Yeast communities associated with sugarcane in Campos, Rio de Janeiro, Brazil

Yeast communities associated with sugarcane leaves, stems and rhizosphere during different phases of plant development were studied near Campos, in Rio de Janeiro, Brazil. Atmospheric temperature, soil granulometry and pH, and sugar cane juice °Brix and pH were determined. Yeast communities associated with sugarcane were obtained after cellular extraction by shaking, blending and shaking plus sonication, and cultured on Yeast Nitrogen Base Agar plus glucose (0.5%) and Yeast Extract-Malt Extract Agar. No significant differences in yeast counts were found among the cellular extraction treatments and culture media. 230 yeast cultures were identified according to standard methods, and distinct yeast communities were found for each substrate studied. The prevalent species isolated from sugarcane were Cryptococcus laurentii, Cryptococcus albidus, Rhodotorula mucilaginosa and Debaryomyces hansenii

Bacterial community structure in two sediments with different organic matter content of a tropical coastal lagoon (Brazil)

Palavras-chave: bactérias, estrutura da comunidade, sedimento, lagoa tropical, Brazil

Análise Fenotípica e Genotípica de Bactérias Isoladas do Solo da Floresta Nacional dos Tapajós, pará, Brasil, sob Efeito de Estresse Hídrico

Soils from the National Forest of Tapajos are nutrient-poor, acidic, podzolic clay types, with high aluminum content. The Dry Forest Project was developed to assess the impact of drought on a tropical forest. This project includes plots of Primary Forest (FP, control) and Dry Forest (FS, with exclusion of rain). This study assessed the effect of dryness on the microbial populations of soils collected in these plots. Twelve soil samples were analyzed for counts of total bacteria, fungi, and cellulolytic, proteolytic and phosphate solubilizer populations. A decrease of microbial counts was detected at the dry forest plot in comparison with the control, being more significant (two orders of magnitude) for cellulolytic populations. The majority of 286 isolated cultures were Gram-positive bacilli (47% for FP and 62% for FS) and the prevalent genera were Bacillus, Corynebacterium, Listeria and Micrococcuss. Box-PCR profiles of the bacteria from both plots showed high genetic diversity. The exclusion BATISTA, Selma Baia Centro de Ciências Biológicas e da Saúde (CCBS) Universidade Federal do Mato Grosso. Av. Fernando Correia da Costa. Bairro Boa Esperança, Cuiabá-MT. CEP 78060-900. Brasil. Tel. (65) 63615-8970. E-mail: [email protected] HARGREAVES, Paulo Iiboshi; MENDONÇA-HAGLER, Leda Cristina Instituto de Microbiologia Prof. Paulo de Góes (IMPPG) UFRJ; Laboratório de Ecologia Microbiana e Taxonomia; Centro de Ciências da Saúde (CCS), Bloco I, sala 44, Ilha do Fundão-RJ. CEP 21941-590. Brasil. Tel. (21) 2562-6739. SOUSA, Oscarina Viana de Instituto de Ciências do Mar – LABOMAR UFC; Av. da Abolição, 3207 – Meireles – Fortaleza-CE. CEP 60165-081. Tel. (85) 3366-7000 of rain can produce a negative effect on the microbial populations of tropical forest soil. The diversity, at the genus level, does not appear to be affected by drought, and the high diversity found for bacteria at the species/ subspecies level at both sites suggested a resilience of the soil microbiota to this environmental stress.Os solos da Floresta Nacional dos Tapajós são classificados como argilosos e podzólicos, possuem acidez elevada, altos teores de alumínio e são pobres em nutrientes. Visando avaliar o impacto das secas na floresta, foi desenvolvido o projeto "Dry Forest". Este projeto inclui as parcelas Floresta Primária (FP, controle) e Floresta Seca (FS, com exclusão de chuvas). O presente estudo avaliou o efeito do estresse hídrico sobre a microbiota do solo nessas parcelas. Foram analisadas 12 amostras de solo por parcela quanto às populações microbianas, incluindo organismos celulolíticos, proteolíticos e solubilizadores de fosfato. Foi observada uma redução nas contagens microbianas no solo sob estresse hídrico, podendo atingir duas ordens de grandeza, sendo mais expressiva para os microrganismos celulolíticos. Das 286 culturas bacterianas isoladas, os bastonetes Gram positivos representaram 47% (FP) e 62% (FS) destes isolados. Os gêneros prevalentes foram Bacillus, Corynebacterium, Listeria e Micrococcus. Foi encontrada significativa diversidade genotípica entre as estirpes isoladas (FP e FS) nos perfis de BOX-PCR. Os resultados permitem concluir que a exclusão de chuvas na parcela seca pode provocar redução nas populações microbianas. No entanto, a diversidade encontrada, em nível de gênero, foi pouco influenciada. A elevada diversidade bacteriana detectada ao nível de espécie/subespécie sugere uma resiliência dos solos de ambas as parcelas ao estresse ambiental

Taking Root: Enduring Effect of Rhizosphere Bacterial Colonization in Mangroves

Mangrove forests are of global ecological and economic importance, but are also one of the world's most threatened ecosystems. Here we present a case study examining the influence of the rhizosphere on the structural composition and diversity of mangrove bacterial communities and the implications for mangrove reforestation approaches using nursery-raised plants.A barcoded pyrosequencing approach was used to assess bacterial diversity in the rhizosphere of plants in a nursery setting, nursery-raised transplants and native (non-transplanted) plants in the same mangrove habitat. In addition to this, we also assessed bacterial composition in the bulk sediment in order to ascertain if the roots of mangrove plants affect sediment bacterial composition. We found that mangrove roots appear to influence bacterial abundance and composition in the rhizosphere. Due to the sheer abundance of roots in mangrove habitat, such an effect can have an important impact on the maintenance of bacterial guilds involved in nutrient cycling and other key ecosystem functions. Surprisingly, we also noted a marked impact of initial nursery conditions on the rhizosphere bacterial composition of replanted mangrove trees. This result is intriguing because mangroves are periodically inundated with seawater and represent a highly dynamic environment compared to the more controlled nursery environment.In as far as microbial diversity and composition influences plant growth and health, this study indicates that nursery conditions and early microbial colonization patterns of the replants are key factors that should be considered during reforestation projects. In addition to this, our results provide information on the role of the mangrove rhizosphere as a habitat for bacteria from estuarine sediments

Mangrove microniches determine the structural and functional diversity of enriched petroleum hydrocarbon-degrading consortia

In this study, the combination of culture enrichments and molecular tools was used to identify bacterial guilds, plasmids and functional genes potentially important in the process of petroleum hydrocarbon (PH) decontamination in mangrove microniches (rhizospheres and bulk sediment). In addition, we aimed to recover PH-degrading consortia (PHDC) for future use in remediation strategies. The PHDC were enriched with petroleum from rhizosphere and bulk sediment samples taken from a mangrove chronically polluted with oil hydrocarbons. Southern blot hybridization (SBH) assays of PCR amplicons from environmental DNA before enrichments resulted in weak positive signals for the functional gene types targeted, suggesting that PH-degrading genotypes and plasmids were in low abundance in the rhizosphere and bulk sediments. However, after enrichment, these genes were detected and strong microniche-dependent differences in the abundance and composition of hydrocarbonoclastic bacterial populations, plasmids (IncP-1 alpha, IncP-1 beta, IncP-7 and IncP-9) and functional genes (naphthalene, extradiol and intradiol dioxygenases) were revealed by in-depth molecular analyses [PCR-denaturing gradient gel electrophoresis and hybridization (SBH and microarray)]. Our results suggest that, despite the low abundance of PH-degrading genes and plasmids in the environmental samples, the original bacterial composition of the mangrove microniches determined the structural and functional diversity of the PHDC enriched.Deutsche Forschungsgemeinschaft [SM59/4-1, 4-2]; FAPERJ-Brazil; European Commission [003998, 211684]; Alexander-von-Humboldt-Stiftung; CONICET (Argentina)info:eu-repo/semantics/publishedVersio

Assessment of variation in bacterial composition among microhabitats in a mangrove environment using DGGE fingerprints and barcoded pyrosequencing

Here, we use DGGE fingerprinting and barcoded pyrosequencing data, at six cut-off levels (85-100%), of all bacteria, Alphaproteobacteria and Betaproteobacteria to assess composition in the rhizosphere of nursery plants and nursery-raised transplants, native plants and bulk sediment in a mangrove habitat. When comparing compositional data based on DGGE fingerprinting and barcoded pyrosequencing at different cut-off levels, all revealed highly significant differences in composition among microhabitats. Procrustes superimposition revealed that ordination results using cut-off levels from 85-100% and DGGE fingerprint data were highly congruent with the standard 97% cut-off level. The various approaches revealed a primary gradient in composition from nursery to mangrove samples. The affinity between the nursery and transplants was greatest when using Betaproteobacteria followed by Alphaproteobacteria data. There was a distinct secondary gradient in composition from transplants to bulk sediment with native plants intermediate, which was most prevalent using all bacteria at intermediate cut-off levels (92-97%). Our results show that PCR-DGGE provides a robust and cost effective exploratory approach and is effective in distinguishing among a priori defined groups.This study was funded by the Deutsche Forschungsgemeinschaft SM59/4-1 and 4-2 (www.dfg.de/en/index.jsp), FAPERJ-Brazil (www.faperj.br), Centre for Environmental and Marine Studies (CESAM, Portugal) (www.cesam.ua.pt), Foundation for Science and Technology (FCT, Portugal) PTDC/AAC-CLI/107916/2008 (http://alfa.fct.mctes.pt) and the European Regional Development Fund (ERDF) through COMPETE- (FCOMP-01-0124-FEDER-008657). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.publishe

QUALIDADE MICROBIANA DA ÁGUA, SEDIMENTO, PEIXE E MARISCO EM ALGUMAS REGIÕES DA COSTA BRASILEIRA.

Studies of microorganisms in Brazilian coastal regions have focused largely on pol1ution indicators and pathogens and are briefly reviewed here. Fecal coliform counts taken in Brazilian tropical waters have been confirmed to be mostly Escherichia coli and other Enterobacteriaceoe of probable fecal origin, and to correlate wel1 with other pol1ution parameters including frequency of occurrence of some pathogens. Other microbial counts such as fecal streptococci, yeasts, heterotrophic bacteria, Pseudomonas aeroginosa and Staphylococcus aureus can also be usefull as pollution indicators. Water of Brazilian urban beaches is frequently contaminated to levels above those acceptable for use as bathing or fish harvest areas, Where water is contaminated according to microbial indicators, the associated sediments and animals can have even more elevated levels of pathogens and indicator organisms. Improvement in the sanitary quality of Brazilian coastal waters is needed to protect resources  of economic importance to the tourism and fishing industries.Os estudos sobre a microbiota de ambientes costeiros brasileiros foram basicamente focalizados nos aspectos sanitários envolvendo indicadores de poluição e estão revisados no pre­sente capitulo. As populações de coliformes fecais encontradas nos ambientes estudados foram constituídas predominantemente da espécie Escherichia coli, e outras bactérias da família Enterobacteriaceae, provavelmente de origem fecal. Os indexes de coliformes fecais, encontra­dos em águas costeiras, apresentaram correlação positiva com outros parâmetros indicadores de poluição c com a ocorrência de alguns microrganismos patogênicos. Outros parâmetros microbianos, tais como as contagens de estreptococos fecais, leveduras, bactérias heterotróficas, Pseudomonas aeruginosa e Staphyiococcus aureus podem ser utilizados como indicadores de poluição. As águas de praias brasileiras, localizadas em regiões urbanas, frequentemente apre­sentaram níveis de contaminação fecal superiores aqueles aceitáveis para uso em atividades de recreação e pesca. Os animais e sedimentos associados à ambientes aquáticos contaminados podem apresentar níveis mais elevados de organismos indicadores e patogênicos em relação as populações detectadas na água. Medidas de saneamento básico visando à melhoria da qualidade das águas nas regiões costeiras brasileiras são necessárias para proteção de recursos naturais importantes para as atividades econômicas de turismo e pesca

Fluorescent Pseudomonads associated with the rhizosphere of crops: an overview Pseudomonas spp. associadas à rizosfera de plantas de uso agrícola: um panorama

Environmental concerns have led to the need of sustainable use of natural resources. The conventional agriculture caused considerable impacts on soils and waters. It is important to change certain agricultural managements to environmental cleaner techniques. The sustainable agriculture has pointed many approaches and techniques to reduce environmental impact. One of those strategies is the utilization of the soil microbiota to induce plant growth, control of plant diseases and biodegradation of xenobiotic compounds. Studies on the relationship between roots and microbiota are essential to achieve viable agricultural applications. These studies indicate that one of the most abundant microorganisms in the rhizosphere (area around the roots) is fluorescent Pseudomonas spp. They have been considered as an alternative to agrochemicals for controlling plant diseases and increasing plant development. This review addresses the main findings on fluorescent Pseudomonads. It summarizes and discusses significant aspects of this general topic, including (i) rhizosphere as a microhabitat; (ii) taxonomic, genetic and ecological aspects of fluorescent Pseudomonads in the rhizosphere; (iii) mechanisms of Plant Growth Promoting and Biological Control and (iv) commercial use of PGPR in agriculture.<br>As preocupações com o meio ambiente têm levado à necessidade do uso sustentável dos recursos naturais. A agricultura convencional tem causado impactos consideráveis no solo e nas águas. É importante mudar certas técnicas agrícolas por outras consideradas mais limpas para o meio ambiente. Uma estratégia é a utilização da microbiota do solo para induzir o crescimento de plantas, controlar fitomoléstias e para fazer a biodegradação de compostos xenobióticos. Estudos sobre a relação entre as raízes e a microbiota são essenciais para conseguir aplicações viáveis na agricultura. Estes estudos têm indicado que um dos mais abundantes microrganismos na rizosfera (região ao redor da raiz) é Pseudomonas spp. do grupo fluorescente. Estes têm sido considerados como alternativa tanto aos agrotóxicos no controle de doença de plantas como na indução do seu desenvolvimento. Esta revisão mostra os principais conhecimentos sobre Pseudomonas spp. do grupo fluorescente. Esta resume e discute aspectos significantes deste tópico, incluindo, (i) rizosfera como microhabitat; (ii) aspectos taxonômicos, genéticos e ecológicos de Pseudomonas spp. do grupo das fluorescentes na rizosfera; (iii) mecanismos de Promoção de Crescimento de Plantas e Controle Biológico e (iv) uso comercial de PGPR na agricultura