Mammals in São Paulo State: diversity, distribution, ecology, and conservation / Mamíferos do Estado de São Paulo: diversidade, distribuição, ecologia e conservação

Abstract Mammals are charismatic organisms that play a fundamental role in ecological functions and ecosystem services, such as pollination, seed dispersal, nutrient cycling, and pest control. The state of São Paulo represents only 3% of the Brazilian territory but holds 33% of its mammalian diversity. Most of its territory is dominated by agriculture, pastures, and urban areas which directly affect the diversity and persistence of mammals in the landscape. In addition, São Paulo has the largest port in Latin America and the largest offshore oil reservoir in Brazil, with a 600 km stretch of coastline with several marine mammal species. These human-made infrastructures affect the diversity, distribution, ecology, and the future of mammals in the state. Here, we answer five main questions: 1) What is the diversity of wild mammals in São Paulo state? 2) Where are they? 3) What is their positive and negative impact on human well-being? 4) How do mammals thrive in human-modified landscapes? 5) What is the future of mammals in the state? The state of São Paulo holds 255 species of native mammals, with four endemic species, two of them globally endangered. At least six species (two marsupials, Giant otter, Pampas deer, Brazilian dwarf brocket deer, and Giant armadillo) were extirpated from the state due to hunting and habitat loss. The intense human land use in the state forced many mammalian species to change their diet to cope with the intense fragmentation and agriculture. Large-scale monoculture has facilitated the invasion of exotic species such as wild boars (javali) and the European hare. Several "savanna-dwelling" species are expanding their ranges (Maned wolf, Brocket deer) over deforested areas and probably reflect changes towards a drier climate. Because the state has the largest road system, about 40,000 mammals from 33 species are killed per year in collisions causing an economic loss of 12 million dollars/year. The diversity of mammals is concentrated in the largest forest remnants of Serra do Mar and in the interior of the State, mainly in the regions of Ribeirão Preto and Jundiaí. Sampling gaps are concentrated throughout the interior of the state, particularly in the northwest region. Wild mammals play a fundamental role in many ecosystem services, but they can also be a concern in bringing new emergent diseases to humans. Although the taxonomy of mammals seems to be well known, we show that new species are continuously being discovered in the state. Therefore, continuous surveys using traditional and new technologies (eDNA, iDNA, drones), long-term population monitoring, investigation of the interface of human-wildlife conflict, and understanding of the unique ecosystem role played by mammals are future avenues for promoting sustainable green landscapes allied to human well-being in the state. The planting of forest or savanna corridors, particularly along with major river systems, in the plateau, controlling illegal hunting in the coastal areas, managing fire regimes in the Cerrado, and mitigating roadkill must be prioritized to protect this outstanding mammal diversity.

Resumo Os mamíferos são organismos carismáticos que desempenham um papel fundamental na função ecológica e nos serviços ecossistêmicos, como polinização, dispersão de sementes, ciclagem de nutrientes e controle de pragas. O Estado de São Paulo representa apenas 3% do território brasileiro, mas detém 33% da diversidade de mamíferos. A maior parte de seu território é dominado pela agricultura, pastagens e áreas urbanas que afetam diretamente a diversidade e a persistência dos mamíferos na paisagem. Além disso, São Paulo possui o maior porto da América Latina e o maior reservatório de petróleo costeiro do Brasil, com 600 km de extensão de litoral com diversas espécies de mamíferos marinhos. Essas infraestruturas afetam a diversidade, distribuição, ecologia e o futuro dos mamíferos no estado. Aqui, respondemos cinco perguntas principais: 1) Qual é a diversidade de mamíferos silvestres no Estado de São Paulo? 2) Onde eles ocorrem? 3) Qual é o seu impacto positivo e negativo no bem-estar humano? 4) Como os mamíferos persistem em paisagens modificadas pelo homem? 5) Qual é o futuro dos mamíferos no estado? O estado de São Paulo possui 255 espécies de mamíferos nativos, com quatro espécies endêmicas, duas delas globalmente ameaçadas de extinção. Pelo menos seis espécies (dois marsupiais, ariranha, veado-campeiro, veado-cambuta e tatu-canastra) foram extirpadas do estado devido à caça e perda de habitat. O intenso uso humano da terra no estado forçou muitas espécies de mamíferos a mudar sua dieta para lidar com a intensa fragmentação e agricultura. A monocultura em larga escala facilitou a invasão de espécies exóticas, como porcos selvagens (javaporco) e a lebre europeia. Várias espécies de áreas abertas estão expandindo suas áreas de distribuição (lobo-guará, veado-catingueiro) sobre áreas desmatadas e provavelmente refletem mudanças em direção a um clima mais seco. Como o estado possui o maior sistema rodoviário do Brasil, cerca de 40 mil mamíferos de 33 espécies são mortos por ano em colisões, causando um prejuízo econômico de 12 milhões de dólares/ano. A diversidade de mamíferos está concentrada nos maiores remanescentes florestais da Serra do Mar e no interior do Estado, principalmente nas regiões de Ribeirão Preto e Jundiaí. As lacunas amostrais estão concentradas em todo o interior do estado, principalmente na região noroeste. Os mamíferos silvestres desempenham um papel fundamental em muitos serviços ecossistêmicos, mas também podem ser uma preocupação em trazer novas doenças emergentes para as populações humanas. Embora a taxonomia de mamíferos pareça ser bem conhecida, mostramos que novas espécies estão sendo continuamente descobertas no estado. Portanto, pesquisas usando tecnologias tradicionais e novas (eDNA, iDNA, drones), monitoramento populacional de longo prazo, a investigação da interface do conflito homem-vida selvagem e a compreensão do papel único no ecossistema desempenhado pelos mamíferos são um caminho futuro para promover uma paisagem verde sustentável aliada ao bem-estar humano no estado. O plantio de corredores florestais ou de cerrado, principalmente junto aos principais sistemas fluviais, no planalto, o controle da caça ilegal nas áreas costeiras, o manejo dos regimes de fogo no Cerrado e a mitigação dos atropelamentos devem ser uma prioridade para proteger essa notável diversidade de mamíferos.

I See Golden Mussel! They are Everywhere! Environmental DNA Supports Widespread Dissemination of Limnoperna fortunei in Hydrographic Basins in the Paraná State, Brazil

Abstract The golden mussel is an aquatic invasive species that was introduced in South America in the '90s, including Brazil, and was firstly registered in 2001 in the Paraná state. This bivalve causes macrofouling issues because adhere in substrates and form dense aggregations, affecting especially hydroelectric power plants, and water treatment facilities, apart from the native biodiversity. The present research aimed to diagnose the distribution of Limnoperna fortunei in the Paraná state using environmental DNA (eDNA) from 174 sites from 12 basins, and scientific and technical previous records. L. fortunei eDNA was found in 90 sites from 11 hydrographic basins sampled. Most of the positive samples were detected in Iguaçu (42), Tibagi (15), and Ivaí (10) rivers basins. We also registered the first occurrence for five basins: Cinzas, Itararé, Ivaí, Pirapó e Ribeira rivers. Together, our and previous data recorded L. fortunei in 118 sites, between adult, larvae, and eDNA detection. Moreover, the results evidenced that eDNA is a low coast and reliable tool, and it may be very recommended for L. fortunei early detection and diagnosis. The present research was the greatest and most widespread survey for golden mussel prospection in a state in Brazil, supported a worrying scenario for Parana, with the urgent need for intense and continuous monitoring and prevention actions for controlling and mitigation of the L. fortunei impacts.

Development of a real-time PCR assay for the detection of the golden mussel ( Limnoperna fortunei, Mytilidae) in environmental samples

ABSTRACT The golden mussel, Limnoperna fortunei, is among the most devastating invasive species in freshwater habitats worldwide, leading to severe environmental disturbances and economic losses. Therefore, management efforts would be greatly improved by methods that efficiently detect and quantify the abundance of the golden mussel in freshwater habitats, particularly in early stages of colonization. In this study, we describe a highly-sensitive real-time PCR assay targeting a 100-bp region of the COI mitochondrial gene of the golden mussel. The method was able to detect as little as 0.225 pg of target DNA. This assay represents an important contribution to surveillance methods, as well as to optimize field measures to contain and manage populations of the golden mussel in its introduced range.

History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments / Historia, aplicaciones, aspectos metodológicos y perspectivas para el uso del ADN ambiental (ADNa) en ecosistemas marinos y de agua dulce

Genetic material (short DNA fragments) left behind by species in nonliving components of the environment (e.g. soil, sediment, or water) is defined as environmental DNA (eDNA). This DNA has been previously described as particulate DNA and has been used to detect and describe microbial communities in marine sediments since the mid-1980’s and phytoplankton communities in the water column since the early-1990’s. More recently, eDNA has been used to monitor invasive or endangered vertebrate and invertebrate species. While there is a steady increase in the applicability of eDNA as a monitoring tool, a variety of eDNA applications are emerging in fields such as forensics, population and community ecology, and taxonomy. This review provides scientist an understanding of the methods underlying eDNA detection as well as applications, key methodological considerations, and emerging areas of interest for its use in ecology and conservation of freshwater and marine environments. Rev. Biol. Trop. 62 (4): 1273-1284. Epub 2014 December 01.

El material genético que liberan los organismos en los componentes no vivos del ecosistema (aire, suelo, agua y sedimentos) recibe el nombre de ADN ambiental (ADNa) (eDNA, por su nombre en inglés). Este ADN previamente definido como ADN particulado ha sido utilizado desde mediados de la década de los ochenta y principios de los noventas para describir la composición de las comunidades microbianas en sedimentos marinos y de comunidades microbianas y fitoplanctónicas en la columna de agua. Recientemente el ADNa es utilizado principalmente para la detección y monitoreo de especies invasoras y en peligro. No obstante, existen múltiples áreas en las que este método puede ser utilizado como por ejemplo en ciencias forenses, ecología de poblaciones y comunidades, y taxonomía. Esta revisión proporciona información sobre esta nueva herramienta molecular, sus actuales y futuras aplicaciones, historia, principales consideraciones metodológicas y áreas emergentes para su uso en ecología y conservación de ambientes marinos y de agua dulce.

Influence of different extracellular DNA levels in Staphylococccus epidermidis isolates on the ability of biofilm formation / 中华微生物学和免疫学杂志

ObjectiveTo determine the ability of biofilm formation of Staphylococcus epidermidis isolates and study the influence of different extracellular DNA(eDNA) levels in S.epidermidis isolates on the ability of biofilm formation.MethodsDetect the biofilm-formation ability of 227 S.epidermidis isolates with adhesion assays,amplify the icaA gene fragment with PCR.The S.epidermidis isolates were divided into biofilm formation(BF) group and non-biofilm formation (NBF) group according to adhesion assays and icaA amplification.Detect eDNA levels of S.epidermidis in planktonic culture and microtitre plate static culture.The eDNA in S.epidermidis biofilms stained by AO-PI was observed by CLSM.Results26 isolates were positive in adhesion assays and 32 isolates existed icaA gene among 227 S.epidermidis isolates.Select 20 isolates with positive adhesion assays and positive icaA amplification for BF group.Select 19 isolates with negative adhesion assays and negative icaA amplification for NBF group.The eDNA levels were (32.2±10.1)μg/ml,(33.6±11.9) μg/ml,(34.3±10.0) μg/ml in BF group when cultured in planktonic condition for 2,4,6 h,while the eDNA levels in NBF group were (28.7±8.9) μg/ml,(31.5±11.7) μg/ml,(31.8±12.7) μg/ml respectively.There were no significant differences between the two groups for these three phases(P＞0.05),though the eDNA levels of BF group were higher than that of NBF group.The eDNA levels were (740.0±264.4) ng/A600 in BF group when cultured in static microtitre plate,higher than that of NBF group,(80.1 ±31.1) ng/A600,and the difference between these two groups was significant.The eDNA in BF isolate Y36 biofilms could be visualized by staining with AO and PI when observed by CLSM,while neither biofilm structure nor eDNA appeard when NBF isolate Y26 was cultured for 24 h.ConclusionS.epidermidis isolates have the ability of biofilm formation.eDNA is one of the important matrix components in the S.epidermidis biofilm-forming process.The eDNA of static culture in microtitre plate was more efficient than planktonic culture in the case of estimating the ability of biofilm formation of S.epidermidis.