Symbolic Sequences and Tsallis Entropy

We address this work to investigate symbolic sequences with long-range correlations by using computational simulation. We analyze sequences with two, three and four symbols that could be repeated $l$ times, with the probability distribution $p(l)\propto 1/ l^{\mu}$. For these sequences, we verified that the usual entropy increases more slowly when the symbols are correlated and the Tsallis entropy exhibits, for a suitable choice of $q$, a linear behavior. We also study the chain as a random walk-like process and observe a nonusual diffusive behavior depending on the values of the parameter $\mu$.Comment: Published in the Brazilian Journal of Physic

Logarithmic Clustering in Submonolayer Epitaxial Growth

We investigate submonolayer epitaxial growth with a fixed monomer flux and irreversible aggregation of adatom islands due to their effective diffusion. When the diffusivity D_k of an island of mass k is proportional to k^{-\mu}, a Smoluchowski rate equation approach predicts steady behavior for 0<\mu<1, with the concentration c_k of islands of mass k varying as k^{-(3-\mu)/2}. For \mu>1, continuous evolution occurs in which c_k(t)~(\ln t)^{-(2k-1)\mu/2}, while the total island density increases as N(t)~(\ln t)^{\mu/2}. Monte Carlo simulations support these predictions.Comment: 4 pages, 2 figure

The Contribution of the Smectic-Nematic Interface to the Surface Energy

The contribution of the smectic-nematic interface to the surface energy of a nematic liquid crystal sample is analyzed. By means of a simple model it is shown that the surface energy depends on the thickness of the region over which the transition smectic-nematic takes place. For perfectly flat substrates this thickness is of the order of the correlation length entering in the transition. An estimate of this contribution shows that it is greater than the one arising from the nematic-substrate interaction. Moreover, it is also shown that the surface energy determined in this way presents a non-monotonic behavior with the temperature.Comment: 10 pages, revte

Rhizosphere microbial community composition of common beans with different levels of resistance to Fusarium oxysporum.

Microbial communities in the rhizosphere make significant contributions to plant health, growth and protection against soil pathogens. Plants can take advantage of their rhizosphere microbiomes to fend off pathogens, avoiding microbial infections. Here, we aimed to identify potential microbial groups and functional traits correlated to the suppression of the soil borne Microbial diversity and functioning in the soil ecosystem 145 pathogen Fusarium oxysporum. Through shotgun metagenomics we investigated the rhizosphere microbial communities of four common bean cultivars with different levels of resistance to the fungus, ranging from susceptible to resistant. Plants were grown in mesocosms experiments with two contrasting soils, i.e. Amazon Dark Earth (ADE) and an agricultural soil (AS). The soils presented clear differences in chemical properties, and ADE hosts higher microbial diversity than AS. Chemical analysis indicated a significant increase of pH, Ca, Fe, sum of bases and base saturation, and decrease of K, Mg, exchangeable Al, and Mn in rhizosphere of both soil types. Quantitative PCR showed an increase of 16S rRNA copy number with the increase resistance to the fungus in ADE soil. The rhizosphere of the four bean cultivars is dominated by the same bacterial phyla Proteobacteria, Actinobacteria, Firmicutes, and Chloroflexi, albeit in different relative abundance between soil types. The community structure of rhizosphere was different from the bulk soil, revealing the selection process in this environment. In ADE soil, the most resistant cultivar presented higher taxonomic diversity when compared to other cultivars; in contrast, the functional diversity was lower. Comparing the resistant to the susceptible cultivars there was an increase of Nitrospirae, Solibacteres, Spirochaeta and Chryosiogenetes bacterial classes in the resistant. Also, resistant cultivar presented high number of sequences affiliated to the family Pseudomonadaceae and to the genera Bacillus and Solibacter. Interestingly, the resistant and moderately resistant cultivars, presented high proportion of sequences related to bacteriocin, a narrow spectrum antibiotic, which suggests its role on pathogen suppression. Preliminary analysis showed that the selection of the microbial communities inhabiting the common bean rhizosphere is cultivar and soil type dependent. Further analysis will search for bacterial groups potentially related to the fungal antagonism. FAPESP 2014/03217-3

Analysis of the rhizosphere microbial communities of common beans resistant and susceptible to Fusarium oxysporum.

The rhizosphere is the narrow zone of soil around the living plant roots that is influenced by the activity of the plants. Many beneficial microorganisms in the rhizosphere provide plants with mineral nutrients, phytohormones, and also help to protect the plant against soil-borne pathogens. Microbiological studies are addressed to understand how rhizosphere microorganisms are recruited from soil and either benefit or harm plant growth, nutrition and health. Here, we aimed to identify potential microbial groups and functional traits correlated to the suppression of the soil borne pathogen Fusarium oxysporum, the causal agent of Fusarium wilt on common beans. We used shotgun metagenomics to investigate the rhizosphere microbiome of two common bean cultivars classified as resistant (Milênio) and susceptible (Alvorada). Plants were grown in mesocosms experiments in Amazon Dark Earth, a soil with high microbial diversity. Chemical analysis indicated a significant increase of pH, Ca, Fe, Zn, Mn, B, nitrate, cation exchange capacity, sum of bases and base saturation in rhizosphere of both common bean types. The microbial community structure of rhizosphere was different from the bulk soil in a deeper taxonomic classification (genera), revealing the selection process in this environment. Quantitative PCR showed an increase of 16S rRNA copy number with the increase resistance to the fungus in ADE soil. The resistant cultivar presented higher taxonomic diversity but lower functional diversity. The most abundant phyla in rhizosphere were Proteobacteria (41%), Actinobacteria (31%), Firmicutes (5%), Acidobacteria (3%) and Chloroflexi (3%). The resistant cultivar presented more abundance of the phyla Chlamydiae, Spirochaetes, Deinococcus-Thermus and Chrysiogenetes in comparison to the susceptible one and bulk soil. Comparing the resistant to the susceptible cultivar in a finer taxonomic level, 24 genera presented higher abundance in the resistant one, highlighting Bacillus and Pseudomonas. Preliminary analysis showed that there is a specific selection of the microbial communities inhabiting the rhizosphere of a resistant common bean cultivar. Further analysis will combine 16S rRNA gene sequencing and metatranscriptome for a deep taxonomical and functional analysis

Metagenomic analysis of the rhizosphere microbiome of the common bean resistant to Fusarium oxysporum.

The rhizosphere microbiome plays a key role in the functioning of the host plant, influencing its physiology and development. It has been suggested that plants use mechanisms present in the rhizosphere microbiome to fend off infections, such as fungal diseases. This work aimed to assess the microbial community inhabiting the common bean rhizosphere in order to identify potential groups related to the suppression of the soil-borne pathogen Fusarium oxysporum. Therefore, using shotgun metagenomic sequencing (Illumina Miseq), we investigated the phylogenetic and potential functional diversity of microbial communities colonizing the rhizosphere of four cultivars of common bean with different levels of resistance to the fungus, ranging from high susceptibility to resistant. Quantitative PCR of total bacteria in rhizosphere samples showed in increase of 16S rRNA copy number with the increase of resistance to the fungus. Mesocosms experiments, including four common bean cultivars cultivated in Amazonian Dark Earth and three replicates, were conducted in greenhouse conditions and we obtained over than 12 million metagenomic sequences. The overall microbial diversity did not present significant variations across common bean cultivars. From the classified sequences, 97,4% were affiliated to Bacteria and 1,48% to Archaea. Proteobacteria represented the most abundant phyla (41,7%), followed by Actinobacteria (29,4%), Firmicutes (5,9%) and Acidobacteria (4,1%). The microbial communities structure were different between bulk soil and rhizosphere samples. Comparing all bean cultivars, the resistant one showed an overrepresention of the phyla Spirochaetes, Nitrospirae and Euryarchaeota. The resistant bean cultivar presented high number of sequences affiliated to the genus Bacillus. Interestingly, the resistant and moderately resistant cultivars, presented high proportion of sequences related to bacteriocin, a narrow spectrum antibiotics. Preliminary analysis showed that different common bean cultivars could select differential microbial groups in the rhizosphere environment. Further analysis will search for bacterial groups potentially related to the fungal antagonism