Abundance and Distribution of Enteric Bacteria and Viruses in Coastal and Estuarine Sediments—a Review

The long term survival of fecal indicator organisms (FIOs) and human pathogenic microorganisms in sediments is important from a water quality, human health and ecological perspective. Typically, both bacteria and viruses strongly associate with particulate matter present in freshwater, estuarine and marine environments. This association tends to be stronger in finer textured sediments and is strongly influenced by the type and quantity of clay minerals and organic matter present. Binding to particle surfaces promotes the persistence of bacteria in the environment by offering physical and chemical protection from biotic and abiotic stresses. How bacterial and viral viability and pathogenicity is influenced by surface attachment requires further study. Typically, long-term association with surfaces including sediments induces bacteria to enter a viable-but-non-culturable (VBNC) state. Inherent methodological challenges of quantifying VBNC bacteria may lead to the frequent under-reporting of their abundance in sediments. The implications of this in a quantitative risk assessment context remain unclear. Similarly, sediments can harbor significant amounts of enteric viruses, however, the factors regulating their persistence remains poorly understood. Quantification of viruses in sediment remains problematic due to our poor ability to recover intact viral particles from sediment surfaces (typically <10%), our inability to distinguish between infective and damaged (non-infective) viral particles, aggregation of viral particles, and inhibition during qPCR. This suggests that the true viral titre in sediments may be being vastly underestimated. In turn, this is limiting our ability to understand the fate and transport of viruses in sediments. Model systems (e.g., human cell culture) are also lacking for some key viruses, preventing our ability to evaluate the infectivity of viruses recovered from sediments (e.g., norovirus). The release of particle-bound bacteria and viruses into the water column during sediment resuspension also represents a risk to water quality. In conclusion, our poor process level understanding of viral/bacterial-sediment interactions combined with methodological challenges is limiting the accurate source apportionment and quantitative microbial risk assessment for pathogenic organisms associated with sediments in aquatic environments

Diversidade de Bacteria e Archaea do solo do Cariri paraibano e prospecção de celulases e xilanases em clones metagenômicos e isolados bacterianos

Soil samples of native pasture (site A) and of soil cultivated with grass Paspalum conjugatum, Bergius (site B) collected from Caatinga vegetation in the semi-arid region in Paraíba state (07°23‟27 S 36°31‟58 W) were utilized for constructing four metagenomic libraries, aiming the evaluation of microbial diversity through amplification of gene 16S rRNA of domains Bacteria and Archaea. The metagenomic DNAs were extracted by utilizing FastDNA® SPIN Kit for Soil (BIO 101), which were amplified by PCR, by using universal primers 27F / 1525R (Bacteria) and 20F / 958R (Archaea). The purified fragments were linked to vector pGEM Teasy and transformed by thermal shock in chemically competent Escherichia coli DH10B. Transformants were cultivated in LB/Ampicillin medium (100 μM/ml), IPTG (800 μg/mL) and XGal (80 μg/mL) at 37ºC/18-20 h. A selection of 250 clones of each library was performed, sequenced and after discarding the low quality sequences and chimerics, 64 and 68 sequences were obtained (Bacteria) and 89 and 141 sequences (Archaea) from soils of sites A and B, respectively, which were compared to public bank of data RDB and NCBI (similarity >95%). In site A the phylum Acidobacteria (48.4%) was the most abundant, followed by phyla Bacteroidetes (10.9%), Proteobacteria (10.9%), and Firmicutes (6.3%). In site B Proteobacteria (45.6%) was the most abundant, followed by Firmicutes (10.3%), Acidobacteria (8.8%), Bacterioidetes (7.3%); and also Cyanobacteria (1.5%) and Planctomycetes (1.5%) which were not found in site A. Among the sequences obtained, 23.4% (site A) and 25.0% (site B) were not classified (similarity <95%). In the domain Archaea the phyla found were Euryarchaeota (3.4 and 45.4%) and Crenarchaeota (2.2 and 3.5%), in sites A and B, respectively; it should be observed that 94.4% and 51.1% of the sequences were not classified (similarity <95%), between sites A and B, respectively. Larger diversity (Shannon‟s índex), richness (Chao 1), and distribution (equity index) of communities were observed at species level, in the phyla Bacteria and Archaea, in both sites. The metagenomic libraries 16S rRNA of Bacteria and Archaea, when compared by using the LIBSHUFF program, differed significantly (p<0.0001). The results of the present study showed the occurrence of a great diversity of bacteria and archaea in that semi-arid environment, with peculiar features of elevated temperature and hydric limitations, emphasizing the possibility of investigations on search of new genes and/or microbial isolates with biotechnological potential.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPESAmostras do solo da pastagem nativa (sítio A) e sob cultivo do capim marrequinho (Paspalum conjugatum, Bergius) (sítio B), coletadas na região semi-árida do bioma Caatinga, Paraíba, (07°23‟27 S 36°31‟58 O), foram utilizadas para construção de quatro bibliotecas de clones metagenômicos, para avaliação da diversidade microbiana pela amplificação do gene 16S rRNA dos domínios Bacteria e Archaea. Os DNA metagenômicos foram extraídos utilizando FastDNA® SPIN Kit for Soil (BIO 101), os quais foram amplificados por PCR utilizando primers universais, 27F / 1525R (Bacteria) e 20F / 958R (Archaea). Os fragmentos purificados foram ligados ao vetor pGEM Teasy e transformados por choque térmico em Escherichia coli DH10B quimicamente competente. Os transformantes foram cultivados em meio Agar LB/Ampicilina (100 μ/mL), IPTG (800 μg/μL) e XGal (80 μg/μL), a 37ºC/18-20 h. Foram selecionados 250 clones de cada biblioteca os quais foram sequenciados e após descarte das sequências de baixa qualidade e quiméricas, foram obtidas 64 e 68, 89 e 141 sequências para Bacteria e Archaea, nos solos dos sítios A e B, respectivamente, as quais foram comparadas em banco de dados públicos RDB e NCBI (≥95% de similaridade). No sítio A o filo Acidobacteria (48,4%) foi o mais abundante, seguido dos filos Bacteroidetes (10,9%), Proteobacteria (10,9%), e Firmicutes (6,3%). No sítio B Proteobacteria (45,6%) foi o de maior destaque, seguido de Firmicutes (10,3%), Acidobacteria (8,8%), Bacterioidetes (7,3%); e ainda Cyanobacteria (1,5%) e Planctomycetes (1,5%), que não foram encontrados no sítio A. Entre as sequências geradas, 23,4% (sítio A) e 25,0% (sítio B) não foram classificadas (similaridade <95%). No domínio Archaea foram encontrados os filos Euryarchaeota (3,4 e 45,4%) e Crenarchaeota (2,2 e 3,5%), nos sítios A e B, respectivamente; destacando-se que 94,4% e 51,1% das sequências não foram classificadas (similaridade <95%), entre os sítios A e B, respectivamente. Uma maior diversidade (índice de Shannon), riqueza (índice Chao 1) e distribuição (índice de equidade) das comunidades foram observadas no nível de espécies, tanto para Bacteria como para Archaea, nos dois sítios. As bibliotecas de clones metagenômicos 16S rRNA de Bacteria e Archaea, quando comparadas, utilizando-se o programa LIBSHUFF, diferiram significativamente (p<0,0001). Os resultados desse estudo mostraram a ocorrência de uma grande diversidade de bactérias e arqueas, nesse tipo de ambiente pouco estudado e com características peculiares de temperatura elevada e limitações hídricas, com possibilidade de busca de novos genes e/ou isolados microbianos, com potencial biotecnológico

The abundance of some pathogenic bacteria in mangrove habitats of Paraiba do Norte estuary and crabmeat contamination of mangrove crab Ucides cordatus

Study on mangrove water and sediment of Paraiba do Norte river (Northeastern Brazil) and crabmeat of Ucides cordatus was carried to investigate the relation between the abundance of bacteria in the mangrove habitat and in the crabmeat. Simultaneous collection of samples of water, sediment and crabs (U. cordatus) was done during the rainy and dry seasons at two areas of mangroves that differed in influence of tide and sewage discharge. The numbers of total heterotrophic bacteria in the mangrove water were between 0.04 and 6 log CFU 100mL-1, and in the sediment between 5 and 6 log CFU g-1. The location closer to waste discharge showed higher incidence of total heterotrophic bacteria, coliforms, Staphylococcus aureus and Salmonella spp. The counts of total heterotrophic bacteria in the crabmeat varied from 1.3 to 4.4 log CFU g-1, and did not differ significantly between the locations analysed. No crabmeat sample showed the presence of coliforms, S. aureus and Salmonella spp.O estudo sobre água e sedimento do mangue do rio Paraíba do Norte (Nordeste do Brasil) e carne de caranguejo-uçá (Ucides cordatus) foi conduzido para investigar a relação entre a abundância de bactérias heterotróficas totais e patogênicas no ambiente e na carne de caranguejo. As amostras de água, sedimento e caranguejos U. cordatus foram coletadas simultaneamente em duas áreas do manguezal que diferiam em influencia da maré e do esgoto lançado no mangue. O número de bactérias heterotróficas totais nas amostras de água do mangue variaram de 0,04 a 6 log UFC 100mL-1, e no sedimento de 5 a 6 log UFC g-1. Em local mais próximo a desembocadura do esgoto evidenciou-se maior incidência de bactérias heterotróficas totais, coliformes, Staphylococcus aureus e Salmonella spp. As contagens de bactérias totais nas amostras da carne de caranguejo variaram de 1,3 a 4,4 log UFC g-1, não diferindo estatisticamente entre as áreas estudadas. Nenhuma amostra da carne de caranguejo apresentou coliformes, S. aureus e Salmonella spp

Situação epidemiológica da tuberculose bovina no Estado de Pernambuco, Brasil

The epidemiological situation of bovine tuberculosis was studied in the state of Pernambuco, Brazil. The state was divided into three regions, and a predetermined number of properties was randomly sampled in each region. In each property, females aged 24 months or older were randomly selected and subjected to the cervical comparative tuberculin test. Altogether, 5,728 animals from 906 properties were tested. In the evaluated properties, an epidemiological questionnaire was applied to identify risk factors related to bovine tuberculosis. The prevalence of infected herds and infected animals and in the state was 2.87% [1.82–4.50] and 0.62% [0.29–1.29], respectively. There was a predominance trend of infected herds in the properties located in the dry areas of Pernambuco, where most dairy properties are found. The risk factors related to the occurrence of positive herds were: presence of 18 or more cows in the herd, milking the cows two or three times a day, and sharing the grazing area. In conclusion, the prevalence of bovine tuberculosis in Pernambuco is low, and the best strategy to be adopted is the implementation of a surveillance system for detection and sanitation of infected herds, preferably by incorporating risk-based surveillance strategies. In addition, the State should implement an effective sanitary program to enable producers to test their animals for bovine tuberculosis before inserting them into the herds, as well as avoid sharing the grazing areas with properties that are not free of bovine tuberculosis.A situação epidemiológica da tuberculose bovina foi estudada no estado de Pernambuco. O estado foi dividido em três regiões e em cada uma delas foi aleatoriamente amostrado um número pré-estabelecido de propriedades. Dentro de cada propriedade, fêmeas com idade igual ou superior a 24 meses foram escolhidas aleatoriamente e submetidas ao teste Tuberculínico Cervical Comparativo. Ao todo foram testados 5.728 animais provenientes de 906 propriedades. Nas propriedades, foi aplicado um questionário epidemiológico para identificar fatores de risco associados à tuberculose bovina. A prevalência de focos no estado foi de 2,87% [1,82; 4,50] e a de animais 0,62% [0,29; 1,29]. Houve tendência de concentração de focos na região do Agreste do estado, caracterizada pelo predomínio de propriedades de leite. Os fatores de risco associados à condição de foco foram ter 18 ou mais vacas no rebanho, ordenhar as vacas 2 ou 3 vezes ao dia e compartilhar pastagem. Concluindo, o estado tem baixa prevalência de tuberculose bovina e a melhor estratégia a ser adotada é a implementação de sistema de vigilância para detecção e saneamento dos focos, de preferência incorporando elementos de vigilância baseada em risco. Além disso, o estado deve realizar uma sólida ação de educação sanitária para que seus produtores passem a testar os animais para tuberculose bovina antes de introduzi-los em seus plantéis e deixem de compartilhar pastagem com propriedades que não sejam livres de tuberculose bovina

Trocas gasosas de cafeeiros (Coffea arabica L.) e seringueiras (Hevea brasiliensis Muell. Arg.) em diferentes sistemas de cultivo na região de larvas, MG Gas exchange in coffe (Coffea arabica L.) and rubber tree (Hevea brasiliensis Muell. Arg.) in different crop systems in lavras, MG

O uso de sistemas de cultivo agrícola que favorecem a conservação dos recursos naturais e a diversidade de produção representa uma alternativa para produtores que visam menores custos em uma produção sustentável. Dentre esses sistemas de cultivo, destaca-se o sistema de consórcio entre cafeeiros e seringueiras, que tem sido estudado na região sul de Minas Gerais. Nesse contexto, avaliaram-se características de trocas gasosas, fluorescência da clorofila e relações hídricas de cafeeiros e seringueiras, em monocultivo e consórcio, na fase de implantação dos cultivos, com o objetivo de verificar o comportamento dessas espécies em diferentes sistemas de cultivo. Os resultados apontaram que um ambiente caracterizado por níveis de radiação e temperatura menores favorece as trocas gasosas do cafeeiro, enquanto maior disponibilidade hídrica e valores elevados de radiação são favoráveis ao desenvolvimento da seringueira quando em sistemas consorciados.<br>Crop systems that improve conservation of natural resources and diversity of production is a promising practice for farmers seeking low costs and a sustainable agriculture. The coffee - rubber tree intercropping has been studied in the south of Minas Gerais - Brazil. Within this context, the objective of this work was to evaluate the characteristics gas exchange, chlorophyll fluorescence and water relations of coffee and rubber tree in both intercropping and monocroping systems, in the early stage of the plantation establishment. The results showed that the reduction in radiation levels and temperature promote gas exchange increase in coffee, while higher photosynthetic radiation values and soil water availability are favorable to rubber tree in intercropping systems