Biodiversity Assessment Research Articles

Ecological networks reveal important taxa for ecosystem function in two subtropical South African estuaries

Biodiversity is essential for estuarine ecosystems' functioning, resilience, and persistence. While biodiversity assessments provide some insight into the ecosystem state, they cannot quantify every aspect of ecosystem-level function. We assessed aspects of estuarine ecosystem function and pinpointed taxa of interest that fulfil specific roles in estuarine ecosystems, using a series of novel food web model ensembles and Ecological Network Analysis. We investigated emergent network properties of two subtropical South African estuaries, the anthropogenically impacted large temporarily closed uMdloti Estuary and the ‘near natural’ predominantly open uMlalazi Estuary, during a drought period induced by the El Niño Southern Oscillation. In addition, important network components were identified to elucidate the importance of estuarine/marine taxa in maintaining ecosystem function. The key findings included (1) estuaries exhibit system-specific functional responses under drought conditions, and (2) estuarine/marine taxa are critical for overall ecosystem function. Both estuaries showed seasonal differences in ecosystem activity and reliance on trophic level I (microalgae and detritus) to fuel the food web, and persistently low cycling (<9.3 %). However, compared to uMdloti Estuary, uMlalazi Estuary showed less variation in mean seasonal activity (1597–2095 mgC m−2 d−1), and higher reliance on detritus to fuel the food web (D:H > 2.02), indicating greater ecosystem functional resilience to external perturbations. uMlalazi Estuary ecosystem function could be attributed to predominantly open mouth conditions maintaining a salinity gradient, and subsequent large contributions to overall ecosystem function from typically estuarine/marine invertebrate taxa. In contrast, the uMdloti Estuary, dominated by freshwater/brackish taxa under prolonged closed mouth conditions, showed greater seasonal variations in mean system activity (1084–2289 mgC m−2 d−1) and generally high reliance on microalgae (D:H < 1.26), indicative of decreased resilience to external perturbations. During this study, a single mouth breach acted as a ’biological reset’ of uMdloti Estuary, enabling recruitment of estuarine/marine taxa, and a temporary recovery in ecosystem function reflected in increased system cycling (FCI >14.05 %) and decreased reliance on microalgae (D:H > 1. 41). These findings suggest that future predicted drought impacts on estuarine ecosystem function may be partially system-specific due to differing estuarine types, anthropogenic impact, and invertebrate community composition. This study provides a scientific link between ecosystem-level indicators and the role of individual taxa within the system, which is a valuable complement to biodiversity assessments and ecosystem state evaluation.

Monitoring the rewilding of the Brazilian Atlantic Forest on tree and mammal diversity: From a biodiversity hotspot to a biodiversity hopespot

The implementation of rewilding initiatives is crucial for biodiversity recovery, particularly in biodiversity hotspots such as the Brazilian Atlantic Forest. Long-term monitoring of rewilding initiatives is critical for assessing progress and informing management choices. This study assesses the efficiency of different reforestation practices for biodiversity recovery, including passive restoration, active reforestation with different native seedlings, and plantations of exotic species. We applied an ecosystem approach to estimate the tree and mammal diversity, collected through forest plots and camera traps. We selected differently managed areas and included the oldest forest patches as reference points for the assessment of biodiversity; a naturally disturbed montane forest in the area was included as a control category for the disturbance analysis. Moreover, we investigated the influence of ecological variables, such as biodiversity, aboveground biomass, and altitude, on rewilding processes. Our results suggest that Eucalyptus plantations, a simplified ecosystem made up of monocultures of exotic species, support lower biodiversity. On the contrary, active reforestation with different native species resulted in an ecological status comparable to naturally regrown secondary forests. We show that active reforestation can reduce the time required for rewilding. We also found a positive correlation between tree and mammal species richness. These results underscore the importance and potential of responsible restoration efforts in recovering local biodiversity, contributing to the vision of a future where the Brazilian Atlantic Forest can be acknowledged not only as a biodiversity hotspot but also as a “hopespot.”

Development of DNA Barcoding for the Rapid Assessment of Biodiversity: 2024 Benjamin Franklin Medal in Earth and Environmental Science presented to Paul D. N. Hebert, Ph.D., FRSC, O.C.

Development of DNA Barcoding for the Rapid Assessment of Biodiversity: 2024 Benjamin Franklin Medal in Earth and Environmental Science presented to Paul D. N. Hebert, Ph.D., FRSC, O.C.

Evaluating the feasibility of using plant‐specific metabarcoding to assess forest types from soil eDNA

AbstractQuestionsAn essential aspect of variation in natural systems is that species respond to complex environmental gradients. Recognizing plant composition gradients associated with abiotic factors (ecoclines) can be foundational for defining habitat types, which, in turn, helps map natural variation. Typically, ecoclinal structures are assessed through visual evaluation of above‐ground vegetation and analysis of covarying abiotic factors. However, the correlation between ecological structures detected by soil eDNA plant assessments and those identified by visual assessment remains largely unexplored.LocationHvaler archipelago, southern Norway.MethodsPlant diversity assessments were conducted using metabarcoding of the trnL (UUA) intron p6 loop and ITS2 from 31 soil samples collected across six forest types. These forest types span gradients related to drought risk and calcium richness.ResultsThe barcode amplicons identified 70 plant taxa, primarily vascular plants (67), with most assigned to the species level (59), representing common forest taxa across the sites. Comparisons between soil eDNA compositions and theoretical forest‐type compositions showed a low to medium correspondence (26% to 76%) between the two. Ordinations of soil eDNA compositions revealed two axes without clear ecological interpretation and correlated poorly with the calcium–richness gradient previously identified by visual assessments.ConclusionsOverall, our results emphasize the necessity for comprehensive sequence reference libraries to conduct thorough plant biodiversity assessments. They also highlight the potential of soil eDNA to assess plant composition, which can aid in ecosystem mapping.

Benthic taxonomic and functional diversity change across a depth gradient in the Southern Benguela Shelf ecoregion

Functional trait-based approaches improve biodiversity assessment and have consequently been gaining traction in ecology, including marine benthic studies. However, taxonomic diversity is still the default biodiversity metric applied to monitor benthic community responses to environmental variation despite not always representing functional diversity change. Therefore, we used Biological Traits Analysis (BTA) to quantify functional diversity for infauna and epifauna communities collected from the same locations across a depth gradient in the Southern Benguela Shelf ecoregion. Infauna experienced an increase in functional uniqueness with depth, whereas epifauna experienced an increase in functional redundancy with depth. As a result, the epifauna species assemblage predicted 43 % of the epifauna trait assemblage, whereas the infauna species assemblage predicted only 8 % of the infauna trait assemblage. These findings suggest that taxonomic diversity and functional diversity changes are not congruent within and between marine benthic faunal groups. We emphasize the need to utilise both biodiversity metrics when quantifying marine biodiversity for conservation and management objectives.

Cross‐validation matters in species distribution models: a case study with goatfish species

In an era of ongoing biodiversity, it is critical to map biodiversity patterns in space and time for better‐informing conservation and management. Species distribution models (SDMs) are widely applied in various types of such biodiversity assessments. Cross‐validation represents a prevalent approach to assess the discrimination capacity of a target SDM algorithm and determine its optimal parameters. Several alternative cross‐validation methods exist; however, the influence of choosing a specific cross‐validation method on SDM performance and predictions remains unresolved. Here, we tested the performance of random versus spatial cross‐validation methods for SDM using goatfishes (Actinopteri: Syngnathiformes: Mullidae) as a case study, which are recognized as indicator species for coastal waters. Our results showed that the random versus spatial cross‐validation methods resulted in different optimal model parameterizations in 57 out of 60 modeled species. Significant difference existed in predictive performance between the random and spatial cross‐validation methods, and the two cross‐validation methods yielded different projected present‐day spatial distribution and future projection patterns of goatfishes under climate change exposure. Despite the disparity in species distributions, both approaches consistently suggested the Indo‐Australian Archipelago as the hotspot of goatfish species richness and also as the most vulnerable area to climate change. Our findings highlight that the choice of cross‐validation method is an overlooked source of uncertainty in SDM studies. Meanwhile, the consistency in richness predictions highlights the usefulness of SDMs in marine conservation. These findings emphasize that we should pay special attention to the selection of cross‐validation methods in SDM studies.

Identification of Two Species of the Family Sparidae for eDNA Sequences using a Representative 16SrRNA Reference Library for Omani Fish

Identification of fish species accurately is required to support efforts for conserving fishery biodiversity assessment and sustainable management. Recently, environmental DNA (eDNA) was suggested for regular monitoring of species for effective management of biodiversity. In Oman, molecular reference library representing fish species from the Omani coastline can support such potential approaches. In this communication, we used a local mtDNA-16SrRNA reference library representing Sparidae fish species from the Omani coastlines to identify two Sparidae eDNA sequences (zotu24 and zotu85, from Muscat and Dhofar, respectively) from Acanthopagrus and Diplodus genera reported by a recent eDNA study from Oman. The two species are found to be Acanthopagrus berda and Diplodus cervinus and their sampling sites matches the locations range of the reference specimens. The results indicate the utility and importance for DNA markers’ reference library representing fish species from the Omani coastline to effectively sustain the marine resources using emerging technologies. Keywords: Sparidae, eDNA; 16SrRNA; Acanthopagrus berda; Diplodus cervinus; Oman.

Performance of DNA metabarcoding, standard barcoding and morphological approaches in the identification of insect biodiversity.

For two decades, DNA barcoding and, more recently, DNA metabarcoding have been used for molecular species identification and estimating biodiversity. Despite their growing use, few studies have systematically evaluated these methods. This study aims to evaluate the efficacy of barcoding methods in identifying species and estimating biodiversity, by assessing their consistency with traditional morphological identification and evaluating how assignment consistency is influenced by taxonomic group, sequence similarity thresholds and geographic distance. We first analysed 951 insect specimens across three taxonomic groups: butterflies, bumblebees and parasitic wasps, using both morphological taxonomy and single-specimen COI DNA barcoding. An additional 25,047 butterfly specimens were identified by COI DNA metabarcoding. Finally, we performed a systematic review of 99 studies to assess average consistency between insect species identity assigned via morphology and COI barcoding and to examine the distribution of research effort. Species assignment consistency was influenced by taxonomic group, sequence similarity thresholds and geographic distance. An average assignment consistency of 49% was found across taxonomic groups, with parasitic wasps displaying lower consistency due to taxonomic impediment. The number of missing matches doubled with a 100% sequence similarity threshold and COI intraspecific variation increased with geographic distance. Metabarcoding results aligned well with morphological biodiversity estimates and a strong positive correlation between sequence reads and species abundance was found. The systematic review revealed an 89% average consistency and also indicated taxonomic and geographic biases in research effort. Together, our findings demonstrate that while problems persist, barcoding approaches offer robust alternatives to traditional taxonomy for biodiversity assessment.

Assessment of Biodiversity, Physicochemical water parameters, Length-weight Relationship and Condition factor of fish species in Tiga Lake, Kano State, Nigeria

Assessment of Biodiversity, Physicochemical water parameters, Length-weight Relationship and Condition factor of fish species in Tiga Lake, Kano State, Nigeria

The value of multi-taxon approaches to improve biodiversity assessment at municipal scales

The value of multi-taxon approaches to improve biodiversity assessment at municipal scales

Human-animal contact to inform zoonotic disease risk across gradients of agricultural land use change in the Central River Region (CRR) of The Gambia (ZooContact): a formative study.

Pilot studies are important initial steps in research, providing a preliminary assessment of the practicality, feasibility, and potential challenges of a proposed study. This study attempts to assess the feasibility, practicality, and acceptability of a study that integrates a human-animal contact (HAC) questionnaire, animal biodiversity survey using acoustic analysis, and zoonotic disease investigation in animals among rural households in the Central River Region (CRR) of The Gambia. The pilot study revealed granular insights that would otherwise go unnoticed, providing vital information that directly guided the design and implementation of the subsequent full-scale study on zoonotic disease risk. A pilot study was conducted in five villages in the CRR of The Gambia. Community sensitization was carried out together with the village leadership, followed by a familiarization tour of the study setting. Questionnaire-based interview was conducted among participants (n = 50) randomly selected to assess the acceptability and reliability of the questionnaire. The feasibility and acceptability of biodiversity surveys and animal sampling were assessed using verbal inquiries from participants and community leaders. The recruitment rate was 96%, and most participants, 50 out of 52, were willing to participate without compensation for lost time during interviews. For animal sampling, 45 out of 50 participants were willing to allow the study team to sample blood and feces from their animals without any form of incentive. All five village heads agreed to the usage of sound recorders to be placed within their community for animal biodiversity assessment. For the survey effort, one field assistant interviewed 25 participants per week. It took a total of 1 h to complete an interview, including random household selection, consenting, and questionnaire interview. The pilot study confirmed the feasibility of the research and informed the design of the larger study. Key parameters, such as community access, acceptability, recruitment success, and logistical requirements, contributed to robust sample size calculations and realistic project cost estimates. Additionally, the study enabled the research team to familiarize themselves with the communities and refine the methods for the full study.

A Comparative Assessment of Soil Biodiversity and Physicochemical Characteristics in Conservation and Conventional Smallholder Farms in Kenya

A Comparative Assessment of Soil Biodiversity and Physicochemical Characteristics in Conservation and Conventional Smallholder Farms in Kenya

Deepdive: Leveraging Pre-trained Deep Learning for Deep-Sea ROV Biota Identification in the Great Barrier Reef

Understanding and preserving the deep sea ecosystems is paramount for marine conservation efforts. Automated object (deep-sea biota) classification can enable the creation of detailed habitat maps that not only aid in biodiversity assessments but also provide essential data to evaluate ecosystem health and resilience. Having a significant source of labelled data helps prevent overfitting and enables training deep learning models with numerous parameters. In this paper, we contribute to the establishment of a significant deep-sea remotely operated vehicle (ROV) image classification dataset with 3994 images featuring deep-sea biota belonging to 33 classes. We manually label the images through rigorous quality control with human-in-the-loop image labelling. Leveraging data from ROV equipped with advanced imaging systems, our study provides results using novel deep-learning models for image classification. We use deep learning models including ResNet, DenseNet, Inception, and Inception-ResNet to benchmark the dataset that features class imbalance with many classes. Our results show that the Inception-ResNet model provides a mean classification accuracy of 65%, with AUC scores exceeding 0.8 for each class.

EDNA State and Medium Affect DNA Degradation Patterns in Seminatural Systems of Southern African Waterholes

ABSTRACTEnvironmental DNA (eDNA) has evolved into a valuable asset of the ecologists' toolkit, enabling time‐ and cost‐efficient biodiversity assessments in a wide variety of ecosystems. Since eDNA can be isolated from a broad range of environmental substrates, its persistence times in those media are of decisive importance for drawing inferences about species presence. For the first time, we characterize eDNA persistence in water and sediment samples of seminatural waterholes in a savanna system in South Africa to gain a better understanding of eDNA decay in these waterbodies. Using mesocosm experiments, we tracked eDNA decay in two different DNA states (extracellular and membrane bound), during two different seasons (wet and dry), and from two different substrates (surface water and sediment). Extracellular DNA degraded rapidly in a first‐order exponential decay fashion and membrane‐bound DNA exhibited a slower decline with more intricate patterns, involving initial reduction followed by a subsequent increase in measured DNA concentrations. The latter we attribute to cell disassociation and cell lysis at 24–48 h after introduction into the environment. Higher stochasticity of membrane‐bound DNA capture in the dry season highlights the need for higher sampling efforts in natural systems in which eDNA is presumably more patchily distributed. Additionally, we observed longer eDNA persistence in sediments than in water samples, presumably due to better protection from nucleases. We could not reveal any effects of environmental parameters on eDNA decay, emphasizing that further research is needed to better understand eDNA dynamics in those waterbodies in order to exploit their full potential for eDNA‐based bioassessments in those systems.

Review of biodiversity assessment and resource management orientation for sustainable rural development in Lang Son province, Vietnam

This study examines the conservation and biodiversity management efforts in Lang Son province, Vietnam, in the context of global environmental concerns. Under Decision No 2447/QD-UBND, the province’s Special-use Forest Planning focuses on conserving areas such as the Huu Lien Nature Reserve and the Mau Son special-use forests. This initiative covers a substantial planned land area to sustain biodiversity and foster rural development up to 2030. Recent surveys indicate a notable increase in plant species within these areas, from 842 species in 2017 to 961 in 2019, and significant efforts towards conserving endangered species like the Asiatic black bear and the Annam flying frog. The province encompasses diverse ecosystems spread across 832,075.82 ha, characterized by varied terrains and climates contributing to its rich biodiversity. These regions are crucial for various species, including those listed in conservation documents, such as the 77 plant species recorded. RAP-Plant analysis and Monte Carlo simulation indicate that Lang Son’s biodiversity, with a Shannon index of 2.85 and Simpson index of 0.75, is threatened by a projected forest area decline to 514,578.61 ha by 2040, risking extinction for rare species like Hoang dan and Lan kim tuyen. Furthermore, Lang Son’s strategic initiatives towards sustainable agricultural practices, forest management, and restoration efforts highlight the integration of biodiversity conservation into broader socio-economic development plans. The province’s approach aligns with global strategies emphasizing the protection of endangered and endemic species as essential to maintaining ecological balances and supporting sustainable development. This study underscores the importance of comprehensive regional planning and community engagement in biodiversity conservation efforts to mitigate economic development, illegal activities, and climate change challenges. Threats such as illegal logging and habitat fragmentation persist, necessitating more vital community-based conservation efforts and robust legal frameworks.

Monitoring soil fauna with ecoacoustics.

Ecoacoustics-or acoustic ecology-aids in monitoring elusive and protected species in several ecological contexts. For example, passive acoustic monitoring (PAM), which involves autonomous acoustic sensors, is widely used to detect various taxonomic groups in terrestrial and aquatic ecosystems, from birds and bats to fish and cetaceans. Here, we illustrate the potential of ecoacoustics to monitor soil biodiversity (specifically fauna)-a crucial endeavour given that 59% of species live in soil yet 75% of soils are affected by degradation. We describe the sources of sound in the soil (e.g. biological, geological and anthropogenic) and the ability of acoustic technology to detect and differentiate between these sounds, highlighting opportunities and current gaps in knowledge. We also propose a roadmap for the future development of optimized hardware, analytical pipelines and experimental approaches. Soil ecoacoustics is an emerging field with considerable potential to improve soil biodiversity monitoring and 'soil health' diagnostics. Indeed, early studies suggest soil ecoacoustics can be successfully applied in various ecosystems (e.g. grasslands, temperate, tropical and arid forests) and land uses (e.g. agriculture, viticulture, natural and restored ecosystems). Given the low cost, minimal intrusiveness, and effectiveness in supporting soil biodiversity assessments and biosecurity risks, we advocate for the advancement of soil ecoacoustics for future land management applications.

Microalgal Diversity and Molecular Ecology: A Comparative Study of Classical and Metagenomic Approaches in Ponds of the Eifel National Park, Germany

While molecular methods have begun to transform ecology, most algal biodiversity is still studied using the classical approach of identifying microalgae by light microscopy directly in sample material or using cultures. In this study, we compare both approaches (light microscopy and metagenomics as a molecular approach) using the freshwater ponds of the Eifel National Park in Germany as a case study. The ponds were found to be rich in desmids by light microscopy. A total of 299 species representing 81 genera were identified by light microscopy. While the molecular method does not currently allow species identification in most cases, we were able to identify 207 different algal genera. In total, 157 genera were detected only by metagenomics, 50 genera were found with both methods, and 31 genera were found by light microscopy, highlighting the need to continue using light microscopy in addition to a molecular approach. The metagenomics method has several advantages over the light microscopy method: (1) deeper assessment of alpha biodiversity, (2) better abundance numbers, and (3) complete coverage of all living matter. The latter is also a significant improvement over metabarcoding, as universal PCR primers are not available.

The Past and Future of the Fisheries and Marine Ecosystem Model Intercomparison Project

AbstractClimate change is increasingly affecting the world's ocean ecosystems, necessitating urgent guidance on adaptation strategies to limit or prevent catastrophic impacts. The Fisheries and Marine Ecosystem Model Intercomparison Project (FishMIP) is a network and framework that provides standardised ensemble projections of the impacts of climate change and fisheries on ocean life and the benefits that it provides to people. Since its official launch in 2013 as a small, self‐organized project within the larger Inter‐Sectoral Impact Model Intercomparison Project, the FishMIP community has grown substantially and contributed to key international policy processes, such as the Intergovernmental Panel on Climate Change Assessment Report, and the Intergovernmental Science‐Policy Platform on Biodiversity and Ecosystem Services Global Biodiversity Assessment. While not without challenges, particularly around comparing heterogeneous ecosystem models, integrating fisheries scenarios, and standardising regional‐scale ecosystem models, FishMIP outputs are now being used across a variety of applications (e.g., climate change targets, fisheries management, marine conservation, Sustainable Development Goals). Over the next decade, FishMIP will focus on improving ecosystem model ensembles to provide more robust and policy‐relevant projections for different regions of the world under multiple climate and societal change scenarios, and continue to be open to a broad spectrum of marine ecosystem models and modelers. FishMIP also intends to enhance leadership diversity and capacity‐building to improve representation of early‐ and mid‐career researchers from under‐represented countries and ocean regions. As we look ahead, FishMIP aims to continue enhancing our understanding of how marine life and its contributions to people may change over the coming century at both global and regional scales.

Foundations for a national assessment of soil biodiversity

Foundations for a national assessment of soil biodiversity

Decoding the Baltic Sea’s past and present: A simple molecular index for ecosystem assessment

Marginal sea ecosystems, such as the Baltic Sea, are severely affected by anthropogenic pressures, such as climate warming, pollution, and eutrophication, which increased in the course of the past century. Biodiversity monitoring data and assessment of environmental status in such systems have typically been carried out only for the past few decades, if at all, and knowledge on pre-impact stability and good ecological status is limited. An extension of monitoring time series can potentially be achieved through analyses of paleoecological records, e.g. for phytoplankton, which form the base of the food web and are highly susceptible to environmental changes. Within the phytoplankton community, dinoflagellates and diatoms play a significant role as primary producers, and their relative dominance in the spring bloom, calculated as Dia/Dino index, is used as an indicator for the environmental status of the Baltic Sea. To extend time series on the dominance patterns and include non-fossilized dinoflagellates, we here establish a simple droplet digital PCR (ddPCR) reaction on ancient DNA from sediment cores that decodes phytoplankton dynamics. We focus on two common spring bloom species, the diatom Skeletonema marinoi and the dinoflagellate Apocalathium malmogiense, for which we evaluate a DNA based dominance index. It performs very well in comparison to DNA metabarcoding and modern monitoring and can elucidate past species dominance across the past century and across millennia in different basins of the Baltic. For the past century, we see a dominance shift already starting before the mid-20th century in two of the Baltic Sea basins, thus substantially predating current monitoring programs. Shifts are only partly coeval among the cores and the index shows different degrees of stability. This pattern is confirmed across millennia, where a long-term stable relationship between the diatom and the dinoflagellate is observed in the Eastern Gotland Basin, while data from the Gulf of Finland bear testimony to a much more unstable relationship. This confirms that good ecological status based on the dominance pattern of diatoms and dinoflagellates must be established locally and exemplifies how sediment core DNA can be employed to extend monitoring data.