Rodrigo Josemar Seminoti Jacques

Network topology reveals high connectance levels and few key microbial genera within soils

Microbes have a central role in soil global biogeochemical process, yet specific microbe-microbe relationships are largely unknown. Analytical approaches as network analysis may shed new lights in understanding of microbial ecology and environmental microbiology. We investigated the soil bacterial community interactions through cultivation-independent methods in several land uses common in two Brazilian biomes. Using correlation network analysis we identified bacterial genera that presented important microbial associations within the soil community. The associations revealed nonrandomly structured microbial communities and clusters of operational taxonomic units (OTUs) that reflected relevant bacterial relationships. Possible keystone genera were found in each soil. Irrespective of the biome or land use studied only a small portion of OTUs showed positive or negative interaction with other members of the soil bacterial community. The more interactive genera were also more abundant however, within those genera, the abundance was not related to taxon importance as measured by the Betweenness Centrality. Most of the soil bacterial genera were important to the overall connectance of the network, whereas only few genera play a key role as connectors, mainly belonged to phyla Proteobacteria and Actinobacteria. Finally it was observed that each land use presented a different set of keystone genera and that no keystone genus presented a generalized distribution. Taking into account that species interactions could be more important to soil processes than species richness and abundance, especially in complex ecosystems, this approach might represent a step forward in microbial ecology beyond the conventional studies of microbial richness and abundance.

Biorremediação de solos contaminados com hidrocarbonetos aromáticos policíclicos

Polycyclic aromatic hydrocarbons (PAHs) are mutagenic and carcinogenic compounds to the humans and animals, released through the environment by anthropogenic activities related to the extraction, transport, refine, transformation and use of the petroleum and its derivatives. Most of the soils microorganisms do not possess the capacity to degrade them, which results in its accumulation in the atmosphere and contamination of the ecosystems. A strategy for PAHs elimination from the soil is through the bioremediation, where microorganisms having capacity to metabolize these compounds will transform them in inert substances, CO2 and water. However, this biotechnology can be limited by the lack of specific HAP microbial-degraders in soil, by unfavorable environmental conditions to these microorganisms or by the low bioavailability of those contaminants to the microorganisms. To overcome these limitations and to promote an efficient removal of the pollutants to the atmosphere, several bioremediation techniques were developed as passive bioremediation, bioaugmentation, biostimulation, phytoremediation, landfarming, composting and bioreactors. This revision aims at discussing microbial metabolism of PAHs, present the main chemical and physical factors that influence the survival and the activity of these microorganisms and to show the bioremediation techniques that are being used now for the PAHs removal in soil.

Land-use change and soil type are drivers of fungal and archaeal communities in the Pampa biome

The current study aimed to test the hypothesis that both land-use change and soil type are responsible for the major changes in the fungal and archaeal community structure and functioning of the soil microbial community in Brazilian Pampa biome. Soil samples were collected at sites with different land-uses (native grassland, native forest, Eucalyptus and Acacia plantation, soybean and watermelon field) and in a typical toposequence in Pampa biome formed by Paleudult, Albaqualf and alluvial soils. The structure of soil microbial community (archaeal and fungal) was evaluated by ribosomal intergenic spacer analysis and soil functional capabilities were measured by microbial biomass carbon and metabolic quotient. We detected different patterns in microbial community driven by land-use change and soil type, showing that both factors are significant drivers of fungal and archaeal community structure and biomass and microbial activity. Fungal community structure was more affected by land-use and archaeal community was more affected by soil type. Irrespective of the land-use or soil type, a large percentage of operational taxonomic unit were shared among the soils. We accepted the hypothesis that both land-use change and soil type are drivers of archaeal and fungal community structure and soil functional capabilities. Moreover, we also suggest the existence of a soil microbial core.

Soil-borne bacterial structure and diversity does not reflect community activity in Pampa biome.

The Pampa biome is considered one of the main hotspots of the world’s biodiversity and it is estimated that half of its original vegetation was removed and converted to agricultural land and tree plantations. Although an increasing amount of knowledge is being assembled regarding the response of soil bacterial communities to land use change, to the associated plant community and to soil properties, our understanding about how these interactions affect the microbial community from the Brazilian Pampa is still poor and incomplete. In this study, we hypothesized that the same soil type from the same geographic region but under distinct land use present dissimilar soil bacterial communities. To test this hypothesis, we assessed the soil bacterial communities from four land-uses within the same soil type by 454-pyrosequencing of 16S rRNA gene and by soil microbial activity analyzes. We found that the same soil type under different land uses harbor similar (but not equal) bacterial communities and the differences were controlled by many microbial taxa. No differences regarding diversity and richness between natural areas and areas under anthropogenic disturbance were detected. However, the measures of microbial activity did not converge with the 16S rRNA data supporting the idea that the coupling between functioning and composition of bacterial communities is not necessarily correlated.

Improved Enrichment and Isolation of Polycyclic Aromatic Hydrocarbons (PAH)-Degrading Microorganisms in Soil Using Anthracene as a Model PAH

Lack of attention to soil and microbial characteristics that influence PAHs degradation has been a leading cause of failures in isolation of efficient PAH degraders and bioaugumentation processes with microbial consortia. This study compared the classic method of isolation of PAHs-degraders with a modified method employing a pre-enrichment respirometric analysis. The modified enrichment of PAH degrading microorganisms using in vitro microcosm resulted to reduced enrichment period and more efficient PAH-degrading microbial consortia. Results indicate that natural soils with strong heterotrophic microbial activity determined through pre-enrichment analysis, are better suited for the isolation of efficient PAH degrading microorganisms with significant reduction of the enrichment period.

Enzymatic activity of catechol 1,2-dioxygenase and catechol 2,3-dioxygenase produced by Gordonia polyisoprenivorans

This study aimed to evaluate the environmental conditions for enzyme activity of catechol 1,2-dioxygenase (C1,2O) and catechol 2,3-dioxygenase (C2,3O) produced by Gordonia polyisoprenivorans in cell-free and immobilized extracts. The optimum conditions of pH, temperature, time course and effect of ions for enzyme activity were determined. Peak activity of C1,2O occurred at pH 8.0. The isolate exhibited the highest activity of C2,3O at pH 7.0 and 8.0 for the cell-free extract and immobilized extract, respectively. This isolate exhibited important characteristics such as broad range of pH, temperature and time course for enzyme activity.

Properties of catechol 1,2-dioxygenase in the cell free extract and immobilized extract of Mycobacterium fortuitum

Polycyclic aromatic hydrocarbons (PAH) are carcinogenic compounds which contaminate water and soil, and the enzymes can be used for bioremediation of these environments. This study aimed to evaluate some environmental conditions that affect the production and activity of the catechol 1,2-dioxygenase (C12O) by Mycobacterium fortuitum in the cell free and immobilized extract in sodium alginate. The bacterium was grown in mineral medium and LB broth containing 250 mg L−1 of anthracene (PAH). The optimum conditions of pH (4.0–9.0), temperature (5–70 °C), reaction time (10–90 min) and the effect of ions in the enzyme activity were determined. The Mycobacterium cultivated in LB shown higher growth and the C12O activity was two-fold higher to that in the mineral medium. To both extracts the highest enzyme activity was at pH 8.0, however, the immobilized extract promoted the increase in the C12O activity in a pH range between 4.0 and 8.5. The immobilized extract increased the enzymatic activity time and showed the highest C12O activity at 45 °C, 20 °C higher than the greatest temperature in the cell free extract. The enzyme activity in both extracts was stimulated by Fe3+, Hg2+ and Mn2+ and inhibited by NH4+ and Cu2+, but the immobilization protected the enzyme against the deleterious effects of K+ and Mg2+ in tested concentrations. The catechol 1,2-dioxygenase of Mycobacterium fortuitum in the immobilized extract has greater stability to the variations of pH, temperature and reaction time, and show higher activity in presence of ions, comparing to the cell free extract.

Selection, isolation, and identification of fungi for bioherbicide production

Production of a bioherbicide for biological control of weeds requires a series of steps, from selection of a suitable microbial strain to final formulation. Thus, this study aimed to select fungi for production of secondary metabolites with herbicidal activity using biological resources of the Brazilian Pampa biome. Phytopathogenic fungi were isolated from infected tissues of weeds in the Pampa biome. A liquid synthetic culture medium was used for production of metabolites. The phytotoxicity of fungal metabolites was assessed via biological tests using the plant Cucumis sativus L., and the most promising strain was identified by molecular analysis. Thirty-nine fungi were isolated, and 28 presented some phytotoxic symptoms against the target plant. Fungus VP51 belonging to the genus Diaporthe showed the most pronounced herbicidal activity. The Brazilian Pampa biome is a potential resource for the development of new and sustainable chemical compounds for modern agriculture.

Biodegradação dos herbicidas imazetapir e imazapique em solo rizosférico de seis espécies vegetais

Phytostimulation is a technique of phytoremediation that can be used to reduce the concentration of herbicides in the soil. It is necessary to select plants that stimulate the activity of the rizosphere degrading microorganism. The aim of this study was to evaluate the activity of the biodegradation of the herbicide compound formulated mixture of imazethapyr + imazapic (75 + and 25 g L-1) in rhizosphere soil from six plant species with potential for phytostimulation. Biodegradation of the herbicide in the rhizosphere soil of Canavalia ensiformis, Glycine max, Lolium multiflorum, Lotus corniculatus, Stizolobium aterrimum and Vicia sativa, and a control (soil without plant) was evaluated at doses of 0, 250, 500, 1.000 and 4.000mL 1 ha, by quantifying the production of C-CO2 of the soil and the degradation of the herbicide from the soil by liquid chromatography coupled to mass spectrometry. The production of C-CO2 of the soil after the contamination with the mixture imazethapyr + imazapic was higher in the rhizosphere soil of the six plant species when compared to soil not cultivated. The rhizospheric soil from Stizolobium aterrimum shouwed the highest degradation of the herbicide imazetapyr on the highest doses evaluated, being a promising specie for phytostimulation.

The effects of trace elements, cations, and environmental conditions on protocatechuate 3,4-dioxygenase activity

Phenanthracene is a highly toxic organic compound capable of contaminating water and soils, and biodegradation is an important tool for remediating polluted environments. This study aimed to evaluate the effects of trace elements, cations, and environmental conditions on the activity of the protocatechol 3,4-dioxygenase (P3,4O) enzyme produced by the isolate Leifsonia sp. in cell-free and immobilized extracts. The isolate was grown in Luria Bertani broth medium (LB) amended with 250 mg L-1 of phenanthrene. Various levels of pH (4.0-9.0), temperature (5-80 °C), time (0-90 min), trace elements (Cu2+, Hg2+ and Fe3+), and cations (Mg2+, Mn2+, K+ and NH4+) were tested to determine which conditions optimized enzyme activity. In general, the immobilized extract exhibited higher enzyme activity than the cell-free extract in the presence of trace elements and cations. Adding iron yielded the highest relative activity for both cell-free and immobilized extracts, with values of 16 and 99 %, respectively. Copper also increased enzyme activity for both cell-free and immobilized extracts, with values of 8 and 44 %, respectively. Enzyme activity in the phosphate buffer was high across a wide range of pH, reaching 80 % in the pH range between 6.5 and 8.0. The optimum temperatures for enzyme activity differed for cell-free and immobilized extracts, with maximum enzyme activity observed at 35 oC for the cell-free extract and at 55 oC for the immobilized extract. The cell-free extract of the P3,4O enzyme exhibited high activity only during the first 3 min of incubation, when it showed 50 % relative activity, and dropped to 0 % after 60 min of incubation. By contrast, activity in the immobilized extract was maintained during 90 min of incubation. This isolate has important characteristics for phenanthrene biodegradation, producing high quantities of the P3,4O enzyme that forms part of the most important pathway for PAH biodegradation.