Exploring the Potential of Two Bacterial Consortia to Degrade Cellulosic Biomass for Biotechnological Applications.

This paper outlines two cellulolytic bacterial consortia named SCS and SCB, isolated from soil samples of sugarcane (Saccharum officinarum) crop field, and a sugarcane bagasse deposit in an ethanol mill. Both consortia were able to grow on different carbon sources, such as sugarcane bagasse, corn husk, peanut hulls, and carboxymethylcellulose, releasing up to 11.90 µmol/mL and 15.23 µmol/mL of glucose for SCS and SCB, respectively. In addition, SCS and SCB have several strains capable of producing cellulase, amylase, lipase, and protease. Whole genome sequencing of the SCS consortium revealed that Burkholderia was the most prevalent genus, encompassing approximately 80% of the consortia. In addition, metagenome analysis allowed the identification of genes encoding enzymes related to starch and cellulose degradation, as well as enzymes related to lipases and proteases, confirming our initial findings. The results showed that SCS and SCB had the capability to degrade cellulose, and that they were an efficient source of enzyme production, which would provide a new choice for use in different biotechnological applications.

Land use impact on potentially toxic metals concentration on surface water and resistant microorganisms in watersheds.

Soil and water resources must be conserved and protected. However, the management of production activities causes a change in the quality of these natural resources due to accumulation in soil of potentially toxic metals. The objective of the present study was to identify the variety and paths of potentially toxic metals (PTMs), such as cadmium, lead, copper, chromium, nickel and zinc, which are associated spatially and temporally to soil and water. We also intended to isolate bacteria resistant to PTMs with important characteristics to be used in bioremediation processes. Water samples were collected every two months for one year (February-December/2014) at eight sites (P1-P8) and the soil samples were collected twice (February and August/2014) from twelve sites (S1-S12). Results indicated that agricultural land use impacts the environment, increasing the concentration of potentially toxic metals, mainly copper, zinc and chromium, in soil and water due to crop management. Ten bacteria resistant to all the metals studied were isolated, which could be used as tools for bioremediation of contaminated soils and water with those metals. The results would positively contribute to land use policy, and for the development of enhanced agricultural practices.

Bacterial communities in mining soils and surrounding areas under regeneration process in a former ore mine

Abstract Human activities on the Earth's surface change the landscape of natural ecosystems. Mining practices are one of the most severe human activities, drastically altering the chemical, physical and biological properties of the soil environment. Bacterial communities in soil play an important role in the maintenance of ecological relationships. This work shows bacterial diversity, metabolic repertoire and physiological behavior in five ecosystems samples with different levels of impact. These ecosystems belong to a historical area in Iron Quadrangle, Minas Gerais, Brazil, which suffered mining activities until its total depletion without recovery since today. The results revealed Proteobacteria as the most predominant phylum followed by Acidobacteria, Verrucomicrobia, Planctomycetes, and Bacteroidetes. Soils that have not undergone anthropological actions exhibit an increase ability to degrade carbon sources. The richest soil with the high diversity was found in ecosystems that have suffered anthropogenic action. Our study shows profile of diversity inferring metabolic profile, which may elucidate the mechanisms underlying changes in community structure in situ mining sites in Brazil. Our data comes from contributing to know the bacterial diversity, relationship between these bacteria and can explore strategies for natural bioremediation in mining areas or adjacent areas under regeneration process in iron mining areas.

Bacterial communities in mining soils and surrounding areas under regeneration process in a former ore mine.

Human activities on the Earth's surface change the landscape of natural ecosystems. Mining practices are one of the most severe human activities, drastically altering the chemical, physical and biological properties of the soil environment. Bacterial communities in soil play an important role in the maintenance of ecological relationships. This work shows bacterial diversity, metabolic repertoire and physiological behavior in five ecosystems samples with different levels of impact. These ecosystems belong to a historical area in Iron Quadrangle, Minas Gerais, Brazil, which suffered mining activities until its total depletion without recovery since today. The results revealed Proteobacteria as the most predominant phylum followed by Acidobacteria, Verrucomicrobia, Planctomycetes, and Bacteroidetes. Soils that have not undergone anthropological actions exhibit an increase ability to degrade carbon sources. The richest soil with the high diversity was found in ecosystems that have suffered anthropogenic action. Our study shows profile of diversity inferring metabolic profile, which may elucidate the mechanisms underlying changes in community structure in situ mining sites in Brazil. Our data comes from contributing to know the bacterial diversity, relationship between these bacteria and can explore strategies for natural bioremediation in mining areas or adjacent areas under regeneration process in iron mining areas.

Agricultural management of an Oxisol affects accumulation of heavy metals.

Soil contamination may result from the inadequate disposal of substances with polluting potential or prolonged agricultural use. Therefore, cadmium (Cd), chromium (Cr) and nickel (Ni) concentrations were assessed in a Eutroferric Red Oxisol under a no-tillage farming system with mineral fertilizer applications, a conventional tillage system with mineral fertilizer application and a conventional tillage system with sewage sludge application in an area used for agriculture for more than 80 years. We evaluated the spatial distributions of these elements in the experimental area and the effect of the different management practices on the soil retention of these metals. The concentrations of metals extracted from 422 soil samples by open-system digestion with HNO3, H2O2 and HCl were assessed by flame atomic absorption spectroscopy. The pH and soil organic matter were also assessed, and spatial distribution maps were designed. The mean concentrations of Cd, Cr and Ni (1.0, 50 and 14 mg kg-1, respectively) in the native forest were higher than the reference values (100, 25 and 8% greater, respectively) in Brazilian legislation, indicating that the source material was the determining factor of the high metal concentrations in the study soils. Soil management with sewage sludge was the major contributor to the accumulation of Cd and Ni, whereas Cr concentration did not vary with management type. Approximately 0.3, 12 and 16% of the experimental area is contaminated with Ni, Cd and Cr, respectively, because their concentrations exceeded the values for alertness or prevention in Brazilian legislation.

Freshwater quality of a stream in agricultural area where organic compost from animal and vegetable wastes is used / Qualidade da água de um córrego em área agrícola onde é usado composto orgânico de resíduos animais e vegetais

ABSTRACT Organic compost from biomass residues constitutes a viable alternative for partial or total replacement of mineral fertilizers for growing vegetables. This study evaluated the effects of compost on the water quality of a stream used mainly for irrigation of agricultural crops cultivated in nearby soil that has been treated with organic compost produced by carcasses, animal and vegetable waste for the last ten years. We sampled water biannually for two years, 2013 and 2014, from five locations along the stream. Physical variables and some chemical variables were analyzed. We also analyzed the total number of coliforms (Escherichia coli). Bacterial populations were compared by carbon substrate consumption. Total phosphorus contents in the samples from 2014 exceeded 0.1 mg L-1. The concentrations of other chemical species analyzed and the results for the physical variables were in accordance with the expected values compared with national and international water quality standards. The environment showed differential carbon source consumption and a high diversity of microorganisms, but our results did not show any evidence that the applied compost is changing the microbial population or its metabolic activity. This study shows that the use of the organic compost in agricultural areas seen does not negatively influence the quality of surface water in the study area. These results are important because the process of composting animal and vegetable waste and the use of compost obtained can be an alternative sustainable for adequate destination of these wastes.

RESUMO Composto orgânico produzido a partir de biomassa residual constitui uma alternativa viável para a substituição parcial ou total de fertilizantes minerais no cultivo de hortaliças. Neste estudo foram avaliados os efeitos do composto, sobre a qualidade da água de um córrego, usado principalmente para a irrigação de culturas agrícolas cultivadas em solo nas proximidades, tratado nos últimos dez anos com composto orgânico produzido a partir de carcaças, resíduos animais e vegetais. Amostras de água foram coletadas semestralmente, em 2013 e 2014, em cinco pontos ao longo do córrego. Foram analisadas variáveis físicas, algumas variáveis químicas e o número total de coliformes (Escherichia coli). As populações bacterianas foram comparadas pelo consumo de substratos de carbono. Os teores de fósforo total nas amostras de 2014 ultrapassaram 0,1 mg L-1. As concentrações das demais espécies químicas analisadas e os resultados para as variáveis fisicas ficaram de acordo com valores estabelecidos em normas nacionais e internacionais de qualidade de água. O ambiente mostrou consumo diferencial de fontes de carbono e grande diversidade de micro-organismos, mas os resultados não mostraram qualquer evidência de que o composto aplicado seja o fator responsável pela alteração da população microbiana ou sua atividade metabólica. Este estudo mostra que o uso do composto orgânico em áreas agrícolas parece não influenciar negativamente a qualidade da água superficial na área estudada. Estes resultados são importantes porque o processo de compostagem de resíduos animais e vegetais e o uso do composto obtido podem ser uma alternativa sustentável para o destino adequado desses resíduos.

Liming in the sugarcane burnt system and the green harvest practice affect soil bacterial community in northeastern São Paulo, Brazil.

Here we show that both liming the burnt sugarcane and the green harvest practice alter bacterial community structure, diversity and composition in sugarcane fields in northeastern São Paulo state, Brazil. Terminal restriction fragment length polymorphism fingerprinting and 16S rRNA gene cloning and sequencing were used to analyze changes in soil bacterial communities. The field experiment consisted of sugarcane-cultivated soils under different regimes: green sugarcane (GS), burnt sugarcane (BS), BS in soil amended with lime applied to increase soil pH (BSL), and native forest (NF) as control soil. The bacterial community structures revealed disparate patterns in sugarcane-cultivated soils and forest soil (R = 0.786, P = 0.002), and overlapping patterns were shown for the bacterial community structure among the different management regimes applied to sugarcane (R = 0.194, P = 0.002). The numbers of operational taxonomic units (OTUs) found in the libraries were 117, 185, 173 and 166 for NF, BS, BSL and GS, respectively. Sugarcane-cultivated soils revealed higher bacterial diversity than NF soil, with BS soil accounting for a higher richness of unique OTUs (101 unique OTUs) than NF soil (23 unique OTUs). Cluster analysis based on OTUs revealed similar bacterial communities in NF and GS soils, while the bacterial community from BS soil was most distinct from the others. Acidobacteria and Alphaproteobacteria were the most abundant bacterial phyla across the different soils with Acidobacteria Gp1 accounting for a higher abundance in NF and GS soils than burnt sugarcane-cultivated soils (BS and BSL). In turn, Acidobacteria Gp4 abundance was higher in BS soils than in other soils. These differential responses in soil bacterial community structure, diversity and composition can be associated with the agricultural management, mainly liming practices, and harvest methods in the sugarcane-cultivated soils, and they can be detected shortly after harvest.

Properties of Polyhydroxyalkanoate Granules and Bioemulsifiers from Pseudomonas sp. and Burkholderia sp. Isolates Growing on Glucose.

A Burkholderia and Pseudomonas species designated as AB4 and AS1, respectively, were isolated from soil containing decomposing straw or sugar cane bagasse collected from Brazil. This study sought to evaluate the capacities of culture media, cell-free medium, and crude lysate preparations (containing PHB inclusion bodies) from bacterial cell cultures to stabilize emulsions with several hydrophobic compounds. Four conditions showed good production of bioemulsifiers (E24 ≥ 50 %), headed by substantially cell-free media from bacterial cell cultures in which bacterial isolates from Burkholderia sp. strain AB4 and Pseudomonas sp. strain AS1 were grown. Our results revealed that the both isolates (AB4 and AS1 strains) exhibited high emulsification indices (indicating usefulness in bioremediation) and good stabilities.

Draft genome sequence of the nitrogen-fixing symbiotic bacterium Bradyrhizobium elkanii 587.

The draft sequence of the genome of Bradyrhizobium elkanii 587 is presented. This was obtained using Illumina Next-Gen DNA sequencing combined with Sanger sequencing. Genes for the pathways involved in biological nitrogen fixation (the nif gene cluster), nod genes including nodABC, and genes for the type III protein secretion system (T3SS) are present.

Genomics-based design of defined growth media for the plant pathogen Xylella fastidiosa.

Based on the genetic analysis of the phytopathogen Xylella fastidiosa genome, five media with defined composition were developed and the growth abilities of this fastidious prokaryote were evaluated in liquid media and on solid plates. All media had a common salt composition and included the same amounts of glucose and vitamins but differed in their amino acid content. XDM(1) medium contained amino acids threonine, serine, glycine, alanine, aspartic acid and glutamic acid, for which complete degradation pathways occur in X. fastidiosa; XDM(2) included serine and methionine, amino acids for which biosynthetic enzymes are absent, plus asparagine and glutamine, which are abundant in the xylem sap; XDM(3) had the same composition as XDM(2) but with asparagine replaced by aspartic acid due to the presence of complete degradation pathway for aspartic acid; XDM(4) was a minimal medium with glutamine as a sole nitrogen source; XDM(5) had the same composition as XDM(4), plus methionine. The liquid and solidified XDM(2) and XDM(3) media were the most effective for the growth of X. fastidiosa. This work opens the opportunity for the in silico design of bacterial defined media once their genome is sequenced.