The high biodiversity of benthic organisms in a coastal ecosystem revealed by an integrative approach / A alta biodiversidade de organismos bentônicos em um ecossistema costeiro revelada por uma abordagem integrativa

Abstract Increasing habitat modification and species loss demand consistent efforts to describe and understand biodiversity patterns. The BIOTA/FAPESP Program was created in this context and it has been a successful initiative to promote studies on biodiversity and conservation in Brazil. The BIOTA/Araçá is an interdisciplinary project that provided a detailed evaluation of the biodiversity of Araçá Bay, a coastal seascape located on the North coast of the state of São Paulo, Southeast Brazil. The bay encompasses multiple habitats, such as beaches, mangroves, rocky shores, and a tidal flat, and provides important ecosystem services. Unfortunately, the bay is the subject of complex social-environmental conflicts that oppose economic, social, and environmental demands (i.e., the expansion of neighboring harbor activities vs. small-scale artisanal fisheries and protection of biodiversity). The present study presents a survey of the benthic species occurring in the different habitats of Araçá Bay, including data obtained during the BIOTA/Araçá project and previous assessments of the area. The benthic species play an important role in marine environments and studying the diversity of these organisms that live associated with the bottom is indispensable for comprehending the environment's functioning. The macrofauna, meiofauna, and microorganisms associated with soft and hard bottom were listed, and additional information, such as the habitat and geographical distribution, were provided for each species. The checklist includes 826 species, almost 70% recorded during the BIOTA/Araçá project. The most speciose taxa were the annelids (225 spp.), mollusks (194 spp.), and crustaceans (177 spp.). Seven benthic species are endemic to Araçá Bay, 14 are considered threatened, and seven are economically exploited. Furthermore, the bay is the type locality of many taxa, and 11 new benthic species were described based on specimens sampled during the project. This project shows the importance of Araçá Bay as a unique biologically rich environment and highlights the need for conservation efforts in light of the current threats.

Resumo O aumento da modificação dos habitats e da perda de espécies demanda esforços consistentes para descrever e compreender os padrões de biodiversidade. O programa BIOTA/FAPESP foi criado nesse contexto e é uma iniciativa de sucesso para promover estudos em biodiversidade e conservação no Brasil. O BIOTA/Araçá é um projeto interdisciplinar que promoveu uma avaliação detalhada da biodiversidade da Baía do Araçá, um ecossistema costeiro localizado ao Norte do estado de São Paulo, Sudeste do Brasil. A baía engloba múltiplos habitats, tais como praias, manguezais, costões rochosos, e uma planície de maré, e também fornece importantes serviços ecossistêmicos. Infelizmente, a baía está sujeita à conflitos sócio-ambientais complexos que contrastam demandas econômicas, sociais e ambientais (i.e. a expansão das atividades do porto vizinho vs. a pesca artesanal de pequena escala e a proteção da biodiversidade). O presente estudo apresenta um levantamento das espécies bentônicas que ocorrem nos diferentes habitats da Baía do Araçá, incluindo dados obtidos durante o projeto BIOTA/Araçá e de investigações realizadas anteriormente na área. As espécies bentônicas desempenham um papel importante no ambiente marinho, e estudar a diversidade desses organismos que vivem associados ao fundo é indispensável para compreender o funcionamento do meio ambiente. A macrofauna, meiofauna, e microorganismos associados aos fundos consolidado e inconsolidado foram listados, e informações adicionais foram fornecidas para cada espécie, tais como a distribuição geográfica e nos habitats. O checklist inclui 826 espécies, quase 70% registradas durante o projeto BIOTA/Araçá. Os taxa mais especiosos foram os anelídeos (225 spp.), moluscos (194 spp.), e crustáceos (177 spp.). Entre as espécies bentônicas listadas, sete são endêmicas da Baía do Araçá, 14 são consideradas ameaçadas de extinção, e sete são exploradas economicamente. A baía é a localidade tipo de vários taxa, e 11 novas espécies bentônicas foram descritas com base em espécimes amostrados durante o projeto. Este projeto mostra a importância da Baía do Araçá como um ambiente de riqueza biológica única e demonstra a necessidade de esforços para a sua conservação considerando as atuais ameaças.

Machine learning algorithms accurately identify free-living marine nematode species.

Background: Identifying species, particularly small metazoans, remains a daunting challenge and the phylum Nematoda is no exception. Typically, nematode species are differentiated based on morphometry and the presence or absence of certain characters. However, recent advances in artificial intelligence, particularly machine learning (ML) algorithms, offer promising solutions for automating species identification, mostly in taxonomically complex groups. By training ML models with extensive datasets of accurately identified specimens, the models can learn to recognize patterns in nematodes' morphological and morphometric features. This enables them to make precise identifications of newly encountered individuals. Implementing ML algorithms can improve the speed and accuracy of species identification and allow researchers to efficiently process vast amounts of data. Furthermore, it empowers non-taxonomists to make reliable identifications. The objective of this study is to evaluate the performance of ML algorithms in identifying species of free-living marine nematodes, focusing on two well-known genera: Acantholaimus Allgén, 1933 and Sabatieria Rouville, 1903. Methods: A total of 40 species of Acantholaimus and 60 species of Sabatieria were considered. The measurements and identifications were obtained from the original publications of species for both genera, this compilation included information regarding the presence or absence of specific characters, as well as morphometric data. To assess the performance of the species identification four ML algorithms were employed: Random Forest (RF), Stochastic Gradient Boosting (SGBoost), Support Vector Machine (SVM) with both linear and radial kernels, and K-nearest neighbor (KNN) algorithms. Results: For both genera, the random forest (RF) algorithm demonstrated the highest accuracy in correctly classifying specimens into their respective species, achieving an accuracy rate of 93% for Acantholaimus and 100% for Sabatieria, only a single individual from Acantholaimus of the test data was misclassified. Conclusion: These results highlight the overall effectiveness of ML algorithms in species identification. Moreover, it demonstrates that the identification of marine nematodes can be automated, optimizing biodiversity and ecological studies, as well as turning species identification more accessible, efficient, and scalable. Ultimately it will contribute to our understanding and conservation of biodiversity.

Two new species of Cyatholaimidae (Nematoda: Chromadorida) from the Southeastern Brazilian coast with emphasis on the pore complex and lateral pore-like structures.

Cyatholaimidae is a common and diverse family of mainly marine nematodes, potentially, with a large number of species to be discovered. The taxonomy of the group is marked by a lack of information about the evolutionary history of the characters and of detailed descriptions of morphological structures that may be taxonomically relevant. Two new species of the family are described from a sublittoral region in Southeastern Brazil, emphasizing the importance of the distribution and morphology of pore complex and pore-like structures present on the cuticle. The taxonomic importance of the cuticle ornamentation and spicule shape for the Biarmifer species, as well as the precloacal supplements structures of Pomponema species, are discussed. Biarmifer nesiotes sp. nov. differs from other species of the genus by the presence of eight longitudinal rows of pore complex on the cuticle and by the shape of the copulatory structure. Pomponema longispiculum sp. nov. differs from the most similar species, P. stomachor Wieser, 1954, by the smaller number of turns of the amphidial fovea, the shorter tail and the beginning of the cuticle lateral differentiation (3/4 of the pharynx length vs. end of the pharynx, respectively). We also obtained the SSU rDNA sequence from Pomponema longispiculum sp. nov., which is closely related to Pomponema sp. (MN250093) by about 91%. Updated tabular keys to species identification of each genus (Biarmifer and Pomponema) are included, containing morphometric data, characters related to cuticle ornamentation, and copulatory structures.

Feeding on Host Plants with Different Concentrations and Structures of Pyrrolizidine Alkaloids Impacts the Chemical-Defense Effectiveness of a Specialist Herbivore.

Sequestration of chemical defenses from host plants is a strategy widely used by herbivorous insects to avoid predation. Larvae of the arctiine moth Utetheisa ornatrix feeding on unripe seeds and leaves of many species of Crotalaria (Leguminosae) sequester N-oxides of pyrrolizidine alkaloids (PAs) from these host plants, and transfer them to adults through the pupal stage. PAs confer protection against predation on all life stages of U. ornatrix. As U. ornatrix also uses other Crotalaria species as host plants, we evaluated whether the PA chemical defense against predation is independent of host plant use. We fed larvae from hatching to pupation with either leaves or seeds of one of eight Crotalaria species (C. incana, C. juncea, C. micans, C. ochroleuca, C. pallida, C. paulina, C. spectabilis, and C. vitellina), and tested if adults were preyed upon or released by the orb-weaving spider Nephila clavipes. We found that the protection against the spider was more effective in adults whose larvae fed on seeds, which had a higher PA concentration than leaves. The exceptions were adults from larvae fed on C. paulina, C. spectabilis and C. vitellina leaves, which showed high PA concentrations. With respect to the PA profile, we describe for the first time insect-PAs in U. ornatrix. These PAs, biosynthesized from the necine base retronecine of plant origin, or monocrotaline- and senecionine-type PAs sequestered from host plants, were equally active in moth chemical defense, in a dose-dependent manner. These results are also partially explained by host plant phylogeny, since PAs of the host plants do have a phylogenetic signal (clades with high and low PA concentrations in leaves) which is reflected in the adult defense.