Biodiversity Monitoring Programs Research Articles

The Neotropical Biodiversity Mapping Initiative: Transforming Venezuelan biodiversity monitoring and capacity building

Tropical Latin America is home to an enormous share of the world's biodiversity. Despite its immense natural wealth, the region faces a significant deficit of reliable biodiversity data and lacks the local capacity necessary to collect such data. The Neotropical Biodiversity Mapping Initiative (NeoMaps or NeoMapas) is a long-term biodiversity monitoring program. NeoMaps has not only addressed these gaps in biodiversity data in one of the megadiverse tropical countries, Venezuela, but has also emerged as a model for efficiently surveying biodiversity while strengthening the local capacity needed to conduct these surveys. After three nationwide systematic surveys and international field courses in 2006, 2009, and 2010, NeoMaps assembled an invertebrate collection and biodiversity database with over 170,000 records of occurrence and abundance for birds, dung beetles, and butterflies. NeoMaps activities lead to direct outcomes by reducing biodiversity knowledge gaps for three taxonomic groups and training more than 60 conservationists from Venezuela, Colombia, Mexico, Peru, Bolivia, Brazil, Uruguay, and Spain. NeoMaps had a broader impact on national capacity building programs, and made important contributions for improving, sharing and applying national biodiversity knowledge.

Evaluating the eDNA spatial signal in natural populations and its application for the monitoring of the threatened Harttiella (Siluriformes, Loricariidae)

AbstractTo face the current downward trajectory of freshwater biodiversity loss, the implementation of effective biodiversity monitoring programs is of utmost importance. Environmental DNA offers unprecedented opportunities for this aim but several challenges still need to be addressed before implementing efficient species monitoring using eDNA. One of them is optimizing the eDNA sampling scheme to maximize the eDNA detection probability. For instance, in flowing freshwaters, the transport of eDNA downstream from its source can impact the eDNA detection probability, and blur the link between eDNA detection and the local occurrence of the species. Here, we investigated the eDNA spatial range of Harttiella lucifer (Siluriformes, Loricariidae), a threatened neotropical siluriform fish inhabiting French Guianese mountain streams, and confined to waterfalls and fast‐flowing environments. Environmental samples were collected at 11 sites from the H. lucifer population to 2000 m downstream. A species‐specific dPCR approach was applied to quantify the amount of DNA present in each sample and evaluate the eDNA detection probability of H. lucifer according to the distance from its source. Results showed an accumulation of eDNA at 50 and 100 m downstream from H. lucifer population. The evaluation of detection probabilities revealed that 300 m downstream from H. lucifer population, the probability of detection drops to 50%. This study suggests that eDNA drift in neotropical small streams is limited to a few tens meters downstream. These findings demonstrate that in neotropical small streams, eDNA provides a picture of the local fish fauna rather than integrating information over large spatial scales.

A circumpolar study of surface zooplankton biodiversity of the Southern Ocean based on eDNA metabarcoding

Under pressure from climate change and fishing, the Southern Ocean ecosystems have been changing. Zooplankton plays a vital role in the food web of the Southern Ocean and is crucial for maintaining ecosystem stability. Investigating the circumpolar-scale species composition and biodiversity of zooplankton is crucial for ensuring ecosystem-based conservation and management of the Southern Ocean in a changing climate. Here, we utilized eDNA metabarcoding to assess the biodiversity of zooplankton in the surface seawater surrounding the Antarctica based on samples collected during two expeditions spanning from 2021 to 2022. The main purpose of this paper is to provide more baseline information about circumpolar zooplankton biodiversity based on the emerging eDNA metabarcoding tool. This comprehensive approach led to the identification of over 300 distinct zooplankton species, forming a diverse community dominated by Jellyfish, Mollusca and Polychaete. Surprisingly, common dominant taxonomic groups such as krill and copepods in the Southern Ocean did not show high relative abundance (reads) in surface seawater. The results of redundancy analysis (RDA) and correlation analysis highlighted that water temperature and chlorophyll a had the most significant impact on the reads and diversity of zooplankton. Notably, the influence of water temperature on zooplankton seemed to be primarily indirect, potentially mediated by its effects on primary productivity. Increasing in primary production might lead to lower zooplankton biodiversity in the Southern Ocean in future. This research underscores the effectiveness of eDNA metabarcoding as a valuable tool for monitoring zooplankton diversity in open seas. Given the ongoing changes in temperature, sea ice extent and their impact on primary production, our findings lay a crucial foundation for using eDNA techniques to establish long-term biodiversity monitoring programs across extensive marine ecosystems in the future.

Challenges for the Post-Market Environmental Monitoring in the European Union Imposed by Novel Applications of Genetically Modified and Genome-Edited Organisms.

Information on the state of the environment is important to achieve the objectives of the European Green Deal, including the EU's Biodiversity Strategy for 2030. The existing regulatory provisions for genetically modified organisms (GMOs) foresee an obligatory post-market environmental monitoring (PMEM) of potential adverse effects upon release into the environment. So far, GMO monitoring activities have focused on genetically modified crops. With the advent of new genomic techniques (NGT), novel GMO applications are being developed and may be released into a range of different, non-agricultural environments with potential implications for ecosystems and biodiversity. This challenges the current monitoring concepts and requires adaptation of existing monitoring programs to meet monitoring requirements. While the incorporation of existing biodiversity monitoring programs into GMO monitoring at the national level is important, additional monitoring activities will also be required. Using case examples, we highlight that monitoring requirements for novel GMO applications differ from those of GM crop plants previously authorized for commercial use in the European Union.

Quantification of large-spatial scale and in-stream factors affecting the structure of benthic macroinvertebrate communities in mountain streams

Habitat diversity plays a crucial role in shaping the structure and distribution of benthic macroinvertebrate communities. However, few studies have investigated the concurrent effects of such drivers operating at different spatial scales in mountain streams. Here, we assessed which environmental factors at different spatial scales, related to stream/river type and substrate, influence the diversity of benthic macroinvertebrate assemblages in mountain streams and rivers. Within the framework of the aquatic investigations of the Biodiversity Monitoring South Tyrol (BMS) – a newly-established, regional-based, long-term biodiversity monitoring program – benthic macroinvertebrates and a set of environmental factors describing water quality, stream/river hydromorphology and in-stream habitat characteristics were collected and analysed. The variation in total density, taxonomic richness, Shannon evenness and % Ephemeroptera–Plecoptera–Trichoptera taxa of stream benthic macroinvertebrates was assessed at multi-scale habitat levels, in 48 sampling sites across the mountainous region of the Autonomous Province of Bolzano/Bozen (Italy). The effects of stream/river type, substrates and different environmental factors on community composition of benthic macroinvertebrates were quantified, using a stepfoward Redundancy Analysis (RDA) and generalized additive models (GAMs). In addition, we performed an Indicator Value analysis to detect taxa that were significantly associated with a specific substrate and/or stream/river type. Overall, we observed significant differences in benthic biological metrics among both stream/river and substrate types. We also found at least one indicator taxa for each stream/river type, with environmental factors acting at reach and large-spatial scale – temperature, stream channel stability, elevation – being the key drivers in shaping macroinvertebrate distribution patterns in the analysed mountain rivers. While significant differences in macroinvertebrate community structures were found among substrates, the influence of stream/river type conditions was particularly evident. Apart from ranking environmental variables worth including in a long-term aquatic biodiversity monitoring program in mountain areas, our study provides a baseline for practical applications. For instance, depending on the desired outcome of habitat heterogeneity restoration, it can suggest the optimal scale (landscape vs. reach vs. patch) for prioritizing in-field interventions.

Cost-effort analysis of Baited Remote Underwater Video (BRUV) and environmental DNA (eDNA) in monitoring marine ecological communities.

Monitoring the diversity and distribution of species in an ecosystem is essential to assess the success of restoration strategies. Implementing biomonitoring methods, which provide a comprehensive assessment of species diversity and mitigate biases in data collection, holds significant importance in biodiversity research. Additionally, ensuring that these methods are cost-efficient and require minimal effort is crucial for effective environmental monitoring. In this study we compare the efficiency of species detection, the cost and the effort of two non-destructive sampling techniques: Baited Remote Underwater Video (BRUV) and environmental DNA (eDNA) metabarcoding to survey marine vertebrate species. Comparisons were conducted along the Sussex coast upon the introduction of the Nearshore Trawling Byelaw. This Byelaw aims to boost the recovery of the dense kelp beds and the associated biodiversity that existed in the 1980s. We show that overall BRUV surveys are more affordable than eDNA, however, eDNA detects almost three times as many species as BRUV. eDNA and BRUV surveys are comparable in terms of effort required for each method, unless eDNA analysis is carried out externally, in which case eDNA requires less effort for the lead researchers. Furthermore, we show that increased eDNA replication yields more informative results on community structure. We found that using both methods in conjunction provides a more complete view of biodiversity, with BRUV data supplementing eDNA monitoring by recording species missed by eDNA and by providing additional environmental and life history metrics. The results from this study will serve as a baseline of the marine vertebrate community in Sussex Bay allowing future biodiversity monitoring research projects to understand community structure as the ecosystem recovers following the removal of trawling fishing pressure. Although this study was regional, the findings presented herein have relevance to marine biodiversity and conservation monitoring programs around the globe.

Characterizing personalized ecologies

AbstractPeople have unique sets of direct sensory interactions with wild species, which change through their days, weeks, seasons, and lifetimes. Despite having important influences on their health and well‐being and their attitudes towards nature, these personalized ecologies remain surprisingly little studied and are poorly understood. However, much can be inferred about personalized ecologies by considering them from first principles (largely macroecological), alongside insights from research into the design and effectiveness of biodiversity monitoring programmes, knowledge of how animals respond to people, and studies of human biology and demography. Here I first review how three major sets of drivers, opportunity, capability and motivation, shape people's personalized ecologies. Second, I then explore the implications of these mechanisms for how more passively and more actively practical improvements can be made in people's personalized ecologies. Particularly in light of the declines in the richness of these ecologies that are being experienced in much of the world (the so‐called ‘extinction of experience’), and the significant consequences, marked improvement in many people's interactions and experiences with nature may be key to the future of biodiversity.

Corrigendum: Development of a multi-scale monitoring programme: approaches for the Arctic and lessons learned from the Circumpolar Biodiversity Monitoring Programme 2002-2022

Corrigendum: Development of a multi-scale monitoring programme: approaches for the Arctic and lessons learned from the Circumpolar Biodiversity Monitoring Programme 2002-2022

Putting eDNA to the test: A field comparison of eDNA metabarcoding to established protocols for assessing biodiversity in Missouri's Ozark Highland streams

AbstractAquatic biodiversity monitoring to inform conservation and management efforts in‐stream systems has increasingly begun to incorporate environmental DNA (eDNA)‐based sampling methods. We conducted a comparison of eDNA metabarcoding to a traditional protocol of combined seining and electrofishing methods to assess fish biodiversity of wadeable stream sites in six separate drainages in the Ozark Highlands of Missouri (USA). The study further focused on the headwaters of the Meramec River, which included 11 sites and seasonal sampling (summer and winter). We compared estimates of diversity across sampling methods, assessed the influences of water flow (depth, velocity, and discharge) and season, and tested the effects of sampling method and site locality on fish assemblage composition. eDNA sampling detected approximately double the number of species compared to traditional methods, providing higher diversity estimates while maintaining the relative ranking of sites. eDNA detection probabilities were positively associated with stream depth and velocity and were generally higher in summer than in winter but not for all species. Estimated species richness was positively associated with discharge for both methods but the relationship was stronger with eDNA sampling. Assemblage differences between tributary and mainstem sites were attributable to a small number of species that were found predominantly in one stream size category or the other, indicating that eDNA was sensitive to within‐drainage assemblage structure relationships. We highlight improved species detection, a more comprehensive understanding of assemblage structural dynamics, and the potential ability to integrate data across sampling methods as important benefits that encourage the use of eDNA metabarcoding as a primary collection method in future stream biodiversity assessment and monitoring programs.

Mountain soil multitrophic networks shaped by the interplay between habitat and pedoclimatic conditions

Our knowledge of the factors influencing the distribution of soil organisms is limited to specific taxonomic groups. Consequently, our understanding of the drivers shaping the entire soil multitrophic network is constrained. To address this gap, we conducted an extensive soil biodiversity monitoring program in the French Alps, using environmental DNA to obtain multi-taxon data from 418 soil samples. The spatial structure of resulting soil multitrophic networks varied significantly between and within habitats. From forests to grasslands, we observed a shift in the abundance of trophic groups from fungal to bacterial feeding channels, reflecting different ecosystem functioning. Furthermore, forest soil networks were more strongly spatially structured which could only partly be explained by abiotic conditions. Grassland soil networks were more strongly driven by plant community composition and soil characteristics. Our findings provide valuable insights into how climate and land-use changes may differentially affect soil multitrophic networks in mountains.

Distinct spatial patterns of genetic structure and diversity in the butterfly Marbled White (Melanargia galathea) inhabiting fragmented grasslands

We adopted a landscape-scale approach to analyze the genetic patterns (diversity, structure, and differentiation) of the Marbled White (Melanargia galathea). This butterfly species is characteristic of semi-dry grasslands, which have substantially declined in Switzerland during past decades. We sampled individuals on a regular grid of the established Biodiversity Monitoring program of Switzerland over five consecutive years, obtaining 1639 genotyped individuals from 185 locations. Results showed that M. galathea populations cluster into five spatially aggregated clusters that largely coincide with the biogeographic regions of Switzerland. Genetic diversity (allelic richness) was higher in the South of the Alps, likely related to immigration dynamics that suggest recolonisation from the South after the last glaciation. Demographic history resulted in distinct isolation by distance (IBD) and by cumulative elevational difference (isolation by altitude, IBA) at large scale, while regional IBD and IBA were less pronounced. This pattern was likely induced by the barrier effect of the high mountains of the Alps impeding continuous northward migration after the last glacial maximum. A temporal analysis revealed that regional genetic diversity did not change strongly during the five sampling years. This result indicates that the genetic diversity pattern in M. galathea has not been noticeably affected by historical land-use change or that the sampling period of five years is too short to detect any changes. Our findings highlight the regionally, topography-induced distinct genetic clusters, relevant for consideration as conservation units and likely reflecting genetic structures similar to those found in other butterfly species of conservation concern.

Environmental DNA detects biodiversity and ecological features of phytoplankton communities in Mediterranean transitional waters

Climate changes and anthropogenic pressures are causing a biodiversity decline in terms of species number and genetic diversity, reducing the adaptability and evolvability of natural communities. Transitional water ecosystems are more sensitive to habitat reduction and degradation and, thus, are more exposed to biodiversity declines requiring biodiversity monitoring programs for their conservation. Environmental DNA (eDNA) metabarcoding represents a high-throughput tool for biodiversity assessment that is facilitating data collection for biodiversity monitoring. In this study, we applied, for the first time, eDNA metabarcoding in a Mediterranean coastal lagoon to assess the ecological features of eukaryotic phytoplankton communities. We sampled water in seven different lagoon sites and amplified the extracted DNA with primers targeting the variable region 4 (V4) of the 18S rRNA gene marker. The results demonstrated the validity of eDNA studies to provide insights into lagoon phytoplankton composition, establish the structure and spatial variation of phytoplankton communities, and evaluate its correlation to abiotic factors. Finally, the genetic distances analysis suggests that the different spatial distribution of OTUs, at least for the Tetraselmis genus, reflects the genetic background.

Development of a multi-scale monitoring programme: approaches for the Arctic and lessons learned from the Circumpolar Biodiversity Monitoring Programme 2002-2022

The Arctic Council working group, the Conservation of Arctic Flora and Fauna (CAFF) established the Circumpolar Biodiversity Monitoring Programme (CBMP), an international network of scientists, governments, Indigenous organizations, and conservation groups working to harmonize and integrate efforts to extend and develop monitoring and assessment of the Arctic’s biodiversity. Its relevance stretches beyond the Arctic to a broad range of regional and global initiatives and agreements. This paper describes the process and approach taken in the last two decades to develop and implement the CBMP. It documents challenges encountered, lessons learnt, and solutions, and considers how it has been a model for national, regional, and global monitoring programmes; explores how it has impacted Arctic biodiversity monitoring, assessment, and policy and concludes with observations on key issues and next steps. The following are overarching prerequisites identified in the implementation of the CBMP: effective coordination, sufficient and sustained funding, improved standards and protocols, co-production of knowledge and equitable involvement of IK approaches, data management to facilitating regional analysis and comparisons, communication and outreach to raising awareness and engagement in the programme, ensuring resources to engage in international fora to ensuring programme implementation.

A new genomic resource to enable standardized surveys of SNPs across the native range of brook trout (Salvelinus fontinalis).

Understanding how genetic diversity is distributed across spatiotemporal scales in species of conservation or management concern is critical for identifying large-scale mechanisms affecting local conservation status and implementing large-scale biodiversity monitoring programmes. However, cross-scale surveys of genetic diversity are often impractical within single studies, and combining datasets to increase spatiotemporal coverage is frequently impeded by using different sets of molecular markers. Recently developed molecular tools make surveys based on standardized single-nucleotide polymorphism (SNP) panels more feasible than ever, but require existing genomic information. Here, we conduct the first survey of genome-wide SNPs across the native range of brook trout (Salvelinus fontinalis), a cold-adapted species that has been the focus of considerable conservation and management effort across eastern North America. Our dataset can be leveraged to easily design SNP panels that allow datasets to be combined for large-scale analyses. We performed restriction site-associated DNA sequencing for wild brook trout from 82 locations spanning much of the native range and domestic brook trout from 24 hatchery strains used in stocking efforts. We identified over 24,000 SNPs distributed throughout the brook trout genome. We explored the ability of these SNPs to resolve relationships across spatial scales, including population structure and hatchery admixture. Our dataset captures a wide spectrum of genetic diversity in native brook trout, offering a valuable resource for developing SNP panels. We highlight potential applications of this resource with the goal of increasing the integration of genomic information into decision-making for brook trout and other species of conservation or management concern.

Social Participation in the Brazilian National Biodiversity Monitoring Program Leads to Multiple Socioenvironmental Outcomes

Social Participation in the Brazilian National Biodiversity Monitoring Program Leads to Multiple Socioenvironmental Outcomes

Coastal rocky reef fish monitoring in the context of the Marine Strategy Framework Directive: Environmental DNA metabarcoding complements underwater visual census

Efficient biodiversity monitoring programs are essential to assess the ecological status of marine ecosystems. In the context of the European Marine Strategy Framework Directive (MFSD), coastal rocky reef fish assemblages are most often surveyed using underwater visual census (UVC). While UVC is well-suited to monitor conspicuous fish, it underestimates hidden, vagrant and/or elusive fishes. Hence, complementary methods are needed to survey the whole fish assemblage. Environmental DNA (eDNA) metabarcoding is increasingly used in this context. Here, we evaluated the effectiveness of eDNA metabarcoding collected from water to provide sound and complementary diversity data to UVC in support of the MFSD. Both methods were used to examine coastal rocky reef fish assemblages in one bay of Brittany (France), along an inshore-offshore gradient and during two seasons. eDNA metabarcoding was carried out following different water sampling strategies: small water volumes (2L) from stationary sampling at the surface and bottom and large water volume (30L) filtered at the surface while moving in close vicinity of the sampling site. A total of 93 (including 57 species) and 33 (including 27 species) taxa were detected with eDNA metabarcoding and UVC, respectively. Eleven species were only recorded by UVC, a result explained for nine of them by a lack of taxonomic resolution of the markers used (12S and 16S) and/or the unavailability of reference sequences. eDNA metabarcoding allows to recover species expected to be present, such as demersal rocky specialist fishes, at a similar species richness level than UVC (14 species for UVC and 12 species for eDNA). It however also unveiled other taxa (pelagic, bentho-pelagic and others demersal fishes) inhabiting the bay and rarely reported through UVC (18 species for UVC and 45 species for eDNA). Despite these differences in species identified by UVC vs. eDNA, both survey methods were consistent in characterizing spatio-temporal variabilities of fish assemblages, highlighting strong site fidelity of eDNA to the source communities. In a well-mixed water column, the eDNA signal was very homogeneous, allowing the use of the cost-effective small water volume eDNA sampling method. eDNA metabarcoding is thus particularly promising to study coastal rocky reef assemblages, and when coupled with UVC, it improves monitoring surveys.

Agricultural land-use and landscape composition: Response of wild bee species in relation to their characteristic traits

In the past centuries, farmland has undergone a fundamental transformation through changed farming practices, such as the use of agrochemicals and advanced machine processing. Particularly since the 1970s, agriculturally driven land-use change has caused destruction of natural and semi-natural habitats, and as a consequence, severe loss of biodiversity. Hence, identifying landscape patterns and habitats that enhance species richness, and detecting species and traits that are most vulnerable to intensive land-use are prerequisites for conservation. To evaluate the effects of agricultural land-use and landscape composition on wild bees, we investigated 340 cross-transects in 34 test areas in the main agricultural regions of Austria within the framework of the biodiversity monitoring program BINATS. Using multivariate models (GLM, DCA), wild bees and potential explanatory parameters (e.g. Shannon landscape diversity index, plant diversity, flower cover) were documented, and their interrelationships analyzed. We found strong negative effects of increased agricultural land cover on species richness, abundance and functional richness. Species richness was positively correlated with an increasing area of semi-natural elements (e.g. extensive grassland, hedgerows, fallows) and the number of different habitat types, while wild bee abundance was best explained by the presence of semi-natural habitats and flower cover. Colletidae were significantly associated with the area of semi-natural elements, and were especially sensitive to agricultural intensification. Many species from communities that are present in complex landscapes disappeared in intensively managed farmland, and the majority of species decreased in response to simplified landscapes. A few species, however, even benefited. Our results emphasize the importance of diverse semi-natural elements and high regional flower cover within farmland for maintaining and enhancing species richness and abundance, and for promoting a positive spillover effect of pollinators to the surrounding agricultural landscape. Especially members of the family Colletidae, with a high proportion of specialized species, will benefit from diverse semi-natural habitat types. Given the unique importance of wild bees as pollinators of wildflowers and crops, it is crucial to improve and expand agri-environmental schemes to combat ongoing biodiversity loss in farmland.

A Conceptual Framework for Biodiversity Monitoring Programs in Conservation Areas

Maintaining and improving the state of biodiversity is a primary factor guiding management activities in conservation areas, including protected areas (PAs) and other effective area-based conservation measures (OECMs). Due to the complex nature of conservation programs, a common management approach cannot be prescribed. Robust monitoring programs supporting management activities are required to evaluate the state of species and habitats. However, limited resources, poor data management practices, and competing requirements of stakeholder groups increase the challenges that must be addressed through realization of monitoring programs. We propose a framework of seven basic questions to guide conservation area managers to implement effective biodiversity monitoring techniques. The result is identification of indicators, site characteristics, and resources to promote the development of a biodiversity monitoring program. We call for adoption of a strategic guideline providing this framework to harmonize decision making processes across national and international networks. Implementation of this robust framework will support comparative monitoring data, contributing to systematic approaches for adaptive management in PAs and OECMs and improving the body of knowledge surrounding global biodiversity.

Monitoring Coastal Water Body Health with Sentinel-2 MSI Imagery

The Australian ‘New South Wales Estuary health assessment and biodiversity monitoring program’ has set state-wide targets for estuary health. A selection of water bodies is being monitored by in situ chlorophyll a concentration and turbidity measurements, indicators for water quality. We investigate whether the current monitoring program can benefit from the use of remote sensing derived data, analyzing chlorophyll a and water clarity estimates by the C2RCC and ACOLITE products based on Sentinel-2 MSI imagery for three lakes along the New South Wales coast. The C2RCC and ACOLITE products were partly successful in predicting chlorophyll a concentration and water clarity. Estimates based on Sentinel-2 MSI imagery were in the range of in situ measurements. However, results varied across years and lakes, and a significant correlation could not be found in every case. It is likely that the physical differences between the systems, such as nutrient input, tannins, and suspended algae/sediment matrix, influence the output of the algorithm. This may preclude the application of a ‘one size fits all’ monitoring approach, given the importance of local ecological phenomena in both influencing remote sensing observations and the nature of appropriate targets. However, the design of a monitoring program that incorporates remote sensing provides a way forward.

Environmental heterogeneity of a tropical river-to-sea continuum and its relationship with structure and phytoplankton dynamics – Lençóis Maranhenses National Park

β-diversity and functional traits of phytoplankton indicators associated with environmental heterogeneity were investigated as environmental quality descriptors in coastal (CS), estuarine (ES), and limnetic (LS) sectors in a tropical river-to-sea ecosystem. Results showed that environmental heterogeneity was marked by spatial differences, contributing to biological heterogeneity. Sporadic and recurrent blooms were associated with environmental spatiotemporal variations and reflected a reduction in ES α-diversity. Salinity acted as an environmental filter that governed the structure and dynamics of the community. The spatial heterogeneity and high turnover of phytoplankton resulted in reliable bioindicators selection. Colonial, bloom-forming and harmful species were associated with highly suspended particulate matter (SPM) because these species are better adapted to these conditions. Species small in size were associated with high concentrations of silicate and chlorophyll-a in the ES because of the occurrence of diatom recurrent blooms. Most flagellates indicators genera have bloom-forming potential. Integrating morphofunctional with taxonomic approaches enabled detailed observations of environmental filters, supporting the selection of priority species and areas for introducing biodiversity monitoring programs and conservation in tropical ecosystems.