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Gut microbiomes play an essential role in host survival and local adaptation and thus can facilitate the invasion of host species. Biological invasions have been shown to be linked to the genetic properties of alien host species. It is thus plausible that the holobiont, the host, and its associated microbiome act as an entity to drive invasion success. The bighead carp and silver carp (bigheaded carps), invasive species that exhibit extensive hybridization in the Mississippi River Basin (MRB), provided a unique model to test the holobiont hypothesis of invasion. Here, we investigated the microbiomes of foreguts and hindguts in bigheaded carps and their reciprocal hybrids reared in aquaculture ponds using 16S amplicons and the associated gene prediction. We found an admixed pattern in the gut microbiome community in bigheaded carp hybrids. The hybrid gut microbiomes showed special characteristics such as relatively high alpha diversity in the foregut, an increasing dissimilarity between foreguts and hindguts, and a remarkable proportion of genes coding for putative enzymes related to their digestion of main food resources (Cyanobacteria, cellulose, and chitin). The pond‐reared hybrids had advantageous features in genes coding for putative enzymes related to their diet. The above results collectively suggested that the gut microbiomes of hybrids could be beneficial to their local adaptation (e.g., food resource utilization), which might have facilitated their invasion in the MRB. The gut microbial findings, along with the intrinsic genomic features likely associated with life‐history traits revealed in our recent study, provide preliminary evidence supporting the holobiont hypothesis of invasion.

Aim: The aim was to evaluate the effects of climate warming on biodiversity across spatial scales (i.e., alpha-, beta- and gamma-diversity) and the effects of patch openness and experimental context on diversity responses. Location: Global. Time period: 1995-2017. Major taxa studied: Fungi, invertebrates, phytoplankton, plants, seaweed, soil microbes and zooplankton. Methods: We compiled data from warming experiments and conducted a meta-analysis to evaluate the effects of warming on different components of diversity (such as species richness and equivalent numbers) at different spatial scales (alpha-, beta- and gamma-diversity, partitioning beta-diversity into species turnover and nestedness components). We also investigated how these effects were modulated by system openness, defined as the possibility of replicates being colonized by new species, and experimental context (duration, mean temperature change and ecosystem type). Results: Experimental warming did not affect local species richness (alpha-diversity) but decreased effective numbers of species by affecting species dominance. Warming increased species spatial turnover (beta-diversity), although no significant changes were detected at the regional scale (gamma-diversity). Site openness and experimental context did not significantly affect our results, despite significant heterogeneity in the effect sizes of alpha- and beta-diversity. Main conclusions: Our meta-analysis shows that the effects of warming on biodiversity are scale dependent. The local and regional inventory diversity remain unaltered, whereas species composition across temperature gradients and the patterns of species dominance change with temperature, creating novel communities that might be harder to predict.

Although we are currently experiencing worldwide biodiversity loss, local species richness does not always decline under anthropogenic pressure. This conservation paradox may also apply in protected areas but has not yet received conclusive evidence in marine ecosystems. Here, we survey fish assemblages in six Mediterranean no-take reserves and their adjacent fishing grounds using environmental DNA (eDNA) while controlling for environmental conditions. We detect less fish species in marine reserves than in nearby fished areas. The paradoxical gradient in species richness is accompanied by a marked change in fish species composition under different managements. This dissimilarity is mainly driven by species that are often overlooked by classical visual surveys but detected with eDNA: cryptobenthic, pelagic, and rare fishes. These results do not negate the importance of reserves in protecting biodiversity but shed new light on how under-represented species groups can positively react to fishing pressure and how conservation efforts can shape regional biodiversity patterns.

This thesis shows how the metals of natural and anthropic origin change significantly the composition of the prokaryotic communities (mainly the composition of bacteria). The β-diversity is the most sensitive variable to the effects of metals, unlike α-diversity, which is hardly affected or even benefited. In scenarios with high and chronic metal pollution, the resident community (DNA fraction) suffers changes in its composition that can be detected at phylum or class taxonomic level. However, in fluvial ecosystems, subjected to lower levels of metal pollution, only the RNA fraction is affected by selecting more active OTUs/ASVs. In addition, the knowledge about the bacterial composition of communities and, consequently, the selection of specific taxa is useful to find some potential prokaryotes functions important in stress response caused by metals Esta tesis muestra cómo los metales de origen natural y antrópico cambian la composición de las comunidades de procariotas, sobre todo de las bacterias. La β-diversidad es la variable más sensible a los efectos de los metales, a diferencia de la α-diversidad, que no se muestra casi afectada o incluso es beneficiada. En escenarios con contaminación alta y crónica de metales, la comunidad residente (fracción de ADN) sufre cambios en su composición que pueden ser detectados a nivel de filo o clase. Sin embargo, en ecosistemas fluviales sometidos a niveles más bajos de contaminación de metales sólo la fracción de ARN se ve afectada selecionando los OTUs/ASVs más activos. El conocimiento de la composición de la comunidad bacteriana y por consiguiente la elección de algunos taxones como bioindicadores, ayuda a encontrar funciones potenciales de las bacterias que podrían ser importantes en las respuestas al estrés causado por metales This thesis has been funded by the Spanish Ministry of Economy and Competitiveness through the STREAMFISH Project (CGL2013-43822-R) and the STRESSFISH Project (CGL2016-80820-R). This research work was also funded by the program of grants for the improvement of the scientific productivity of the research groups of the University of Girona 2016-2018 (MPCUdG2016/120) with the Project: “Fluvial microbial microfilms under conditions of stress”. María Argudo Fernández was supported by FI-DGR pre-doctoral scholarship 2016 FI-B 00284 from the Agency for Management of University and Research Grants (AGAUR) of Government of Catalonia

In this work, we hypothesized that two spore-based methods, direct analysis of field samples and trap cultures, simultaneously used for assessment of occurrence and species richness of arbuscular mycorrhizal fungi (AMF) may vary in their efficiency according to the environmental conditions and the total AMF species richness of the evaluated ecosystem. The performance of both methods was analyzed based on two datasets: 1) a complete site x species matrix compiled from two studies in different land uses in the Amazon using direct analysis of field samples and trap cultures. 2) Total number of AMF morphotypes detected by both methods in published manuscripts across several ecosystems. From dataset 1, direct analysis of field samples revealed 57 morphotypes, whereas only 21 of these were detected by trap culture. Community variation (beta diversity) analysis revealed that field samples are far more sensitive in detecting shifts in AMF community composition among land uses than trap cultures in the Amazon region, with the combined results of both methods being not better than that obtained only by direct analysis of field samples. Analysis of dataset 2 showed that the relative performance of trap cultures, using direct analysis of field sample as reference, was inversely related to the total observed AMF species richness.

Information on temporal dynamics of phytoplankton communities and their responses to environmental factors can provide insights into mechanisms driving succession of phytoplankton communities that is useful in programs to manage and or remediate undesirable assemblages. Populations of phytoplankton can be controlled by bottom-up factors such as nutrients and temperature or top-down such as predation by zooplankton. Traditionally, taxonomic diversity based on morphologies has been the measure used for analysis of responses to environmental factors. Recently, according to functional groupings, including functional groups (FG), morpho-FG (MFG), and morphology-based FG (MBFG), functional diversity has been used to represent functional aspects of phytoplankton communities. However, to what extent these taxonomic and functional groupings are congruent at seasonal time-scales and the main environmental factors, which drive succession, have remained less studied. Here, we analyzed absolute and relative proportions of a phytoplankton community during a 3-year period in Lake Erhai, a eutrophic highland lake in China. Alpha diversity and beta diversity, as measured by Shannon-Wiener and Bray-Curtis indices of taxonomic grouping and three functional groupings (FG, MFG, and MBFG) were applied to investigate environmental factors determining diversity. Significant, positive relationships were observed between taxonomic diversity and functional diversity that were strongly linked through seasons. In order to exclude the influence of dominant species' tolerance to extreme environments, the dominant species were excluded one by one, and the results showed that residual communities still exhibited similar patterns of succession. This synchronous temporal pattern was not principally driven by the dominant genera (Microcystis, Psephonema, and Mougeotia). Instead, the entire phytoplankton community assemblages were important in the pattern. Most diversity indices of taxonomic and functional groupings were significantly correlated with solar irradiance, but not nutrient concentrations. Because the lake is eutrophic and there were already sufficient nutrients available, additional nutrients had little effect on seasonal taxonomic and functional diversity of phytoplankton in Lake Erhai.

The community of microbes in the rhizosphere region is diverse and contributes significantly to plant growth and crop production. Being an important staple and economic crop, the maize rhizosphere microbiota has been studied in the past using culture-dependent techniques. However, these limited culturing methods often do not help in understanding the complex community of microbes in the rhizosphere. Moreover, the vital biogeochemical processes carried out by these organisms are yet to be fully characterized. Herein, shotgun metagenomics, which enables the holistic study of several microbial environments, was employed to examine the community structure and functional potentials of microbes in the maize rhizosphere and to assess the influence of environmental variables on these. The dominant microbial phyla found in the soil environments include Actinobacteria, Microsporidia, Bacteroidetes, Thaumarchaeota, Proteobacteria and Firmicutes. Carbohydrate metabolism, protein metabolism and stress metabolism constitute the major functional categories in the environments. The beta diversity analysis indicated significant differences (p = 0.01) in the community structure and functional categories across the samples. A correlation was seen between the physical and chemical properties of the soil, and the structural and functional diversities. The canonical correspondence analysis carried out showed that phosphorus, N-NO3, potassium and organic matter were the soil properties that best influenced the structural and functional diversities of the soil microbes. It can be inferred from this study that the maize rhizosphere is a hotspot for microorganisms of agricultural and biotechnological importance which can be used as bioinoculants for sustainable agriculture.

The establishment of grazing areas in humid tropical environments is one of the causes of amphibian population decline. This work evaluates the consequences of the establishment of grazing areas on amphibian communities in an area of the Sierra Madre Oriental using analyses of alpha and beta diversity. Sampling was conducted at 28 locations, 7 in tropical evergreen forest (TEF), 7 in mountain cloud forest (MCF), 7 in tropical grazing areas (TGA), and 7 in cloud forest grazing areas (CFGA) using the method of direct sampling. Amphibian diversity is reduced when the grazing areas are established in tropical environments (TGA, 8 species; 7.1 effective species and TEF, 10 species; 7.7 effective species); in contrast, the CFGA has a greater diversity (11 species; 9.3 effective species) compared with MCF (8 species; 3.9 effective species). The most dissimilar composition was found between the 2 communities of undisturbed forests (MCF-TEF; Jaccard dissimilarity 0.78). Establishment of grazing areas in TEF strongly influences the reduction of amphibian populations when compared with MCF.

ResumenOaxaca es el segundo estado con mayor diversidad de mamíferos; sin embargo, las actividades antropogénicas han provocado su reducción. Los trabajos mastozoológicos que evalúen el efecto de la alteración en la Sierra Sur del estado son nulos; por lo que el objetivo fue comparar la diversidad de mamíferos pequeños en 2 sitios con diferente grado de alteración causada por los asentamientos humanos, plantaciones de café y otros cultivos. El trabajo fue realizado mensualmente desde junio de 2009 hasta mayo de 2010. En cada sitio se seleccionó 1ha, donde se describió la vegetación y se registraron los mamíferos pequeños usando redes de niebla, trampas Sherman y observaciones visuales. En el sitio 1, con menor alteración, se capturaron 431 individuos de 21 especies; mientras que en el sitio 2, más alterado, se registraron 190 individuos de 16 especies. La diversidad de árboles y arbustos fue significativamente mayor en el sitio 1 y, aunque las diferencias en la diversidad alfa de mamíferos pequeños (marsupiales-roedores y murciélagos) no fueron significativas entre sitios, la abundancia se redujo para la mayoría de las especies.AbstractOaxaca ranks second in mammal diversity; however, human activities have led to its reduction. Mammalian studies conducted at the Sierra Sur of Oaxaca are scarce; therefore, the objective was to compare small mammal diversity in 2 sites with different degree of disturbance, caused by human settlements, coffee plantations and other crops. The study was conducted monthly from June 2009 to May 2010. At each site, 1hectare was selected, where vegetation and small mammals were recorded using mist nets, Sherman traps, and visual observations. At site 1, less-disturbed, 431 individuals belonging to 21 species were captured; meanwhile at site 2, more-disturbed, 190 individuals belonging to 16 species were recorded. Tree and shrub diversity was significantly greater in site 1. Even differences in alpha diversity for small mammals (marsupials-rodents and bats) were not significant between sites, abundance was reduced for the most species.

Only a few studies comparing flea composition on the coast and in the mountains have been conducted. We investigated differences in flea communities infesting small mammals in selected habitats in northern, central and southern Poland. We predicted: (1) a greater number of flea species in the southeastern Poland and a lower number in the north; (2) a greater number of flea species in fertile and wet habitats than in poor and arid habitats; (3) a low similarity of flea species between flea communities in western and eastern Poland. We found negative effect of increasing latitude on flea species richness. We suppose that the mountains providing a variety of environments and the limits of the geographic ranges of several flea subspecies in southeastern Poland, result in a higher number of flea species. There was positive effect of increasing wetness of habitat on flea species richness. We found a high diversity in flea species composition between western and eastern Poland (beta diversity = 11) and between central and eastern Poland (beta diversity = 12). Re-colonization of Poland by small mammals and their ectoparasites from different (western and eastern) refugies can affect on this high diversity of flea species. grant no. SFRH/BD/ 31602/2006 from the Science and Technology Foundation (Portuguese Ministry of Science, Technology and Higher Education); budget of the Department of Systematic Zoology (Faculty of Biology AMU, Poznań) Parasitology Research

We determined the environmental correlates of vascular plant biodiversity in the Baetic-Rifan region, a plant biodiversity hotspot in the western Mediterranean. A catalog of the whole flora of Andalusia and northern Morocco, the region that includes most of the Baetic-Rifan complex, was compiled using recent comprehensive floristic catalogs. Hierarchical cluster analysis (HCA) and detrended correspondence analysis (DCA) of the different ecoregions of Andalusia and northern Morocco were conducted to determine their floristic affinities. Diversity patterns were studied further by focusing on regional endemic taxa. Endemic and nonendemic alpha diversities were regressed to several environmental variables. Finally, semi-partial regressions on distance matrices were conducted to extract the respective contributions of climatic, altitudinal, lithological, and geographical distance matrices to beta diversity in endemic and nonendemic taxa. We found that West Rifan plant assemblages had more similarities with Andalusian ecoregions than with other nearby northern Morocco ecoregions. The endemic alpha diversity was explained relatively well by the environmental variables related to summer drought and extreme temperature values. Of all the variables, geographical distance contributed by far the most to spatial turnover in species diversity in the Baetic-Rifan hotspot. In the Baetic range, elevation was the most significant driver of nonendemic species beta diversity, while lithology and elevation were the main drivers of endemic beta diversity. Despite the fact that Andalusia and northern Morocco are presently separated by the Atlantic Ocean and the Mediterranean Sea, the Baetic and Rifan mountain ranges have many floristic similarities – especially in their western ranges – due to past migration of species across the Strait of Gibraltar. Climatic variables could be shaping the spatial distribution of endemic species richness throughout the Baetic-Rifan hotspot. Determinants of spatial turnover in biodiversity in the Baetic-Rifan hotspot vary in importance between endemic and nonendemic species.

Esta investigación fue realizada en pinares en Alturas de Pizarra de la Empresa Agroforestal Minas, con el objetivo de determinar la estructura y composición de estos pinares, para el manejo de los mismos. Se seleccionaron dos áreas; en cada área fueron establecidas 30 parcelas circulares de 15 metros de radio; se consideraron tres estratos en la vegetación para cuantificar las especies presentes y hacer los análisis correspondientes. Se calculó la diversidad alfa y beta, se evaluó la estructura horizontal mediante el índice de importancia ecológica y la distribución por clases diamétricas, se describió la estructura vertical a través de la riqueza de especies en cada estrato, así como su posición sociológica. En ambos pinares se identificaron en total 36 familias, 47 géneros y 61 especies de plantas, 42 especies en el área de Pinus caribaea y 36 especies en el área de Pinus tropicalis, observándose diferencias en cuanto a la composición de la vegetación acompañante en sus estratos. Las especies que mayor valor de importancia ecológica alcanzaron en las áreas estudiadas fueron Pinus caribaea con 205.96 y Pinus tropicalis con 175.59, siendo la abundancia y la frecuencia relativas los parámetros que más influyeron. Las parcelas, según la composición de especies, se agruparon en cuatro grupos diferenciándose por la altitud, altura de los árboles, el área basal y la abundancia de árboles muertos presentes en las mismas. Los resultados obtenidos en este estudio, al precisar en algunos de los parámetros de esta formación vegetal en Cuba, constituyen un referente el manejo de estos pinares. This study was conducted in Alturas de Pizarra in the Minas Agroforestry Enterprise, in Cuba, in order to determine its composition and structure of the pine forest vegetation for future management. Two areas were selected: one corresponding to Pinus caribaea and the other to Pinus tropicalis. In each area, 30 circular plots of 15 m radius were established. Three strata were considered in the vegetation in order to quantify the species present and conduct the corresponding analyses. Alpha and beta diversity values were determined, the horizontal structure was evaluated by calculating the index of ecological importance and distribution by diametric classes. The vertical structure was described through the richness of species in each stratum as well as its sociological position. The two pine forests contained 36 families, 47 genera and 61 species of plants, with 42 species in Pinus caribaea area and 36 in the Pinus tropicalis area. Differences were observed in the composition of the accompanying vegetation in their strata. Pinus caribaea attained an importance value of 205.96 and Pinus tropicalis attained 175.59, relative abundance and relative frequency were the parameters that most influenced the index of ecological importance. Plots, according to the composition of species, were divided into groups of four, differing in altitude, tree height, basal area and number of dead trees found in each. By specifying some of the parameters of this vegetation type in Cuba, the results obtained in this study constitute a reference for the management of these pine groves.