Water reuse is increasingly pursued to alleviate global water scarcity. However, wastewater treatment process does not achieve full removal of biological contaminants from wastewater, and hence some microorganisms and their genetic elements can be disseminated into the reclaimed water distribution systems (RWDS). A systematic identification and characterization of these biological contaminants is required. However, a broad characterization for large-scale data are limited. In this study, reclaimed water samples are investigated through metagenomic analyses to assess their bacterial and functional (metal resistance genes (MRGs); virulence factors (VFs)) communities at the entry and exit points of the RWDS. Furthermore, water quality data are investigated to evaluate the potential relationship with these metagenomic annotations. This study found that the organic carbon content was likely relevant to the increase of bacteria and functional genes in RWDS. It was also found that the variation of functional genes was not associated with their host, inferring the role of horizontal gene transfers or promiscuity of hosts for various functional genes. Furthermore, Pseudomonas was identified in one RWDS with significant increase at both bacterial and functional levels.

The Operable Unit 5 (OU 5) area of Hill Air Force Base currently has two trichloroethene-contaminated groundwater plumes underneath residential areas in Sunset and Clinton, Utah. Bioremediation by biological reductive dechlorination can be an important mechanism for the removal of chlorinated compounds from the plumes. The presence of suitable bacteria to carry on reductive dechlorination is the key in the bioremediation process. The goal of this study was to determine the distribution and population density of the 16S rRNA genes of Bacteria, Dehalococcoides ethenogenes, Desulfuromonas michiganensis, Geobacter spp and Rhodoferax ferrireducens-like bacteria, as well as the functional genes trichloroethene reductive dehalogenase (tceA) and vinyl chloride reductase gene (vcrA). This study also evaluated the influence of the physical-chemical properties of the OU 5 aquifer material on the observed bacterial distribution. Twenty OU 5 soil cores were obtained from a 14-ha area that included a trichloroethene (TCE) plume. DNA was extracted from each core. Molecular analysis with qRT-PCR was used to quantify the densities of the mentioned 16S rRNA and functional genes. Separately, total arsenic and iron in the II and II+III oxidation states were extracted by two methods (HCl and hydroxylamine HCl in HCl) in each core. Concentrations of TCE, cis-dichloroethene (cis-DCE), vinyl chloride (VC) and ethane in well water were included. Dehalococcoides population density was low and its distribution was uneven with densities lower than 3.2x104 copies/g (detection limit of 2.5x103). D. michiganensis distribution was not uniform but was clustered near the TCE-source area with densities of 7.9x103-1x105 copies/g (detection limit of 6.3x103). Geobacter spp. distribution was uneven but broader, with densities of 4x103-1.6x106 copies/g (detection limit of 3.2x103). The vcrA gene distribution was relatively uniform and broad. Densities were the lowest measured (detection limit of 63 copies/g). TceA was measured in two cores with densities close to detection limit of 1.6x103 copies/g. Rhodoferax ferrireducens-like bacteria had a broader distribution with the highest densities of 1.6x106-1.3x108 copies/g (detection limit of 7.9x103). Total Bacteria were measured in all cores with densities 3.2x104-3.2x106 copies/g (detection limit of 1x103). Three multivariate statistical methods were used to determine the effect of physical-chemical properties on the target gene distributions. Cluster and discriminant analysis selected five properties (pH, sand and silt content, NO3--N and NH4+-N) as the most discriminating factors among thirty-one physical-chemical properties. However, no effect in the bacterial distribution was observed. The tree classification method identified nine variables that described higher or lower densities of the target genes. Variables such as Bacteria, Fe(II+III) (by hydroxylamine HCl in HCl), organic matter and cis-DCE were selected by the method.. All methods agreed on the selection of pH and sand content as the physical/chemical factors most influencing in the bacterial distribution. Based on the findings of low densities of dechlorinating bacteria and dechlorinating-associated functional genes, low available carbon donor and sandy mineral composition, the partial TCE-dechlorination at this site can be ascribed to the nature of the site and incomplete set of required factors for complete reductive dechlorination.

O estudo buscou avaliar a diversidade de genes funcionais microbianos em solos da Amazônia, submetidos a diferentes formas de uso, empregando o Geochip. Este é um microarranjo com sondas para genes relacionados a diversos processos funcionais, incluindo ciclos biogeoquímicos. Foram avaliados solos de floresta primária, pastagens e floresta secundária. A conversão de floresta para pastagem causou alteração da estrutura funcional da comunidade e redução da diversidade de genes, e o crescimento da floresta secundária restabeleceu a estrutura e diversidade original. Fatores físico-químicos do solo correlacionaram significativamente com a estrutura da comunidade, indicando importância dos mesmos para o perfil observado. A análise de associação de genes aos ambientes revelou diferentes respostas, e um maior número de genes associados às duas florestas. Os resultados mostraram que o uso do solo para pastagem causa impactos sobre a diversidade e a abundância de genes de importância ambiental e um restabelecimento do potencial funcional na floresta secundária. / The functional gene diversity of Amazon soils under different land use systems was accessed by Geochip, which is a microarray targeting genes related to a variety of processes, including biogeochemical cycles. Soils from a primary forest, three pastures and a secondary forest were analyzed. The forest to pasture conversion led to functional structure changes and functional gene diversity loss, whereas the secondary forest growth promoted the recovery of a profile found in primary forest. Correlation of soil physical-chemical properties with the community structure was found, suggesting that soil characteristics may be driving the biological profile observed. The association index showed a range of responses and a greater number of genes associated to both forests. The results revealed an impact of pasture establishment on the diversity and abundance of environmentally important genes, and a recovery of the functional potential with secondary forest growth.

Existe uma preocupação mundial com as mudanças climáticas causadas pelo aumento da concentração de gases do efeito estufa (GEE) e consequente acréscimo na temperatura média da superfície terrestre. A queima de combustíveis fósseis é a maior causadora do aquecimento global e responsável por danos à saúde humana. É notável o esforço global em diversificar a matriz mundial de combustíveis líquidos, priorizando a substituição de fontes fósseis por renováveis. Tal substituição reforça a necessidade de avaliações de todas as emissões de GEE na cadeia produtiva da cana-de-açúcar. O Brasil é o maior produtor de etanol proveniente de cana-de-açúcar. Um importante co-produto deste processo produtivo é a vinhaça, sendo produzida em elevadas quantidades e constituída por uma expressiva carga orgânica. Esta é comumente aplicada ao solo por fertirrigação. Apesar de atuar beneficamente no solo, pouco se sabe sobre a capacidade deste co-produto de aumentar as emissões de GEE no solo. Assim, o objetivo foi avaliar o efeito da aplicação da vinhaça nas emissões de N2O e CH4 e na comunidade de bactérias desnitrificantes e metanogênicas do solo. As amostragens de GEE e solo foram em áreas de cana sem queima a partir da aplicação de doses vinhaça (0, 150, 300 e 450 m3 ha-1). O delineamento experimental realizado foi em cinco blocos casualizados, totalizando 25 câmaras de coleta de gases do efeito estufa. Amostras de solo foram coletadas em quatro períodos de amostragem após aplicação de vinhaça (0, 7, 15 e 30 dias), em dois anos consecutivos. Foram analisados os GEE, N2O e CH4, além da abundancia de genes por meio da técnica de qPCR. A fertirrigação via aplicação de vinhaça no solo, nos dois anos, proporcionou aumento nas emissões de N-N2O, principalmente nos primeiros dias após a aplicação. Contudo os fluxos de C-CH4 oscilaram indicando a capacidade do solo de servir ora como fonte ora como sumidouro deste GEE. Os fatores de emissão obtidos para aplicação de N na forma de vinhaça, dose de 300 m3 ha-1, foram de 0,08% para o primeiro ano e 0,07% para o segundo ano. A partir da técnica de qPCR, a abundância dos genes indicou que a introdução deste resíduo ao solo pode aumentar significativamente o total de bactérias no solo e a atividade do gene nosZ, contudo o mesmo não ocorre com o potencial de desnitrificação biológica (gene nirK) e nem com o gene mcrA (redução de CH4). Os resultados demonstram que a aplicação da vinhaça no solo influencia as emissões de GEE, assim como a comunidade microbiana do solo / There is a global concern with climate change caused by increased concentration of greenhouse gases (GHG) and consequent increase in the average temperature of the Earth surface. Fossil fuels burning is the major cause of global warming and it is responsible for damages to human health. Remarkable global efforts in diversifying liquid fuels have been attempted, giving priority to the replacement of fossil fuels to renewables. Such substitution reinforces the need of an evaluation of all GHG emissions in the production chain of sugarcane. Brazil is the largest producer of ethanol with source from sugarcane. An important co-product of the production process is vinasse, which is being produced in large quantities comprising a significant organic load. This is commonly applied over the ground by fertigation. Despite being good for the soil, little is known about the ability of this co-product of increasing GHG emissions. This work aimed to evaluate the effect of the application of vinasse in the emissions of N2O and CH4 and in the soil community of denitrifying and methanogenic bacteria. Sampling of GHG and soil were performed in areas of sugarcane without burning with the application of different vinasse doses (0, 150, 300 and 450 m3 ha-1). The experiment was conducted in five blocks, totaling 25 collection chambers of greenhouse gases. Soil samples were collected in four sampling periods after application of vinasse (0, 7, 15 and 30 days), in two consecutive years. We analyzed the GHG, N2O and CH4, and the abundance of genes by qPCR technique. The fertigation via vinasse application on the ground in two years provided an increase in emissions of N-N2O, especially in the first couple of days after application. However the flow of C-CH4 was variable indicating the ability of the soil to serve either as source or as sink of this GHG. The emission factor obtained for N application in the form of vinasse dose of 300 m3 ha-1 was 0.08% for the first year and 0.07% for the second year. By qPCR technique, the abundance of the genes indicated that the use of this residue to the soil can significantly increase the amount of bacteria in the soil and nosZ gene activity. However it does not occur with the potential for biological denitrification (nirK gene) or with the gene mcrA (reduction of CH4). These results demonstrate that the application of vinasse in the soil influences GHG emissions as well as the soil microbial community

Metastasis is one of the critical hallmarks of malignancy tumor and the principal cause of death in patients with cancer. Cell migration is the basic and essential step in cancer metastasis process. To systematically investigate functional genes regulating cell migration and cancer metastasis on large scale, we developed a novel on-chip method, SAMcell (self-assembled cell microarray). This method was demonstrated to be particularly suitable for loss-of-function high-throughput screening because of its unique advantages. The first application of SAMcell was to screen human genome miRNAs, considering that more and more miRNAs had been proved to govern cancer metastasis. We found that over 20 % of miRNAs have migratory regulation activity in diverse cell types, indicating a general involvement of miRNAs in migratory regulation. Through triple-round screenings, we discovered miR-23b, which is down-regulated in human colon cancer samples, potently mediates the multiple steps of metastasis, including cell motility, cell growth and cell survival. In parallel, the second application of SAMcell was to screen human genome kinase genes, considering that more and more kinase genes had become successful diagnostic marker or drug targets. We found over 11% migratory kinase genes, suggesting the important role of kinase group in metastasis regulation. Through both functional screening and bioinformatics analysis, we discovered and validated 6 prospective metastasis-related kinase genes, which can be new potential targets in cancer therapy. These findings allow the understanding of regulation mechanism in human cancer progression, especially metastasis and provide the new insight into the biological and therapeutical importance of miRNAs or kinases in cancer.

Existe uma preocupação mundial com as mudanças climáticas causadas pelo aumento da concentração de gases do efeito estufa (GEE) e consequente acréscimo na temperatura média da superfície terrestre. A queima de combustíveis fósseis é a maior causadora do aquecimento global e responsável por danos à saúde humana. É notável o esforço global em diversificar a matriz mundial de combustíveis líquidos, priorizando a substituição de fontes fósseis por renováveis. Tal substituição reforça a necessidade de avaliações de todas as emissões de GEE na cadeia produtiva da cana-de-açúcar. O Brasil é o maior produtor de etanol proveniente de cana-de-açúcar. Um importante co-produto deste processo produtivo é a vinhaça, sendo produzida em elevadas quantidades e constituída por uma expressiva carga orgânica. Esta é comumente aplicada ao solo por fertirrigação. Apesar de atuar beneficamente no solo, pouco se sabe sobre a capacidade deste co-produto de aumentar as emissões de GEE no solo. Assim, o objetivo foi avaliar o efeito da aplicação da vinhaça nas emissões de N2O e CH4 e na comunidade de bactérias desnitrificantes e metanogênicas do solo. As amostragens de GEE e solo foram em áreas de cana sem queima a partir da aplicação de doses vinhaça (0, 150, 300 e 450 m3 ha-1). O delineamento experimental realizado foi em cinco blocos casualizados, totalizando 25 câmaras de coleta de gases do efeito estufa. Amostras de solo foram coletadas em quatro períodos de amostragem após aplicação de vinhaça (0, 7, 15 e 30 dias), em dois anos consecutivos. Foram analisados os GEE, N2O e CH4, além da abundancia de genes por meio da técnica de qPCR. A fertirrigação via aplicação de vinhaça no solo, nos dois anos, proporcionou aumento nas emissões de N-N2O, principalmente nos primeiros dias após a aplicação. Contudo os fluxos de C-CH4 oscilaram indicando a capacidade do solo de servir ora como fonte ora como sumidouro deste GEE. Os fatores de emissão obtidos para aplicação de N na forma de vinhaça, dose de 300 m3 ha-1, foram de 0,08% para o primeiro ano e 0,07% para o segundo ano. A partir da técnica de qPCR, a abundância dos genes indicou que a introdução deste resíduo ao solo pode aumentar significativamente o total de bactérias no solo e a atividade do gene nosZ, contudo o mesmo não ocorre com o potencial de desnitrificação biológica (gene nirK) e nem com o gene mcrA (redução de CH4). Os resultados demonstram que a aplicação da vinhaça no solo influencia as emissões de GEE, assim como a comunidade microbiana do solo / There is a global concern with climate change caused by increased concentration of greenhouse gases (GHG) and consequent increase in the average temperature of the Earth surface. Fossil fuels burning is the major cause of global warming and it is responsible for damages to human health. Remarkable global efforts in diversifying liquid fuels have been attempted, giving priority to the replacement of fossil fuels to renewables. Such substitution reinforces the need of an evaluation of all GHG emissions in the production chain of sugarcane. Brazil is the largest producer of ethanol with source from sugarcane. An important co-product of the production process is vinasse, which is being produced in large quantities comprising a significant organic load. This is commonly applied over the ground by fertigation. Despite being good for the soil, little is known about the ability of this co-product of increasing GHG emissions. This work aimed to evaluate the effect of the application of vinasse in the emissions of N2O and CH4 and in the soil community of denitrifying and methanogenic bacteria. Sampling of GHG and soil were performed in areas of sugarcane without burning with the application of different vinasse doses (0, 150, 300 and 450 m3 ha-1). The experiment was conducted in five blocks, totaling 25 collection chambers of greenhouse gases. Soil samples were collected in four sampling periods after application of vinasse (0, 7, 15 and 30 days), in two consecutive years. We analyzed the GHG, N2O and CH4, and the abundance of genes by qPCR technique. The fertigation via vinasse application on the ground in two years provided an increase in emissions of N-N2O, especially in the first couple of days after application. However the flow of C-CH4 was variable indicating the ability of the soil to serve either as source or as sink of this GHG. The emission factor obtained for N application in the form of vinasse dose of 300 m3 ha-1 was 0.08% for the first year and 0.07% for the second year. By qPCR technique, the abundance of the genes indicated that the use of this residue to the soil can significantly increase the amount of bacteria in the soil and nosZ gene activity. However it does not occur with the potential for biological denitrification (nirK gene) or with the gene mcrA (reduction of CH4). These results demonstrate that the application of vinasse in the soil influences GHG emissions as well as the soil microbial community

O estudo buscou avaliar a diversidade de genes funcionais microbianos em solos da Amazônia, submetidos a diferentes formas de uso, empregando o Geochip. Este é um microarranjo com sondas para genes relacionados a diversos processos funcionais, incluindo ciclos biogeoquímicos. Foram avaliados solos de floresta primária, pastagens e floresta secundária. A conversão de floresta para pastagem causou alteração da estrutura funcional da comunidade e redução da diversidade de genes, e o crescimento da floresta secundária restabeleceu a estrutura e diversidade original. Fatores físico-químicos do solo correlacionaram significativamente com a estrutura da comunidade, indicando importância dos mesmos para o perfil observado. A análise de associação de genes aos ambientes revelou diferentes respostas, e um maior número de genes associados às duas florestas. Os resultados mostraram que o uso do solo para pastagem causa impactos sobre a diversidade e a abundância de genes de importância ambiental e um restabelecimento do potencial funcional na floresta secundária. / The functional gene diversity of Amazon soils under different land use systems was accessed by Geochip, which is a microarray targeting genes related to a variety of processes, including biogeochemical cycles. Soils from a primary forest, three pastures and a secondary forest were analyzed. The forest to pasture conversion led to functional structure changes and functional gene diversity loss, whereas the secondary forest growth promoted the recovery of a profile found in primary forest. Correlation of soil physical-chemical properties with the community structure was found, suggesting that soil characteristics may be driving the biological profile observed. The association index showed a range of responses and a greater number of genes associated to both forests. The results revealed an impact of pasture establishment on the diversity and abundance of environmentally important genes, and a recovery of the functional potential with secondary forest growth.

Decomposition of soil organic matter by microbial processes results in carbon sequestration within soils and/or carbon loss via atmospheric emission of carbon dioxide and methane. Natural as well as anthropogenic factors have been documented to impact soil microbial diversity and the associated biogeochemical functions. The soil microbial communities co-inhabiting Miami-Dade County soils, Florida are under threat because of the ongoing restoration efforts in the adjoining Florida Everglades Parks, predicted climatic changes such as sea-level rise and high rainfall, as well as urbanization. Therefore, an improved understanding of the current microbial functional communities is essential to better assess the impact of soil communities when anthropogenic or climatic disturbances occur. The objectives of the current study were to characterize the biodiversity and distribution of: a) cellulose degrading microbial community, and b) methanogenic guilds responsible for producing the gas methane, across four different Miami-Dade County, Florida soil types using the high throughput technique of GeoChip 5.0 functional microarray. In addition, the influence of vegetation cover, organic content, soil moisture content, pH, and soil texture in shaping the soil functional microbial community was also investigated. The function of cellulose degradation was distributed across wide range of taxonomic lineages with the majority belonging to the bacterial groups of Actinobacteria, Firmicutes, Alphaproteobacteria, and Gammaproteobacteria, whereas Ascomycota and Basidiomycota were the only detected fungal phyla. The cellulolytic bacterial community correlated more with the vegetation cover while fungal groups showed influence of moisture and organic content as well as percent silt. Six out of the seven methanogenic orders, with the greatest numbers found in the Methanomicrobiales, Methanosarcinales, and Methanomassiliicoccales, were identified across all four soil types of Miami-Dade. The abundance of the mcrA gene sequences was significantly greater with respect to soil moisture content. Additionally, the recently classified order Methanomassiliicoccales was identified across all four soils, including soils with lower moisture content not thought to provide ideal redox conditions to support methanogens. The greater number of correlation network interactions amongst the methanogenic guilds in the Florida Everglades wetlands versus the urbanized Miami-Dade County soils depicted the impact of the historical drainage of the Florida Everglades on the methanogenic community. Overall, the current study characterized the biodiversity of cellulolytic and methanogenic organisms across dry and saturated soils of Miami-Dade County and demonstrated that microbial guilds were functionally redundant and were influenced to some extent by the soil abiotic factors. Also, results from network analyses provide a platform to assess the future impacts of disturbances on the microbial community.