Upper mesophotic reef fish assemblages at Bahía de Banderas, Mexico.

There is no information on the species associated with the mesophotic reefs of Banderas Bay, located in the central Mexican Pacific. This study analysed the reef fish assemblage from three depths (50, 60 and 70 m) in three sampling sites of the southern submarine canyon of the Bay: Los Arcos, Bajo de Emirio and Majahuitas. Several analyses were performed to test the hypothesis that there are important differences in fish abundance and species composition between sites and depths. Twenty-two species of bony fishes grouped in 14 families were recorded. PERMANOVA results showed that there were no significant differences in fish diversity parameters between sites, indicating a certain uniformity in their distribution. However, nine species were exclusive to one site and depth (five singleton species with only one individual recorded and four unique species recorded only once). On the other hand, there were significant differences between depths, mainly between 50 and 70 m. Diversity decreases with depth and species composition changes. SIMPER, Shade Plot and NMDS analysis show the most representative species at each depth, with at least half of the species (11) recorded only at 50 m and four species at the deeper levels (60 - 70 m). The observed assemblage includes several of the most caught species in the shallow water artisanal fishery, which is the most traditional and common type of fishery in the Bay. In addition, the Pomacanthuszonipectus (Cortés angelfish) is of particular interest, as it has a special protection status in the official Mexican standard (NOM-059-SEMARNAT, 2010) due to its use as an ornamental species in aquaria. We hypothesised that the mesophotic zone may serve as a refuge for these fishes, so we propose that the information obtained is an important basis for new research aimed at the sustainable management of fisheries in the area.

Taxonomical and functional diversity dynamics of conspicuous echinoderms in the northeastern tropical Pacific over a decade.

Understanding what determines spatio-temporal changes in echinoderm assemblages from an integrative perspective that considers biodiversity, species evenness, and species' niches could permit superior community-scale characterizations of habitat resilience to disturbance. Such an approach was taken herein by tracking a Central Mexican Pacific echinoderm assemblage between 2012 and 2021, and higher richness, diversity, evenness, and functional entity counts were associated with more heterogeneous benthic assemblages. Echinoderm taxonomic composition was influenced by ENSO events, with higher functional diversity found during La Niña events. Conservation strategies should focus on species with unique functional traits to maintain the balance of coral community functionality.

Testing the effectiveness of natural and artificial substrates for coral reef restoration at Isla Isabel National Park, Mexico

Introduction: The branching coral Pocillopora is the main reef-building species in the Eastern Tropical Pacific (ETP) region. However, their populations have been threatened due to the intense effect of thermal-stress events in the last three decades. As a mitigating response, active restoration strategies have been developed. However, it has not been possible to establish specific protocols along the ETP's reefs. Objective: To evaluate the efficiency of two different substrates (natural vs. artificial), through coral growth comparison (extension rate and tissue area) in three Pocillopora coral morphospecies within a year. Methods: Coral growth was estimated by two techniques: extension rate and tissue area of P. cf. verrucosa, P. cf. capitata, and P. cf. damicornis every three months during a year. Results: The extension rate and superficial area growth vary among the coral morphospecies P. cf. verrucosa (16.33 mm yr-1 and 168.49 mm2 yr-1), P. cf. capitata (16.25 mm yr-1 and 176.83 mm2 yr-1), and P. cf. damicornis (12.38 mm yr-1 and 87.62 mm2 yr-1). The data reveals that substrate type did not affect Pocillopora growth, yet there was an effect caused by seasonal changes. Conclusions: This study demonstrates that coral restoration can be implemented using both natural and artificial substrata, with no differences in coral growth. We recommend the implementation of coral reef restoration programs, highlighting the importance of initiate during the warm season due to optimal growth performance of P. cf. verrucosa and P. cf capitata species, which improves the effectiveness of management actions in Isla Isabel National Park.

Introducción: Los corales ramificados del género Pocillopora son los constructores arrecifales más importantes del Pacífico Tropical Oriental (PTO). Sin embargo, sus poblaciones han disminuido por efectos de eventos de estrés térmico ocurridos las últimas décadas. Por ello, se han desarrollado estrategias de restauración activa como respuesta de mitigación, pero no ha sido posible establecer protocolos específicos para estas especies en el PTO. Objetivo: Evaluar la eficiencia de dos tipos de sustrato (natural vs. artificial) con base en la comparación del crecimiento de coral (tasa de extensión y área de tejido) en tres morfoespecies de Pocillopora a lo largo de un año. Métodos: Las estimaciones del crecimiento coralino se hicieron con dos técnicas (extensión lineal y área superficial) en P. cf. verrucosa, P. cf. capitata and P.cf. damicornis cada tres meses durante un año. Resultados: Las tasa de extensión y crecimiento del área superficial variaron entre las morfoespecies de P. cf. verrucosa (16.33 mm año-1 y 168.49 mm2 año-1), P. cf. capitata (16.25 mm año -1 y 176.83 mm2 año-1), y P.cf. damicornis (12.38 mm año-1 y 87.62 mm2 año-1). Los resultados mostraron que los tipos de sustratos no afectaron el crecimiento de los corales Pocillopora, aunque existió un efecto causado por el cambio de la estación climática, donde la estación cálida promueve un incremento su crecimiento. Conclusiones: Este estudio demuestra que la restauración de corales puede ser implementada con sustrato artificial o natural, sin diferencias en el crecimiento de corales entre ellos. Nosotros recomendamos continuar con la implementación de los programas de restauración de arrecifes de coral, resaltando, la importancia de iniciarlos en la estación cálida cuando existe un desempeño más óptimo en el crecimiento, particularmente de las especies P. cf. verrucosa y P. cf. capitata, lo cual ayudará a mejorar la efectividad de las acciones de manejo en el Parque Nacional Isla Isabel.

Palabras clave: Isla Isabel; coral hermatípico; Pacífico Central Mexicano Central; restauración arrecifal.

Metabarcoding of the phytotelmata of Pseudalcantarea grandis (Bromeliaceae) from an arid zone.

BACKGROUND: Pseudalcantarea grandis (Schltdl.) Pinzón & Barfuss is a tank bromeliad that grows on cliffs in the southernmost portion of the Chihuahuan desert. Phytotelmata are water bodies formed by plants that function as micro-ecosystems where bacteria, algae, protists, insects, fungi, and some vertebrates can develop. We hypothesized that the bacterial diversity contained in the phytotelma formed in a bromeliad from an arid zone would differ in sites with and without surrounding vegetation. Our study aimed to characterize the bacterial composition and putative metabolic functions in P. grandis phytotelmata collected in vegetated and non-vegetated sites. METHODS: Water from 10 individuals was sampled. Five individuals had abundant surrounding vegetation, and five had little or no vegetation. We extracted DNA and amplified seven hypervariable regions of the 16S gene (V2, V4, V8, V3-6, 7-9). Metabarcoding sequencing was performed on the Ion Torrent PGM platform. Taxonomic identity was assigned by the binning reads and coverage between hit and query from the reference database of at least 90%. Putative metabolic functions of the bacterial families were assigned mainly using the FAPROTAX database. The dominance patterns in each site were visualized with rank/abundance curves using the number of Operational Taxonomic Units (OTUs) per family. A percentage similarity analysis (SIMPER) was used to estimate dissimilarity between the sites. Relationships among bacterial families (identified by the dominance analysis and SIMPER), sites, and their respective putative functions were analyzed with shade plots. RESULTS: A total of 1.5 million useful bacterial sequences were obtained. Sequences were clustered into OTUs, and taxonomic assignment was conducted using BLAST in the Greengenes databases. Bacterial diversity was 23 phyla, 52 classes, 98 orders, 218 families, and 297 genera. Proteobacteria (37%), Actinobacteria (19%), and Firmicutes (15%) comprised the highest percentage (71%). There was a 68.3% similarity between the two sites at family level, with 149 families shared. Aerobic chemoheterotrophy and fermentation were the main metabolic functions in both sites, followed by ureolysis, nitrate reduction, aromatic compound degradation, and nitrogen fixation. The dominant bacteria shared most of the metabolic functions between sites. Some functions were recorded for one site only and were related to families with the lowest OTUs richness. Bacterial diversity in the P. grandis tanks included dominant phyla and families present at low percentage that could be considered part of a rare biosphere. A rare biosphere can form genetic reservoirs, the local abundance of which depends on external abiotic and biotic factors, while their interactions could favor micro-ecosystem resilience and resistance.

Contrasting Metabolic Fingerprints and Seed Protein Profiles of Cucurbita foetidissima and C. radicans Fruits from Feral Plants Sampled in Central Mexico.

Cucurbita foetidissima and C. radicans are scarcely studied wild pumpkin species that grow in arid and semi-arid areas of Mexico and the United States. This study describes the morphological, proximal composition, metabolic finger-prints and seed protein profiles of C. foetidissima and C. radicans fruits collected in the wild during a one-year period in different locations of central-western Mexico. The results obtained complement the limited information concerning the fruit composition of C. foetidissima and greatly expand information in this respect regarding C. radicans. Morphology and proximal composition of their fruits varied significantly. Different metabolic fingerprints and seed protein profiles were detected between them and also with the chemical composition of domesticated Cucurbita fruits. The neutral lipids in seed, pulp and peels were rich in wax content and in unsaturated compounds, probably carotenoids and tocopherols, in addition to tri-, di- and mono-acylglycerols. The tri- and diacylglycerol profiles of their seed oils were different from commercial seed oils and between each other. They also showed unusual fatty acid compositions. Evidence of a possible alkaloid in the pulp and peel of both species was obtained in addition to several putative cucurbitacins. An abundance of phenolic acids was found in all fruit parts, whereas flavonoids were only detected in the peels. Unlike most cucurbits, globulins were not the main protein fraction in the seeds of C. radicans, whereas the non-structural carbohydrate and raffinose oligosaccharide content in their fruit parts was lower than in other wild cucurbit species. These results emphasize the significantly different chemical composition of these two marginally studied Cucurbita species, which was more discrepant in C. radicans, despite the notion regarding C. foetidissima as an aberrant species with no affinity to any other Cucurbita species.

Species richness and biogeographical affinities of the marine molluscs from Bahía de Chamela, Mexico.

For more than 10 years (2007-2018), the benthic macroinvertebrates of Bahía de Chamela (Mexican Pacific) were sampled at 31 sites (0-25 m depth). A total of 308 species of the five main classes of benthic molluscs were obtained (106 bivalves, 185 gastropods, 13 polyplacophorans, two scaphopods and two cephalopods). This is a significant increase in the number of species (246 new records) compared to the 62 species previously recorded more than 10 years ago. The distribution in the 31 localities of the bay is given for the first time for most of the species, together with information on its ecological rarity (incidence in the samples). Two families of bivalves (Veneridae and Mytilidae) and three families of gastropods (Calyptraeidae, Muricidae and Collumbellidae) comprised ~ 30% of all species. Ecological rarity was evident with 45 families (45.0%) with only one species and 178 species (57.8%) collected in one site and 67 (21.8%) in two sites. The molluscs of Bahía de Chamela represent 12.2% of all species recorded in the Mexican Pacific. Their biogeographic affinities are mostly related to the Tropical Eastern Pacific (TEP) including the oceanic islands and a few are restricted to the Tropical Mexican Pacific (TMP). Some have broader distributions to adjacent northern and southern temperate regions of the American Pacific, one to the western Atlantic, two pantropical (PAN) and two cosmopolitans (COS). The range distribution of each species was reviewed and updated, thus finding that seven species have extended their ranges of geographic distribution.

Gamma-diversity partitioning of gobiid fishes (Teleostei: Gobiidae) ensemble along of Eastern Tropical Pacific: Biological inventory, latitudinal variation and species turnover.

Gobies are the most diverse marine fish family. Here, we analysed the gamma-diversity (γ-diversity) partitioning of gobiid fishes to evaluate the additive and multiplicative components of α and ß-diversity, species replacement and species loss and gain, at four spatial scales: sample units, ecoregions, provinces and realms. The richness of gobies from the realm Eastern Tropical Pacific (ETP) is represented by 87 species. Along latitudinal and longitudinal gradients, we found that the γ-diversity is explained by the ß-diversity at both spatial scales, ecoregions and provinces. At the ecoregion scale, species are diverse in the north (Cortezian ecoregion) and south (Panama Bight ecoregion) and between insular and coastal ecoregions. At the province scale, we found that the species turnover between the warm temperate Northeast Pacific (WTNP), Tropical East Pacific (TEaP) and the Galapagos Islands (Gala) was high, and the species nestedness was low. At the ecoregion scale, historical factors, and phylogenetic factors have influenced the hotspots of gobiid fish biodiversity, particularly in the Cortezian, Panama Bight and Cocos Island ecoregions, where species turnover is high across both latitudinal and longitudinal gradients. At the provincial level, we found that the contributions of the ß-diversity from north to south, in the WTNP, TEaP and Gala were high, as result of the high number of unique species. Species turnover was also high at this scale, with a low contribution from species nestedness that was probably due to the low species/gene flow within the provinces. These results highlight the importance and successful inclusion of a cryptobenthic fish component in ecological and biogeographical studies.

Correction: Coral Reef Health Indices versus the Biological, Ecological and Functional Diversity of Fish and Coral Assemblages in the Caribbean Sea.

[This corrects the article DOI: 10.1371/journal.pone.0161812.].

Coral Reef Health Indices versus the Biological, Ecological and Functional Diversity of Fish and Coral Assemblages in the Caribbean Sea.

This study evaluated the relationship between the indices known as the Reef Health Index (RHI) and two-dimensional Coral Health Index (2D-CHI) and different representative metrics of biological, ecological and functional diversity of fish and corals in 101 reef sites located across seven zones in the western Caribbean Sea. Species richness and average taxonomic distinctness were used to asses biological estimation; while ecological diversity was evaluated with the indices of Shannon diversity and Pielou´s evenness, as well as by taxonomic diversity and distinctness. Functional diversity considered the number of functional groups, the Shannon diversity and the functional Pielou´s evenness. According to the RHI, 57.15% of the zones were classified as presenting a "poor" health grade, while 42.85% were in "critical" grade. Based on the 2D-CHI, 28.5% of the zones were in "degraded" condition and 71.5% were "very degraded". Differences in fish and coral diversity among sites and zones were demonstrated using permutational ANOVAs. Differences between the two health indices (RHI and 2D-CHI) and some indices of biological, ecological and functional diversity of fish and corals were observed; however, only the RHI showed a correlation between the health grades and the species and functional group richness of fish at the scale of sites, and with the species and functional group richness and Shannon diversity of the fish assemblages at the scale of zones. None of the health indices were related to the metrics analyzed for the coral diversity. In general, our study suggests that the estimation of health indices should be complemented with classic community indices, or should at least include diversity indices of fish and corals, in order to improve the accuracy of the estimated health status of coral reefs in the western Caribbean Sea.

Species composition, richness, and distribution of marine bivalve molluscs in Bahía de Mazatlán, México.

We describe the composition and distribution of bivalve molluscs from the sandy and rocky intertidal and the shallow subtidal environments of Bahía de Mazatlán, México. The bivalve fauna of the bay is represented by 89 living species in 28 families, including 37 new records and four range extensions: Lithophaga hastasia, Adula soleniformis, Mactrellona subalata, and Strigilla ervilia. The number of species increases from the upper (44) and lower intertidal (53) to the shallow subtidal (76), but only 11 (17%) have a wide distribution in the bay (i.e., found in all sampling sites and environments). The bivalve assemblages are composed of four main life forms: 27 epifaunal species, 26 infaunal, 16 semi-infaunal, and 20 endolithic. A taxonomic distinctness analysis identified the sampling sites and environments that contribute the most to the taxonomic diversity (species to suborder categories) of the bay. The present work increased significantly (31%) to 132 species previous inventories of bivalves of Bahía de Mazatlán. These species represent 34% of the bivalve diversity of the southern Golfo de California and approximately 15% of the Eastern Tropical Pacific region.

The tourism carrying capacity of underwater trails in Isabel Island National Park, Mexico.

The popularity of ecotourism in the marine protected areas of Mexico has increased over the last 10 years; in particular there is a large development of a SCUBA diving industry in the Mexican Pacific including Isabel Island. Given the risks associated with human activity in the marine environments around this island, we propose two ecotourism management strategies: (1) the creation and use of underwater trails, and (2) the estimation of the specific tourism carrying capacity (TCC) for each trail. Six underwater trails were selected in sites that presented elements of biological, geological, and scenic interest, using information obtained during field observations. The methodology used to estimate the TCC was based upon the physical and biological conditions of each site, the infrastructure and equipment available, and the characteristics of the service providers and the administrators of the park. Correction factors of the TCC included elements of the quality of the visit and the threat and vulnerability of the marine environment of each trail (e.g., divers' expertise, size and distance between groups of divers, accessibility, wind, coral coverage). The TCC values ranged between 1,252 and 1,642 dives/year/trail, with a total of 8,597 dives/year for all six trails. Although these numbers are higher than the actual number of recreational visitors to the island (~1,000 dives per year), there is a need for adequate preventive management if the diving sites are to maintain their esthetic appeal and biological characteristics. Such management might be initially directed toward using only the sites and the TCC proposed here.