are well-documented, but their lasting effects remain unknown. When unoccupied for centuries, archaeological sites are appropriate for studying the long-term effects of past human occupancy on natural ecosystems, including the soil compartment. In this work, the soil chemical and bacterial compositions were compared between the Roman fort of Hegra (Saudi Arabia) abandoned for 1500 years, and a preserved area located at 120 m of the southern wall of the Roman fort where no human occupancy was detected. We show that the four centuries of human occupancy have deeply and lastingly modified both the soil chemical and bacterial compositions inside the Roman fort. We also highlight different bacterial putative functions between the two areas, notably associated with human occupancy. Finally, this work shows that the use of soils from archaeological sites causes little disruption and can bring relevant information, at a large scale, during the initial surveys of archaeological sites.

Deforestation strengthens environmental filtering and competitive exclusion in Neotropical streams and rivers

Understanding how anthropization impacts the assembly of species onto communities is pivotal to go beyond the observation of biodiversity changes and reveal how disturbances affect the environmental and biotic processes shaping biodiversity. Here, we propose a simple framework to measure the assembly processes underpinning functional convergence/divergence patterns. We applied this framework to northern Amazonian fish communities inventoried using environmental DNA in 35 stream sites and 64 river sites. We found that the harsh and unstable environmental conditions characterizing streams conveyed communities towards functional convergence, by filtering traits related to food acquisition and, to a lower extent, dispersal. Such environmental filtering also strengthened competition by excluding species having less competitive food acquisition traits. Instead, random species assembly was more marked in river communities, which may be explained by the downstream position of rivers facilitating the dispersion of species. Although fish assembly rules differed between streams and river fish communities, anthropogenic disturbances reduced functional divergence in both ecosystems, with a reinforcement of both environmental filtering and weaker competitor exclusion. This may explain the substantial biodiversity alterations observed under slight deforestation levels in Neotropical freshwater ecosystems and underlines their vulnerability to anthropic disturbances that not only affect species persistence but also modify community assembly rules.

Species invasiveness and community invasibility of North American freshwater fish fauna revealed via trait-based analysis

While biological invasions are recognized as a major threat to global biodiversity, determining non-native species' abilities to establish in new areas (species invasiveness) and the vulnerability of those areas to invasions (community invasibility) is challenging. Here, we use trait-based analysis to profile invasive species and quantify the community invasibility for >1,800 North American freshwater fish communities. We show that, in addition to effects attributed to propagule pressure caused by human intervention, species with higher fecundity, longer lifespan and larger size tend to be more invasive. Community invasibility peaks when the functional distance among native species was high, leaving unoccupied functional space for the establishment of potential invaders. Our findings illustrate how the functional traits of non-native species determining their invasiveness, and the functional characteristics of the invaded community determining its invasibility, may be identified. Considering those two determinants together will enable better predictions of invasions.