Farming practices may reshape the structure of watersheds, water quality, and the health of aquatic organisms. Nutrient enrichment from agricultural pollution increases disease pressure in many host–pathogen systems, but the mechanisms underlying this pattern are not always resolved. For example, nutrient enrichment should strongly influence pools of aquatic environmental bacteria, which has the potential to alter microbiome composition of aquatic animals and their vulnerability to disease. However, shifts in the host microbiome have received little attention as a link between nutrient enrichment and diseases of aquatic organisms. We examined nutrient enrichment through the widespread practice of integrated pig–fish farming and its effects on microbiome composition of Brazilian amphibians and prevalence of the globally distributed amphibian skin pathogen Batrachochytrium dendrobatidis (Bd). This farming system drove surges in fecal coliform bacteria, disturbing amphibian skin bacterial communities such that hosts recruited higher proportions of Bd-facilitative bacteria and carried higher Bd prevalence. Our results highlight previously overlooked connections between global trends in land use change, microbiome dysbiosis, and wildlife disease. These interactions may be particularly important for disease management in the tropics, a region with both high biodiversity and continually intensifying anthropogenic pressures on aquatic wildlife habitats.

RESUMOAmbientes naturais ou criados pelo homem abrigam uma diversidade biológica ainda não totalmente conhecida e altamente ameaçada. No presente trabalho, analisamos a artropodofauna edáfica em dois ambientes florestais distintos (bosque de Eucalyptus grandis e uma área de mata nativa), localizados no município de São José do Cedro -SC. As coletas ocorreram no período de maio a dezembro de 2016, caracterizado por um inverno notadamente seco e um verão chuvoso. Utilizou-se um conjunto 30 armadilhas de queda (pitfall-trap), empregadas em três transectos. Foram coletados 8745 indivíduos distribuídos em 18 táxa, destes 3166 indivíduos (36,95%) no bosque de eucalipto (N=15 ordens) e 5579 indivíduos mata nativa (63,05%) (N=19 ordens), sendo que os grupos Hymenoptera, Collembola e Diptera apresentaram as maiores porcentagens de indivíduos coletados, 32,9%, 22,4% e 13,9% respectivamente. A análise de dados obtidos indicou que uma maior diversidade de artrópodes de solo abrigados em remanescentes florestais de Mata Atlântica, e que as monoculturas, tais como as plantações de Eucalyptus spp. influenciaram na diminuição da diversidade da artropodofauna. Palavras-chave:Edáfica; Pitfall-trap; Mata Atlântica; Artrópodes. ABSTRACTNatural or man-made environments harbor a biological diversity not yet fully known and highly threatened biological diversity. In the present work, we analyze the arthropod fauna in two distinct forest environments (Eucalyptus Forest Eucalyptus grandis and an area of native forest), located at São José do Cedro -SC. The collections occurred at the period from May to December 2016. A set of 30 pitfall-traps were used, placed in three transects. A total of 8.745 individuals were collected from 18 taxa, being them, 3.231individuals (36.95%) in the eucalyptus plantation (N = 15 orders) and 5.514 individuals (63.05%) in the native forest (N = 19 orders). Groups Hymenoptera, Collembola and Diptera presented the highest percentages of collected individuals, 32.9%, 22.4% and 13.9% respectively. The results presented show a great diversity of sheltered in forest remnants of the Atlantic Forest soil arthropods, and that the monocultures, such as Eucalyptus spp. influenced in the reduction of the diversity of the arthropodofauna.

Microbial diversity positively influences community resilience of the host microbiome. However, extinction risk factors such as habitat specialization, narrow environmental tolerances, and exposure to anthropogenic disturbance may homogenize host-associated microbial communities critical for stress responses including disease defense. In a dataset containing 43 threatened and 90 non-threatened amphibian species across two biodiversity hotspots (Brazil’s Atlantic Forest and Madagascar), we found that threatened host species carried lower skin bacterial diversity, after accounting for key environmental and host factors. The consistency of our findings across continents suggests the broad scale at which low bacteriome diversity may compromise pathogen defenses in species already burdened with the threat of extinction.

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