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

Effects of Dry and Wet Sieving of Soil on Identification and Interpretation of Microbial Community Composition

Soil aggregates are microhabitats for microorganisms, and directly influence microorganisms that live within and are influenced by microorganisms in return. Two methods are used to isolate soil aggregates by their size: dry sieving (sieving air-dried soil) and wet sieving (sieving soil in water). Wet-sieving methods are generally considered to represent separation of aggregate classes that are stable to physical disaggregation in water, a condition considered favorable for protecting soil structure over time. However, little is known about the effect of sieving methods on microbial abundance, diversity, and functions, hindering the understanding of the relationship between soil structure and soil aggregates as habitat and soil microorganisms. In this study, the effect of dry and wet sieving on bacterial diversity, and abundance of microorganisms involved in N fixation (nifH gene), nitrification (amoA bacteria and archaea), and denitrification (narG, nirS and nosZ genes), was determined for four sizes of soil aggregates from a cropland and grassland. Quantitative-PCR (Q-PCR) showed little differences in relative gene abundance between size fractions of soil aggregates, but wet-sieving method significantly increased gene abundance for amoA bacteria, nirS and nosZ genes. When the N functional genes were expressed as percentage of the bacterial 16S rRNA genes, the wet sieving resulted in significantly higher genes percentage for all the genes (except for narG gene), and significant differences between soil aggregate size fractions at the grassland site. The different sieving methods resulted in different bacterial community compositions, but only the wet-sieving method was able to reveal significant differences in bacterial community composition between soil fractions in grassland. The results demonstrate significantly different quantitative and qualitative interpretation of soil microbial community depending on whether aggregate samples were obtained from wet or dry sieving, highlighting the importance in the choice of the sieving method

Relacionamentos de amizade íntima entre jovens adultos

A literatura é consensual quanto ao importante papel dos amigos no ciclo vital, na maior parte do tempo, para melhorias na qualidade de vida. Este estudo teve como objetivo investigar e descrever características dos relacionamentos íntimos de amizade de jovens adultos. Participaram 98 jovens adultos com idade entre 18 e 30 anos. Os procedimentos de amostragem foram baseados na técnica do Respondent Driven Sampling. Foram utilizados três questionários autoaplicados e os dados foram submetidos a tratamento quantitativo. Os resultados demonstraram uma homogeneidade de características entre amigos íntimos, especialmente para o gênero. O companheirismo despontou como aspecto mais marcante na amizade. Todas as funções da amizade apresentaram correlações positivas entre si. Conclui-se que parece haver um filtro de similaridades entre amigos na adultez jovem e que amizades de boa qualidade em uma determinada função costumam ser de boa qualidade em seu total

Responses of microbial community from tropical pristine coastal soil to crude oil contamination

Brazilian offshore crude oil exploration has increased after the discovery of new reservoirs in the region known as pré-sal, in a depth of 7.000 m under the water surface. Oceanic islands near these areas represent sensitive environments, where changes in microbial communities due oil contamination could stand for the loss of metabolic functions, with catastrophic effects to the soil services provided from these locations. This work aimed to evaluate the effect of petroleum contamination on microbial community shifts (Archaea, Bacteria and Fungi) from Trindade Island coastal soils. Microcosms were assembled and divided in two treatments, control and contaminated (weathered crude oil at the concentration of 30 g kg−1), in triplicate. Soils were incubated for 38 days, with CO2 measurements every four hours. After incubation, the total DNA was extracted, purified and submitted for target sequencing of 16S rDNA, for Bacteria and Archaea domains and Fungal ITS1 region, using the Illumina MiSeq platform. Three days after contamination, the CO2 emission rate peaked at more than 20 × the control and the emissions remained higher during the whole incubation period. Microbial alpha-diversity was reduced for contaminated-samples. Fungal relative abundance of contaminated samples was reduced to almost 40% of the total observed species. Taxonomy comparisons showed rise of the Actinobacteria phylum, shifts in several Proteobacteria classes and reduction of the Archaea class Nitrososphaerales. This is the first effort in acquiring knowledge concerning the effect of crude oil contamination in soils of a Brazilian oceanic island. This information is important to guide any future bioremediation strategy that can be required

Data analysis for 16S microbial profiling from different benchtop sequencing platforms

Progress in microbial ecology is confounded by problems when evaluating results from different sequencing methodologies. Contrary to existing expectations, here we demonstrate that the same biological conclusion is reached using different NGS technologies when stringent sequence quality filtering and accurate clustering algorithms are applied

Misguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databases

Controversy surrounding bacterial phylogenies has become one of the most important challenges for microbial ecology. Comparative analyses with nucleotide databases and phylogenetic reconstruction of the amplified 16S rRNA genes from DGGE (Denaturing Gradient Gel Electrophoresis) excised bands have been used by several researchers for the identification of organisms in complex samples. Here, we individually analyzed DGGE-excised 16S rRNA gene bands from 10 certified bacterial strains of different species, and demonstrated that this kind of approach can deliver erroneous outcomes to researchers, besides causing/emphasizing errors in public databases

Aliphatic Hydrocarbon Enhances Phenanthrene Degradation by Autochthonous Prokaryotic Communities from a Pristine Seawater

The microbial diversity and functioning around oceanic islands is poorly described, despite its importance for ecosystem homeostasis. Here, we aimed to verify the occurrence of microbe-driven phenanthrene co-oxidation in the seawater surrounding the Trindade Island (Brazil). We also used Next-Generation Sequencing to evaluate the effects of aliphatic and polycyclic aromatic hydrocarbons (PAHs) on these microbial community assemblies. Microcosms containing seawater from the island enriched with either labelled (9-14C) or non-labelled phenanthrene together with hexadecane, weathered oil, fluoranthene or pyrene, and combinations of these compounds were incubated. Biodegradation of phenanthrene-9-14C was negatively affected in the presence of weathered oil and PAHs but increased in the presence of hexadecane. PAH contamination caused shifts in the seawater microbial community—from a highly diverse one dominated by Alphaproteobacteria to less diverse communities dominated by Gammaproteobacteria. Furthermore, the combination of PAHs exerted a compounded negative influence on the microbial community, reducing its diversity and thus functional capacity of the ecosystem. These results advance our understanding of bacterial community dynamics in response to contrasting qualities of hydrocarbon contamination. This understanding is fundamental in the application and monitoring of bioremediation strategies if accidents involving oil spillages occur near Trindade Island and similar ecosystems