Microbiota can both influence or be influenced by social structure and interactions between individual hosts. The use of social network analyses to test for associations between social structure and microbial diversity has only been applied to a few host species. Such an approach could help to disentangle conflicting findings on the effect of social transmission of microbial communities. Here, we explored the following hypotheses: i) that the social network centrality of hosts increases bacterial diversity (alpha diversity), ii) that the strength of social associations between hosts or iii) roosting in the same locations increases microbiota similarity between individuals (beta diversity). For this, we investigated cloaca- and feather-associated microbiotas of wild-caught common waxbills living in a semi-natural environment. We found no evidence for influences of sociality or roosting location on bacterial alpha or beta diversities. We nonetheless detected differences between birds roosting primarily indoors or outdoors at the amplicon sequence variant (for 16S rRNA) and genus levels of feather bacteria, with the birds roosting primarily outdoors having a higher prevalence and abundance of taxa associated with vegetation and the environment, while birds roosting indoors had a higher prevalence and abundance of some bacteria reported as animal-associated. The absence of major effects of host social network on microbiota suggests that environmental effects and individual host idiosyncrasy, perhaps mediated by genetic factors, are more important than within-group sociality driving microbial variation in common waxbills. These results thus call for research on hosts’ genetic diversity and how it may influence their microbiota. The social structure of gregarious animals may influence the similarity and diversity of their microbiota. Social proximity between hosts may lead to more similar microbiota, and centrality in the host social network may contribute to more diverse microbiota. Despite these expectations, we found no effects of social structure on microbial diversity in a flock of wild common waxbills sharing an open-air mesocosm environment. We found indications that roosting outdoors made waxbills more prone to host environment-associated bacteria and roosting indoors to animal-associated bacteria. The absence of major effects of social structure on the microbiome suggests that, even in gregarious species, environmental factors and individual host idiosyncrasies, perhaps genetic-based, can be the most important for understanding microbial variation.

redução, fragmentação e declínio continuado da qualidade do habitat.

Fish microbiome plays an important role in maintaining host homeostasis, with many bacterial functions directly linked to host fitness. Fish microbiome research is advancing fast, especially in the context of aquaculture where several stressors are known to disrupt stability of host‐associated bacteria, prompting dysbiosis. Therefore, understanding the signatures of dysbiosis in different fish mucosae and their association with such stressors is fundamental to set up efficient health‐monitoring strategies, as well as sound and objective working hypothesis for future research. Herein, we reviewed studies that employed culture‐independent approaches to assess the effects of disease, chemotherapeutics and water quality changes on several diversity metrics of gut, skin and gill microbiomes. We conclude that increases in abundance of potential pathogens and changes to bacterial community structure are reliable indicators of dysbiosis in fish. The gut microbiome emerged as being highly susceptible to salinity changes and chemotherapeutics, whereas external microbiota seems to be more susceptible to dysbiosis caused by disease and temperature changes. Our analysis showed that treatments with tetracyclines and florfenicol are more likely to elicit severe dysbiosis compared to quinolones and disinfectants that cause lesser disturbance to fish microbiome. Bacterial diseases also frequently elicit severe dysbiosis (enteritis in particular), whereas parasitic diseases are far less deleterious. Regarding impacts on water quality, only changes to salinity and temperature are reasonably studied. Recent developments in metagenomics, that include a fast turn‐around time of results, can be used to detect changes to fish homeostasis during critical periods of fish production, assisting aquaculture management.

The Neotropical realm is vastly known for its richness, being the Amazon one of the main cradles of taxonomic diversity in the region. In the last decades, molecular analyses have been further increasing the number of Amazonian vertebrate species, hidden under traditional taxonomy due to morphological convergence. Bats represent an interesting example, as the number of recognized bat species is continuously expanding with the identification of numerous cryptic taxa. Studies combining different lines of evidence, such as morphometric and molecular approaches, have been playing an important role in addressing knowledge gaps on Neotropical bat diversity. Within the Phyllostomidae family, the dwarf little fruit bat Rhinophylla pumilio is a forest-dependent species, with a disjunct distribution in the Amazonian and Atlantic forests. Moreover, different karyotypes have been recovered across the species distribution, suggesting this might be one more example of cryptic diversity. Here, we test this assumption by identifying geographic patterns of morphological and molecular variation within the species' entire range of distribution. Our results point to an overall morphological and morphometric homogeneity, except between Atlantic Forest and Amazonian specimens, with significant dissimilarity among some cranial characters. Furthermore, genetic data suggest a rapid and recent diversification, with these two lineages most likely corresponding to speciating taxa. Within the Amazonian forest, our molecular analyses also recovered four additional lineages, likely encompassing intraspecific diversity. Furthermore, studies are required to confirm the need for a taxonomic rearrangement.

Lymphocystis viral disease (LVD) is a highly transmissible disease known to affect multiple fishes worldwide. Although this disease is usually benign, mortalities can occur in cases where infection is severe or secondary infection with bacterial pathogens and parasites occur. However, little is known about the bacterial dynamics of fish with LVD or what bacterial pathogens may be responsible for secondary infections. Here we assessed the effects of LVD on the skin microbiome of gilthead seabream by comparing 30 symptomatic, asymptomatic and recovered (three weeks after infection) fish using 16S rRNA high-throughput sequencing. Our results show that LVD is associated with significant changes in microbiome structure and function. Importantly, fish pathogens like Tenacibaculum maritimum and some Vibrio species increased their abundance. Moreover, microbial metabolic activities of the commensal microbiota that may confer some protection to fish were suppressed in diseased fish. After reducing fish cage density to treat symptoms and three weeks of recovery, the abundance of pathogens was significantly reduced and microbiome functionality was recovered, although community structure remained significantly different. These results show that LVD can severely disrupt the bacterial communities of the skin of the gilthead seabream, leading to an increase in bacterial pathogens responsible for relevant diseases in gilthead seabream farms.

incêndios, que podem afetar toda a população de uma só vez.Portanto,

Microbial diversity may affect host phenotypes, including morphology and behaviour, but it remains unclear to which extent those could be mediated by host differences in diet or habitat use. We used a population of wild common waxbills living in a large open-air mesocosm to control for such differences and test whether phenotypic variation is associated with cloaca bacteria diversity. We also tested correlations between feather-associated bacteria diversity and plumage colour ornamentation. Albeit weakly correlated, individuals sharing more similar cloaca microbiotas were more similar in their carotenoid-based plumage and bill red colour, suggesting that the gut microbiota can influence ornamentation even when individuals are in the same habitat and have access to the same food resources, perhaps mediating individual differences in feeding or digestion. There were no associations between feather bacteria and plumage colour, nor between cloaca bacteria and body size or several behavioural phenotypes. These results further highlight that investigating associations between microbiota and behaviour in nature should account for variation in extrinsic factors.

Climate change affects ecosystems in different ways. These effects are particularly worrying in the Neotropical region, where species are most vulnerable to these changes because they live closer to their thermal safety limits. Thus, establishing conservation priorities, particularly for the definition of protected areas (PAs), is a priority. However, some PA systems within the Neotropics are ineffective even under the present environmental conditions. Here, we test the effectiveness of a PA system, within an ecotone in northern Brazil, in protecting 24 endangered bird species under current and future (RCP8.5) climatic scenarios. We used species distribution modeling and dispersal corridor modeling to describe the priority areas for conservation of these species. Our results indicate that several threatened bird taxa are and will potentially be protected (i.e., occur within PAs). Nonetheless, the amount of protected area is insufficient to maintain the species in the ecotone. Moreover, most taxa will probably present drastic declines in their range sizes; some are even predicted to go globally extinct soon. Thus, we highlight the location of a potentially effective system of dispersal corridors that connects PAs in the ecotone. We reinforce the need to implement public policies and raise public awareness to maintain PAs and mitigate anthropogenic effects within them, corridors, and adjacent areas, aiming to conserve the richness and diversity of these already threatened species.

Coendou prehensilis é endêmica do Brasil, ocorrendo na Mata Atlântica dos estados de Alagoas, Paraíba e Pernambuco.A espécie é florestal e apresenta extensão de ocorrência (EOO) de 21.142 km2.A área de distribuição da espécie é afetada principalmente pelas atividades agrícolas (cana de açúcar) e expansão urbana, que promovem redução, fragmentação e declínio continuado da qualidade do habitat remanescente.É encontrado em fragmentos urbanos degradados.Porém, no centro de endemismo de Pernambuco, a porcentagem de remanescentes florestais é menor que 10%.Considerando a baixa capacidade de dispersão e a fidelidade a ambientes florestais, suspeita-se que a fragmentação do habitat se reflita em fragmentação severa da população.Por se aproximar de Vulnerável (VU) pelo critério B1ab(iii), Coendou prehensilis foi categorizada como Quase Ameaçada (NT).

uma extensão de ocorrência (EOO) de apenas 9.127 km².Os ambientes naturais onde a espécie ocorre sofreram redução e fragmentação históricas, promovidas, sobretudo, pela expansão da pecuária e urbanização.Essas atividades também promovem declínio continuado da qualidade do habitat.Portanto, por se aproximar de Vulnerável (VU) pelo critério B1b(iii), Sylvilagus tapetillus foi categorizada como Quase Ameaçada (NT).

The South American Tern Sterna hirundinacea is a poorly known migratory seabird distributed along South American marine coasts, including the Falkland Islands (Malvinas). The species presents allochronic isolation (i.e., separation of populations by breeding time), with different populations occupying different environmental spaces during the reproductive periods. Additionally, southern populations appear to undertake long-distance directional migration, but there is limited knowledge of the migratory behaviour of northern populations. In spite of these temporal and spatial segregative behaviour, limited population structure has been inferred from genetic assessments, although only a few localities have been investigated. Morphological variation is also poorly known. Whether intrinsic, environmental, or anthropogenic factors are causing isolation and differentiation between populations is unknown. Here, we first characterize sexual morphological dimorphism in the South American Tern, and then evaluate morphological variation along the species range, using only measurements that did not respond to sexual dimorphism and with a representative number of specimens. We also evaluate genetic variation along the South American Tern distribution to test for population differentiation and estimate the demographic history and diversification time for the species. Overall, we found limited population structure in both morphological and genetic data, but with some differentiation in measurements assessed for specimens from the Southeastern Pacific. A trend for demographic stability after a population expansion was estimated for the species. The connectivity among species' colonies, followed by its likely non-philopatric behaviour, seems to maintain gene flow between South American Tern populations. However, genetic differentiation might still be undetected, given the estimated recent origin and demographic expansion for the species. Although the South American Tern is not considered globally threatened, it is regionally threatened, and conservation implications of our findings are considered.

Abstract The activity of the microbiome of fish mucosae provides functions related to immune response, digestion, or metabolism. Several biotic and abiotic factors help maintaining microbial homeostasis, with disruptions leading to dysbiosis. Diseases and antibiotic administration are known to cause dysbiosis in farmed fish. Pathogen infections greatly affect the production of gilthead seabream, and antibiotic treatment is still frequently required. Here, we employed a 16S rRNA high-throughput metataxonomics approach to characterize changes in the gut, skin, and gill microbiomes occurring due to infection with Photobacterium damselae subsp. piscicida and subsequent antibiotic treatment with oxytetracycline (OTC), as well as during recovery. Although microbiota response differed between studied tissues, overall changes in composition, diversity, structure, and predicted function were observed in all mucosae. The skin and gill microbiomes of diseased fish became largely dominated by taxa that have been frequently linked to secondary infections, whereas in the gut the genus Vibrio, known to include pathogenic bacteria, increased with OTC treatment. The study highlights the negative impacts of disease and antibiotic treatment on the microbiome of farmed fish. Our results also suggest that fish transportation operations may have profound effects on the fish microbiome, but further studies are needed to accurately evaluate their impact.

Host‐associated microbial communities are essential for host homeostasis and health. Most research on microbiotas is restricted to model host species and, since microbe–host dynamics can be species‐specific, we still lack a good taxonomic, ecological and evolutionary understanding of microbiotas in wild hosts, including birds. Given the diversity of avian host species, their habitat specializations, ecological requirements and life‐history traits, we need to characterize the dynamics of microbiotas from taxonomically diverse bird species. Here we describe cloaca and feather microbiotas of a population of common waxbills Estrilda astrild living in a large open‐air mesocosm, and compare it to microbiotas sampled one year later for a subset of this population, and to the microbiotas of free‐ranging waxbills from the same region. We found clear differences between microbiota from the cloaca, which contained some taxa that may be found in seeds, and from feathers, which contained some taxa that have been previously found in plants and soil. We found limited evidence for sexual differences in both cloaca and feather microbiotas, likely due to the gregariousness, similar behaviour and habitat use of both male and female waxbills. Microbial diversities of waxbills from the mesocosm were representative of those found in free‐ranging individuals. Also, structural differences between microbiota from mesocosm and free‐ranging waxbills seemed to be small and comparable to differences found in microbiota from the mesocosm in consecutive years. These results indicate that this mesocosm population could be used as a model in future studies investigating microbiota–host dynamics.

Defining a species' ecological niche is not a trivial task particularly for marine taxa, since physical and biological constraints are not easily perceived in these environments. Yet, coastal habitats are divided into provinces, influenced by different environmental conditions, such as superficial marine currents, causing seasonality in marine productivity and biomass. The South American Tern Sterna hirundinacea is a poorly known, migratory seabird distributed along the Pacific and Atlantic coasts of South America, including the Malvinas/Falkland Islands, and occurring in most of the South American coastal provinces. Limited knowledge on the migratory behaviour of the species points to differential habits between southern and northern populations. The species' breeding season also varies with latitude and season, occurring during spring in the south and in the fall in northern areas of the species occurrence. These observations point to putatively ecologically distinct populations along the species range that seem to be coincident with coastal provinces. To test our hypotheses, we estimated full-range ecological niche models per season, and we used coastal provinces to model ecological niches for each of the known breeding areas/seasons. We also tested for environmental space differentiation between seasons and breeding and non-breeding areas. Overall, the species does not seem to occupy significantly different ecological niches throughout the year, except during the breeding season, particularly between the Warm Temperate Southeastern Pacific and Warm Temperate Southwestern Atlantic provinces in fall. This suggests that the South American Tern migratory behaviour, the selection of different microhabitats and reproductive areas or distinct biological interactors might be influencing the species environmental space. Nonetheless, our models reinforce the gradual migration of this tern species towards the south, spending the summer mostly in the Malvinas/Falkland Islands. Interestingly, the species seems to be resident in Peru coastal area. Thus, despite the absence of ecological divergence, population structure should be tested and demographic trends assessed along the species range.