Linking the composition of bacterial and archaeal communities to characteristics of soil and flora composition in the Atlantic rainforest

The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient-namely, Santa Virginia, Picinguaba and Restinga-we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms-ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning

'Synthetic lipase' production from a newly isolated Sporidiobolus pararoseus strain by submerged fermentation

The lipase produced by a newly isolate Sporidiobolus pararoseus strain has potential catalysis ability for esterification reactions. In order to improve its synthetic activity, this work aimed at optimizing 'synthetic lipase' production by submerged fermentation of a conventional media based on peptone, yeast extract, NaCl and olive oil using experimental design technique. According to the results obtained in the first experimental design (2(4-1)), yeast extract and NaCl concentrations were tested to further optimization by response surface methodology. The maximum 'synthetic lipase' activity obtained was 26.9 U/mL in the optimized media (5.0, 6.8, 7.0 and 1.0% (wt/v) of peptone, yeast extract, NaCl and olive oil, respectively), representing a 6.36-fold increase compared to the initial medium. The time course of 'synthetic lipase' production in the optimized condition was evaluated in terms of synthetic activity, protease activity, biomass and total carbon and the maximum synthetic activity was observed during the stationary phase of growth

Concentration, characterization and application of lipases from Sporidiobolus pararoseus strain

Lipases produced by a newly isolated Sporidiobolus pararoseus strain have potential catalytic ability for esterification reactions. After production, the enzymatic extracts (conventional crude and precipitated, 'CC' and 'CP', and industrial crude and precipitated, 'IC' e 'IP') were partially characterized. The enzymes presented, in general, higher specificity for short chain alcohols and fatty acids. The precipitated extract showed a good thermal stability, higher than that for crude enzymatic extracts. The 'CC' and 'CP' enzymes presented high activities after exposure to pH 6.5 and 40 ºC. On the other hand, the 'IC' and 'IP' extracts kept their activities in a wide range of pH memory but presented preference for higher reaction temperatures. Preliminary studies of application of the crude lipase extract in the enzymatic production of geranyl propionate using geraniol and propionic acid as substrates in solvent-free system led to a reaction conversion of 42 ± 1.5%

The diversity of bacteria and archaea in soils cultivated with sugarcane: a biogeographic approach

A cana-de-açúcar é atualmente a cultura de maior importância agrícola do Estado de São Paulo e tem papel de destaque entre as principais culturas do Brasil. Dentro de um contexto de maior produtividade unida a sustentabilidade, o papel da comunidade microbiana presente nos solos pode ter fundamental importância, auxiliando no melhor desenvolvimento da planta, suprindo a mesma com nutrientes ou diminuindo a ocorrência de doenças e pragas. Contudo, pouco se sabe sobre a comunidade microbiana existente nos solos cultivados com cana-de-açúcar, sendo que um conhecimento da distribuição espacial desta comunidade pode auxiliar para uma melhor compreensão dos processos aos quais estes microrganismos estão envolvidos. Dessa forma, este trabalho teve como objetivo estudar, em um enfoque biogeográfico, a diversidade de bactérias e arquéias existente em solos de cana-de-açúcar do Estado de São Paulo, focando nos grupos de arquéias e bactérias. Uma análise de 285 amostras de solos, obtidas em 10 regiões produtoras distintas, foi realizada utilizando técnicas independentes de cultivo como: quantificação da abundância total por meio da aplicação de PCR em tempo real (qPCR), análises da estrutura da comunidade por polimorfismo de comprimento de fragmentos de restrição terminal (T-RFLP), e determinação da sua afiliação filogenética por sequenciamento em larga escala de genes ribossomais. Os resultados obtidos demonstraram que o principal modulador destas comunidades foram as características física e química do solo (pH, granulometria, matéria orgânica). Além disso, a comunidade de arquéias demonstrou ser influenciada por práticas de manejo (colheita mecanizada e adição de vinhaça e torta de filtro). Adicionalmente, foi observada uma relação inesperada da estruturação destas comunidades com a distribuição geográfica das amostras analisadas. Os resultados demonstram a complexidade da comunidade de bactérias e arquéias ao longo de um gradiente espacial, sugerindo que estudos posteriores devem considerar uma amostragem mais ampla em distintas regiões. Este trabalho é embasador de estudos futuros que visem desenvolver práticas agrícolas baseadas na exploração da funcionalidade dos microbiomas dos solos.Sugarcane is currently the most important culture of the State of São Paulo and has a prominent role among the crops in Brazil. Into the context of a better productivity with greater sustainability, the role of the microbial community present in the soil could have huge importance, aiding a better plant development, supplying it with nutrients or reducing the occurrence of diseases and pests. However, little is known about the microbial community existing in soils cultivated with sugarcane, where a knowledge of the spatial distribution of this community could be helpful to a better understanding of the processes that these organisms are involved. This project aimed to study in a biogeographic approach, the bacteria and archaea diversity in soils of sugarcane in the São Paulo State, focusing on the groups of archaea and bacteria. Analyses of a total of 285 soil samples, obtained in 10 producing distinct regions was performed using independent cultivation techniques such as quantification of total abundance by applying quantitative PCR (qPCR), analysis of the community structure by terminal restriction of length polymorphism (T-RFLP) and determination of its phylogenetic affiliation by high-throughput sequencing of 16S ribosomal genes. The results showed that the main drivers of these communities were the physical and chemical characteristics of the soil (pH, granulometry and organic matter). In addition, the results have shown that archaea community was influenced by management practices (mechanical harvest, vinasse and filter cake adding). Additionally, an unexpected relationship between the structures of these communities with the geographic distribution of the samples was observed. The results demonstrate the complexity of the community of bacteria and archaea along a spatial gradient, suggesting that future studies should consider a broader sampling of the distinct regions. This work supports upcoming studies that aim at developing agricultural practices exploring the soil microbiomes functionality

The communities structures and metabolic characterizations of yeasts in Anthropogenic Dark Earth soils

A Terra Preta Antropogênica (TPA) é considerada um dos solos mais férteis do mundo, constituída de pequenas faixas e distribuídos aleatoriamente pela região Amazônica. Sua denominação é decorrente da presença de grupos pré-históricos que viveram nestes sítios arqueológicos ao longo dos rios da Amazônia, principalmente Central e Oriental. A grande quantidade de material deixado por esses grupos indígenas como fragmentos cerâmicos, carvão, artefatos líticos, restos de animais e vegetais promoveu uma elevada concentração de matéria orgânica, fósforo, cálcio, magnésio, manganês e zinco. Contudo, pouco se conhece sobre a diversidade e funcionalidade microbiana na TPA sendo; tal conhecimento fundamental para auxiliar na formação e manutenção destes solos, levando ao desenvolvimento de práticas sustentáveis de agricultura que conservem a biodiversidade. Dentre os microrganismos, as leveduras apresentam um papel de destaque na indústria e mesmo no ambiente. Este grupo esta correlacionado a processos fermentativos de diversos tipos de açúcares, produção de vitaminas, enzimas, lipídeos e polissacarídeos. Além disso, sua presença em solos é diversificada e variável quanto à abundância e espécies presentes. O objetivo deste trabalho foi avaliar as estruturas das comunidades de leveduras presentes nos solos de TPA, compará-las com as suas adjacências e correlacionar a possíveis diferenças apresentadas com os atributos químicos do solo. Além disso, testes metabólicos para o consumo de carboidratos e produção de micotoxinas foram efetuados buscando uma melhor compreensão da funcionalidade das leveduras nos ambientes estudados. No isolamento foram identificadas 13 espécies na TPA, 9 nos solos adjacentes e seis comuns ao dois ambientes. As leveduras dos solos adjacentes demonstraram-se capazes de consumir um maior número de carboidratos distintos, especialmente: amido, celobiose e L-arabinose. Na análise de DGGE as comunidades de TPAs apresentaram-se distintas e com maiores índices de diversidade e riqueza, quando comparadas aos seus solos adjacentes. Atributos químicos do solo como: P, matéria orgânica (MO), soma de bases (SB), Al, K, Fe e Mg foram determinantes para a diferenciar as comunidades de leveduras dos solos adjacentes e da Terra Preta. Os resultados permitiram concluir que a comunidade de leveduras presentes nos diferentes sítios de TPA e adjacência são diferentes na sua estrutura e diversidade de espécies, estando isto correlacionado as distintas propriedades químicas dos solos estudadosAnthropogenic Dark Earth (ADE) is considered one of the most fertile soils of the world, consisting in small areas and randomly distributed throughout the Amazonian region. Its name derives from the presence of prehistoric groups who lived in these archaeological sites along the Amazonian rivers, mainly Central and Eastern. The large amount of material left by these indigenous groups as pottery fragments, charcoal, lithic artifacts, the remains of animals and vegetables promoted a high concentration of organic matter, phosphorus, calcium, magnesium, manganese and zinc. However, little is known about the microbial diversity and functionality in ADE being this, fundamental to the knowledge of the formation and maintenance of these soils, leading to the development of sustainable farming practices that conserve the biodiversity. Among the microorganisms, the yeasts have interesting functionalities in the industry and even the environment. This group is correlated with fermentation processes of the several kinds of sugars, production of vitamins, enzymes, lipids and polysaccharides. Furthermore, its presence in soil is diverse and variable in abundance and species presence. The aim of this study was to evaluate the structures of the yeast communities present in the soil of ADE, to compare them with their surroundings and to correlate possible differences presented with the soil chemical properties. In addition, tests for metabolic consumption of carbohydrates and mycotoxin production were performed, seeking a better understanding of the yeast functionality in this study. In isolation were identified 13 species in the ADE , 9 in adjacent soil and six were common to both environments. Yeasts presents in adjacent soils shown are able to consume more distinct carbohydrates, especially: starch, cellobiose and L-arabinose. In DGGE analysis, the communities of ADE presented distinct and with higher levels of diversity and richness when compared to their adjacent soils. Soil chemical attributes as: P, organic matter (OM), total bases (SB), Al, K, Fe and Mg were determinates to differentiate yeast communities of adjacent soils and ADE. The results showed that yeast community in the different sites of ADE and adjacency are different in structure and diversity of the species, being this correlated to the different chemical properties found in these soil

Exploring interactions of plant microbiomes

A plethora of microbial cells is present in every gram of soil, and microbes are found extensively in plant and animal tissues. The mechanisms governed by microorganisms in the regulation of physiological processes of their hosts have been extensively studied in the light of recent findings on microbiomes. In plants, the components of these microbiomes may form distinct communities, such as those inhabiting the plant rhizosphere, the endosphere and the phyllosphere. In each of these niches, the "microbial tissue" is established by, and responds to, specific selective pressures. Although there is no clear picture of the overall role of the plant microbiome, there is substantial evidence that these communities are involved in disease control, enhance nutrient acquisition, and affect stress tolerance. In this review, we first summarize features of microbial communities that compose the plant microbiome and further present a series of studies describing the underpinning factors that shape the phylogenetic and functional plant-associated communities. We advocate the idea that understanding the mechanisms by which plants select and interact with their microbiomes may have a direct effect on plant development and health, and further lead to the establishment of novel microbiome-driven strategies, that can cope with the development of a more sustainable agriculture

Exploring interactions of plant microbiomes

A plethora of microbial cells is present in every gram of soil, and microbes are found extensively in plant and animal tissues. The mechanisms governed by microorganisms in the regulation of physiological processes of their hosts have been extensively studied in the light of recent findings on microbiomes. In plants, the components of these microbiomes may form distinct communities, such as those inhabiting the plant rhizosphere, the endosphere and the phyllosphere. In each of these niches, the "microbial tissue" is established by, and responds to, specific selective pressures. Although there is no clear picture of the overall role of the plant microbiome, there is substantial evidence that these communities are involved in disease control, enhance nutrient acquisition, and affect stress tolerance. In this review, we first summarize features of microbial communities that compose the plant microbiome and further present a series of studies describing the underpinning factors that shape the phylogenetic and functional plant-associated communities. We advocate the idea that understanding the mechanisms by which plants select and interact with their microbiomes may have a direct effect on plant development and health, and further lead to the establishment of novel microbiome-driven strategies, that can cope with the development of a more sustainable agriculture

Composição diferencial das comunidades bacterianas na rizosfera de variedas de cana-de-açúcar

A cultura da cana-de-açúcar é de extrema importância no cenário agrícola nacional. No entanto, pouco se sabe sobre a estruturação das comunidades microbianas associadas aos solos e às rizosferas de tais plantas. O objetivo deste trabalho foi avaliar a estrutura e diversidade das comunidades de bactérias associadas ao solo e à rizosfera de seis variedades de cana-de-açúcar cultivadas no Estado de São Paulo (Brasil). As análises foram realizadas com base em métodos independentes de cultivo, em que a técnica de PCR-DGGE revelou alterações na rizosfera para os grupos de bactérias totais e também para os grupos de Alphaproteobacteria e Betaproteobacteria. Após essa análise, quatro amostras (três de rizosfera e uma de solo) foram usadas para o sequenciamento da região V6 do gene 16S DNAr na plataforma Ion Torrent TM. Essa análise gerou um total de 95.812 sequências, dentro das quais houve a predominância das afiliadas aos filos Actinobacteria, Proteobacteria e Acidobateria . Os resultados revelaram que as comunidades bacterianas na rizosfera são distintas daquelas encontradas no solo. Foi possível ainda observar efeito diferencial de plantas das variedades. Alguns grupos bacterianos apresentaram menor frequência na rizosfera (Acidobacteria ), enquanto outros se mostraram fortemente estimulados pela presença das raízes, comumente para todas as variedades (Betaproteobacteria , Nitrospora e Chloroflexi ), ou em respostas variedade-específicas (Bacilli e Sphingobacteria )