Enzymatic Bioremediation of Dyes from Textile Industry Effluents

The use of synthetic dyes began in 1865 with the discoveries of researcher William Henry Perkin. Its production and use only grew due to the high demand of several industrial sectors, mainly textiles. At the same time, concerns about environmental problems arose due to the disposal of wastewater with dyes, being the textile industry’s effluents the most polluting in the world. According to their structure, dyes can be more or less harmful, whereby azo dyes are the most worrisome from an environmental point of view. Problems, such as carcinogenicity, mutagenicity, and genotoxicity, are related to dyes, as well as contamination of water, and soil, and damages to agricultural plantations. Some of the methods used in the treatment of textile industrial effluents are membrane filtration, coagulation, chemical oxidation, biodegradation, photocatalytic degradation, phytoremediation, and enzymatic remediation. Enzyme remediation is considered an efficient, ecological, and innovative technique, through which enzymes can be used in free or immobilized form. The main enzymes involved in the degradation of azo dyes are azoreductases, laccases, and peroxidases. In some cases, harmful by-products are formed during the reactions and require proper management. Thus, this chapter addresses the main aspects of enzymatic bioremediation of dyes present in effluents from the textile industry

Xylella fastidiosa gene expression analysis by DNA microarrays

Xylella fastidiosa genome sequencing has generated valuable data by identifying genes acting either on metabolic pathways or in associated pathogenicity and virulence. Based on available information on these genes, new strategies for studying their expression patterns, such as microarray technology, were employed. A total of 2,600 primer pairs were synthesized and then used to generate fragments using the PCR technique. The arrays were hybridized against cDNAs labeled during reverse transcription reactions and which were obtained from bacteria grown under two different conditions (liquid XDM2 and liquid BCYE). All data were statistically analyzed to verify which genes were differentially expressed. In addition to exploring conditions for X. fastidiosa genome-wide transcriptome analysis, the present work observed the differential expression of several classes of genes (energy, protein, amino acid and nucleotide metabolism, transport, degradation of substances, toxins and hypothetical proteins, among others). The understanding of expressed genes in these two different media will be useful in comprehending the metabolic characteristics of X. fastidiosa, and in evaluating how important certain genes are for the functioning and survival of these bacteria in plants

Polyhydroxybutyrate in Rhizobium and Bradyrhizobium: quantification and phbC gene expression

Polyhydroxyalkanoates (PHAs) are hydroxyalkanoate polymers that are produced and accumulate by many kinds of bacteria. These polymers act as an energy store for bacteria. Polyhydroxybutyrate (PHB) is the most studied polymer in the PHA family. These polymers have awakened interest in the environmental and industrial research areas because they are biodegradable and have thermoplastic qualities, like polypropylene. In this work, we analyzed the PHB production in Bradyrhizobium sp., Rhizobium leguminosarum bv. phaseoli, and Rhizobium huautlense cultured with two different carbon sources. We did biochemical quantification of PHB production during the three phases of growth. Moreover, these samples were used for RNA extraction and phbC gene expression analysis via real-time PCR. The bacteria showed different manner of growth, PHB accumulation and phbC gene expression when different quantity and quality of carbon sources were used. These results showed that under different growth media conditions, the growth and metabolism of different species of bacteria were influenced. These differences reflect the increase or decrease in PHB accumulation.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

Farming and soil urban occupation in the water quality of Jaboticabal and Cerradinho streams

ABSTRACT Since the end of the twentieth century, 100% of the urban sewage from the city of Jaboticabal has been collected by interceptors and routed to a treatment plant. Between 1999 and 2000, studies on the effect of this environmental care showed that it did not efficiently clean up the water from the two streams that run through the city and flow into an agricultural area. This paper focuses on assessing the influence of soil use on the water quality of surface waters from these two streams. The study was conducted 15 years after the implementation of sewage interceptors. The sampling dates were bimonthly at eight points (P1 to P8) in the Cerradinho and Jaboticabal streams, in Jaboticabal (São Paulo State, Brazil). P1 was located at the source of the Jaboticabal stream, P2 was in a farming area, P3, P4 and P5 were in an urban area, and P6, P7 and P8 were in a farming area. The physical and chemical variables of the water were assessed. We compared the ability of microorganisms to metabolize different sources of carbon using the EcoPlate (Biolog). The total phosphorus (TP) concentration exceeded the limit set by the Brazilian legislation as well as values found in previous studies, which was also observed for the chemical oxygen demand. However, the bacterial metabolic profile had no association with urban or farming practices. The results of the analysis indicated the possibility of clandestine discharge of wastewater in the streams studied and the influence of the agricultural soil

Freshwater quality of a stream in agricultural area where organic compost from animal and vegetable wastes is used

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

Molecular identification of fungal communities in a soil cultivated with vegetables and soil suppressiveness to Rhizoctonia solani

Fungi constitute an important part of the soil ecosystem, playing key roles in decomposition, cycling processes, and biotic interactions. Molecular methods have been used to assess fungal communities giving a more realistic view of their diversity. For this purpose, total DNA was extracted from bulk soils cultivated with tomato (STC), vegetables (SHC), and native forest (SMS) from three sites of the Taquara Branca river basin in Sumaré County, São Paulo State, Brazil. This metagenomic DNA was used as a template to amplify fungal 18S rDNA sequences, and libraries were constructed in Escherichia coli by cloning PCR products. The plasmid inserts were sequenced and compared to known rDNA sequences in the GenBank database. Of the sequenced clones, 22 were obtained from the SMS sample, 18 from the SHC sample, and 6 from the STC sample. Although most of the clone sequences did not match the sequences present in the database, individual amplified sequences matched with Glomeromycota (SMS), Fungi incertae sedis (SMS), and Neocallimastigomycota (SHC). Most of the sequences from the amplified taxa represent uncultured fungi. The molecular analysis of variance (AMOVA) indicated that fluctuations observed of haplotypes in the composition may be related to herbicide application. © 2013 Silvana Pompéia Val-Moraes et al

Diversidade de bactérias de solo sob vegetação natural e cultivo de hortaliças

The microorganisms are essential components in the maintenance of the biological and physicochemical balance of the soil. They exert important function including the degradation of residues of plants and animals and the release of nutrients in the alimentary chain. This work had as objective to compare the microbiota of a soil under bush covering (SMS) and other cropped with vegetables (SHC), suppressive or not it Rhizoctonia solani. Total microbial community DNA was extracted of soils, amplification for PCR of the genes 16S rDNA, inserted into pGEM (R)-T cloning vector and sequencing of the genes of the ribosomal RNA. The analysis of the results demonstrated that this methodology was efficient for evaluation of bacteria in ground. In the bush soil suppressive the microorganisms more found belonged to the phyla of the Acidobacterias, Verrucomicrobia and Actinobacterias and in the soil cultivated with vegetables the biggest frequency was of organisms pertaining to the phyla of the Proteobacterias, Firmicutes and Bacteroidetes

Utilização de marcador molecular SCAR na identificação de Fusarium subglutinans, agente causal da malformação da mangueira

O gênero Fusarium é responsável por doenças em diversas plantas economicamente importantes. Entre estas doenças, destaca-se a malformação da mangueira, causada pelo fungo Fusarium subglutinans. O objetivo deste trabalho foi desenvolver oligonucleotídeos iniciadores para reação em cadeia da polimerase (PCR), específicos para o fungo F. subglutinans da mangueira. A amplificação de DNA de oito Fusarium spp. de diferentes hospedeiros, usando o oligonucleotídeo randômico UBC-41 (TTAACCGGGG), produziu um fragmento de aproximadamente 1.300 pb somente para o fungo da mangueira. Tendo em vista que padrões de bandeamento por RAPD não são considerados confiáveis devido à baixa reprodutibilidade dos resultados, o fragmento diferencial foi eluído do gel de agarose, purificado, clonado e seqüenciado. As seqüências nucleotídicas foram utilizadas para identificar e sintetizar quatro pares de oligonucleotídeos específicos, denominados Fs 5, Fs 13, Fs 14 e Fs 15. DNAs de Fusarium spp. de outros hospedeiros (alho, amendoim, cana-de-açúcar, ciclâmen, ervilha, melão e trigo), da planta de mangueira cv. Tommy Atkins sadia e de outros cinco isolados de F. subglutinans de mangueira sintomática, foram submetidos à amplificação com os pares de oligonucleotídeos. Fragmentos amplificados foram visualizados somente para F. subglutinans de mangueira, demonstrando assim a especificidade dos oligonucleotídeos SCAR desenhados.The Fusarium genus is responsible for serious diseases in many economically important crops. Among these diseases it is distinguished the mango flower malformation, caused by the fungus Fusarium subglutinans. The objective of this work was to develop specific oligonucleotide primers for the polymerase chain reaction (PCR) targeting the mango flower malformation by fungus F. subglutinans. The DNA amplification of eight Fusarium spp. collected from different hosts making the use of a random oligonucleotide primer UBC-41 generated a fragment of approximately 1300 pb in size, specifically for the mango flower malformation fungus (Fusarium subglutinans). Since standard RAPD banding patterns are not considered reliable because of their low results of reproducibility, the distinctive fragment was eluted off the agarose gel, purified, cloned and then sequenced. The nucleotide sequences were used to identify and also to synthesize four pairs of specific oligonucleotide named herein Fs 5, Fs 13, Fs 14 and Fs 15. Other Fusarium spp. DNAs sampled from other hosts (garlic, peanut, sugarcane, cyclamen, pea, melon and wheat), from a healthy mango tree cv. Tommy Atkins and other six isolates from symptomatic mango plants were submitted to PCR amplification with these pairs of oligonucleotide. Only fragments from the mango tree fungus Fusarium subglutinans were visualized, showing this way the SCAR oligonucleotide specificity.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

Metagenomic analysis of soil and freshwater from zoo agricultural area with organic fertilization

<div><p>Microbial communities drive biogeochemical cycles in agricultural areas by decomposing organic materials and converting essential nutrients. Organic amendments improve soil quality by increasing the load of essential nutrients and enhancing the productivity. Additionally, fresh water used for irrigation can affect soil quality of agricultural soils, mainly due to the presence of microbial contaminants and pathogens. In this study, we investigated how microbial communities in irrigation water might contribute to the microbial diversity and function of soil. Whole-metagenomic sequencing approaches were used to investigate the taxonomic and the functional profiles of microbial communities present in fresh water used for irrigation, and in soil from a vegetable crop, which received fertilization with organic compost made from animal carcasses. The taxonomic analysis revealed that the most abundant genera were <i>Polynucleobacter</i> (~8% relative abundance) and <i>Bacillus</i> (~10%) in fresh water and soil from the vegetable crop, respectively. Low abundance (0.38%) of cyanobacterial groups were identified. Based on functional gene prediction, denitrification appears to be an important process in the soil community analysed here. Conversely, genes for nitrogen fixation were abundant in freshwater, indicating that the N-fixation plays a crucial role in this particular ecosystem. Moreover, pathogenicity islands, antibiotic resistance and potential virulence related genes were identified in both samples, but no toxigenic genes were detected. This study provides a better understanding of the community structure of an area under strong agricultural activity with regular irrigation and fertilization with an organic compost made from animal carcasses. Additionally, the use of a metagenomic approach to investigate fresh water quality proved to be a relevant method to evaluate its use in an agricultural ecosystem.</p></div

Resistance to antibiotics and toxic compound related functions within the metagenomes from SVG and FW.

<p>The figure displays a heatmap with relative abundance of the features found and highlighted in bold when a significant difference was found between two environments at a p-value < 0.01.</p