Brazilian Microbiome Project: revealing the unexplored microbial diversity--challenges and prospects.

The Brazilian Microbiome Project (BMP) aims to assemble a Brazilian Metagenomic Consortium/Database. At present, many metagenomic projects underway in Brazil are widely known. Our goal in this initiative is to co-ordinate and standardize these together with new projects to come. It is estimated that Brazil hosts approximately 20 % of the entire world's macroorganism biological diversity. It is 1 of the 17 countries that share nearly 70 % of the world's catalogued animal and plant species, and is recognized as one of the most megadiverse countries. At the end of 2012, Brazil has joined GBIF (Global Biodiversity Information Facility), as associated member, to improve the access to the Brazilian biodiversity data in a free and open way. This was an important step toward increasing international collaboration and clearly shows the commitment of the Brazilian government in directing national policies toward sustainable development. Despite its importance, the Brazilian microbial diversity is still considered to be largely unknown, and it is clear that to maintain ecosystem dynamics and to sustainably manage land use, it is crucial to understand the biological and functional diversity of the system. This is the first attempt to collect and collate information about Brazilian microbial genetic and functional diversity in a systematic and holistic manner. The success of the BMP depends on a massive collaborative effort of both the Brazilian and international scientific communities, and therefore, we invite all colleagues to participate in this project.

Characterization of bacterial strains capable of desulphurisation in soil and sediment samples from Antarctica.

The presence of sulphur in fossil fuels and the natural environment justifies the study of sulphur-utilising bacterial species and genes involved in the biodesulphurisation process. Technology has been developed based on the natural ability of microorganisms to remove sulphur from polycyclic aromatic hydrocarbon chains. This biotechnology aims to minimise the emission of sulphur oxides into the atmosphere during combustion and prevent the formation of acid rain. In this study, the isolation and characterization of desulphurising microorganisms in rhizosphere and bulk soil samples from Antarctica that were either contaminated with oil or uncontaminated was described. The growth of selected isolates and their capacity to utilise sulphur based on the formation of the terminal product of desulphurisation via the 4S pathway, 2-hydroxybiphenyl, was analysed. DNA was extracted from the isolates and BOX-PCR and DNA sequencing were performed to obtain a genomic diversity profile of cultivable desulphurising bacterial species. Fifty isolates were obtained showing the ability of utilising dibenzothiophene as a substrate and sulphur source for maintenance and growth when plated on selective media. However, only seven genetically diverse isolates tested positive for sulphur removal using the Gibbs assay. DNA sequencing revealed that these isolates were related to the genera Acinetobacter and Pseudomonas.

The role of mycorrhization helper bacteria in the establishment and action of ectomycorrhizae associations.

More than 95 % short roots of most terrestrial plants are colonized by mycorrhizal fungi as soon as they emerge in the upper soil profiles. The establishment of mycorrhizal association involves profound morphological and physiological changes in root and fungus. It is affected by other rhizospheric microorganisms, specifically by the bacteria. Bacteria may have developed mechanisms of selective interaction with surrounding microorganisms, with neutral or positive effects on mycorrhizal associations, but negative effect on root pathogens in general. Because of the beneficial effect of bacteria on mycorrhizae, the concept of Mycorrhization Helper Bacteria (MHB) was created. Five main actions of MHB on mycorrhizae were proposed: in the receptivity of root to the mycobiont, in root-fungus recognition, in fungal growth, in the modification of rhizospheric soil and in the germination of fungal propagules. MHB appear to develop a gradation of specificity for the mycobiont, but little or no specificity for the host plant in symbiosis. One of the main groups of MHB is the fluorescent Pseudomonas, well represented in diversity and cell density studies of mycorrhizal associations. This review covers the activity of MHB in the establishment of ectomycorrhizae, taking as model the effects of Pseudomonas sp. described in scientific literature.

Detection of horizontal gene transfers from phylogenetic comparisons.

Bacterial phylogenies have become one of the most important challenges for microbial ecology. This field started in the mid-1970s with the aim of using the sequence of the small subunit ribosomal RNA (16S) tool to infer bacterial phylogenies. Phylogenetic hypotheses based on other sequences usually give conflicting topologies that reveal different evolutionary histories, which in some cases may be the result of horizontal gene transfer events. Currently, one of the major goals of molecular biology is to understand the role that horizontal gene transfer plays in species adaptation and evolution. In this work, we compared the phylogenetic tree based on 16S with the tree based on dszC, a gene involved in the cleavage of carbon-sulfur bonds. Bacteria of several genera perform this survival task when living in environments lacking free mineral sulfur. The biochemical pathway of the desulphurization process was extensively studied due to its economic importance, since this step is expensive and indispensable in fuel production. Our results clearly show that horizontal gene transfer events could be detected using common phylogenetic methods with gene sequences obtained from public sequence databases.

Aumento da disponibilidade de N via deposição atmosférica e fenologia reprodutiva de Habenaria caldensis Kraenzl. (Orchidaceae) no Parque Estadual do Itacolomi (PEIT) - MG, Brasil / The increase of N availability via atmospheric deposition and the reproduction phenology in Habenaria caldensis Kraenzl. (Orchidaceae) in the Parque Estadual do Itacolomi (PEIT) - MG, Brazil

Ao lado do aumento da concentração de CO2, a deposição atmosférica de N é atualmente considerada um dos mais importantes fatores de alteração do funcionamento dos ecossistemas nativos, tendo já provocado drásticas mudanças na composição florística e na ciclagem de nutrientes no hemisfério norte. Entretanto, em sistemas tropicais e subtropicais, pouco se sabe sobre os efeitos do enriquecimento de N via deposição atmosférica, sobre o seu funcionamento. A compreensão da amplitude e da direção das respostas de orquídeas ao aumento da concentração de N disponível pode ajudar a alimentar modelos de dinâmica de populações rupícolas em resposta às mudanças globais. Avaliamos as respostas de floração e frutificação em plantas de Habenaria caldensis Kraenzl. (Orchidaceae), espécie de ampla distribuição em Minas Gerais, em consequência do aumento da disponibilidade de N por meio de fertilizações com nitrato de amônio, in situ, por aspersão. Em resposta à adição de N, a antese foi adiantada em cerca de 15 dias em relação aos indivíduos do grupo controle. Pelos resultados obtidos, o aumento da disponibilidade de N via deposição atmosférica pode afetar em curto prazo a ecologia de orquídeas e possivelmente outras plantas de campos rupestres alterando seus padrões fenológicos e alométricos. Em médio e longo prazos, tais modificações podem ter relevante impacto sobre a dinâmica de populações e comunidades desse tipo vegetacional.

Along with the increased concentration of CO2, the atmospheric deposition of nitrogen is currently considered one of the most important factors of change in the functioning of native ecosystems and has caused drastic changes in their floristic composition and nutrient cycling in the northern hemisphere. In tropical and subtropical systems, however, the largest holders of the plants diversity, little is known about the effects of the nitrogen enrichment via deposition on their performance. Understanding the magnitude and direction of the responses of the orchids to the increase of the concentration of available nitrogen might be helpful to modeling of rock outcrops population dynamics in response to global changes. We evaluated the responses of flowering and fruiting in plants of Habenaria caldensis Kraenzl. (Orchidaceae), a species widely distributed in Minas Gerais, as a result of increased nitrogen availability through fertilization with ammonium nitrate, in situ, by spraying. In response to the addition of N, anthesis occurred about 15 days earlier compared to individuals of the control group. The results of this study demonstrated that the increased availability of N via atmospheric deposition can affect in a short term the ecology of orchids and possibly other plants from rock outcrops by changing their phenological and allometric patterns. In a medium and long term, such changes can have an important impact on the dynamics of populations and communities of this vegetation type.

The role of mycorrhization helper bacteria in the establishment and action of ectomycorrhizae associations

More than 95 percent short roots of most terrestrial plants are colonized by mycorrhizal fungi as soon as they emerge in the upper soil profiles. The establishment of mycorrhizal association involves profound morphological and physiological changes in root and fungus. It is affected by other rhizospheric microorganisms, specifically by the bacteria. Bacteria may have developed mechanisms of selective interaction with surrounding microorganisms, with neutral or positive effects on mycorrhizal associations, but negative effect on root pathogens in general. Because of the beneficial effect of bacteria on mycorrhizae, the concept of Mycorrhization Helper Bacteria (MHB) was created. Five main actions of MHB on mycorrhizae were proposed: in the receptivity of root to the mycobiont, in root-fungus recognition, in fungal growth, in the modification of rhizospheric soil and in the germination of fungal propagules. MHB appear to develop a gradation of specificity for the mycobiont, but little or no specificity for the host plant in symbiosis. One of the main groups of MHB is the fluorescent Pseudomonas, well represented in diversity and cell density studies of mycorrhizal associations. This review covers the activity of MHB in the establishment of ectomycorrhizae, taking as model the effects of Pseudomonas sp. described in scientific literature.

Paenibacillus brasilensis sp. nov., a novel nitrogen-fixing species isolated from the maize rhizosphere in Brazil.

Sixteen nitrogen-fixing strains isolated from the rhizosphere of maize planted in Cerrado soil, Brazil, which showed morphological and biochemical characteristics similar to the gas-forming Paenibacillus spp., were phenotypically and genetically characterized. Their identification as members of the genus Paenibacillus was confirmed by using specific primers based on the 16S rRNA gene. SDS-PAGE of whole-cell proteins, API 50CH, morphological and biochemical tests, amplified rDNA-restriction analysis (ARDRA), DNA-relatedness analyses, denaturing-gradient gel electrophoresis (DGGE) and 16S rRNA gene sequence determinations were performed to characterize the novel isolates and to compare them to strains of other nitrogen-fixing Paenibacillus spp. Phenotypic analyses showed that the 16 strains were very homogeneous and shared a high level of relatedness with Paenibacillus polymyxa and Paenibacillus peoriae. However, none of the novel isolates was able to ferment glycerol (positive test for P. polymyxa), L-arabinose or D-xylose (positive tests for P. polymyxa and P. peoriae) or utilize succinate (positive test for P. peoriae). Genetic approaches also indicated a high level of similarity among the novel isolates and P. polymyxa and P. peoriae, but the novel strains clearly could not be assigned to either of these two recognized species. On the basis of the features presented in this study, the 16 novel isolates were considered to represent members of a novel species within the genus Paenibacillus, for which the name Paenibacillus brasilensis is proposed. The type strain is PB1 72(T) (= ATCC BAA-413(T) = DSM 14914(T)).

Molecular microbial ecology: a minireview

Nossos conhecimentos sobre ecologia de microorganismos em ambientes naturais têm sido limitados por se basearem em técnicas clássicas de Microbiologia. Entretanto, os recentes avanços em técnicas de biologia molecular, juntamente com os constantes desenvolvimentos em tecnologias de informaçäo e computadores, têm transformado os estudos de Ecologia Microbiana e abriram uma nova área da Microbiologia denominada Ecologia Molecular Microbiana. Atualmente, estudos sobre comunidades microbianas naturais säo possíveis mesmo sem a necessidade de técnicas baseadas em cultivo, e novas estratégias moleculares têm sido desenvolvidas permitindo a realizaçäo de estudos sobre expressäo gênica, assim como um melhor entendimento sobre as interaçöes entre comunidades microbianas no ecossistema. Algumas das principais e/ou mais recentes técnicas foram revisadas.