Theactive sludge process is one of the most-used techniques for the biodegradation of organic compounds present in effluents from an assortment of wastewaters. This study investigated the bacterial ...community structure of a petroleum industry’s activated sludge and its physical and chemical parameters using high-throughput sequencing. Samples were collected over one year: autumn 2015 (C1), winter 2015 (C2), spring 2015 (C3), and summer 2016 (C4). Total DNA was extracted, and the primers targeting the V4 region of the 16S rRNA gene were used for amplicon sequencing. The majority of the detected microorganisms were considered rare microbiota, presenting a relative abundance below 1% of the total sequences. All of the sequences were classified at the phylum level, and up to 55% of the ASVs (Amplicon Sequence Variants) were associated with known bacterial genera. Proteobacteria was the most abundant phylum in three seasons, while the phylum Armatimonadota dominated in one season. The genus Hyphomicrobium was the most abundant in autumn, winter and summer, and an ASV belonging to the family Fimbriimonadaceae was the most abundant in the spring. Canonical Correspondence Analysis showed that physicochemical parameters of SS, SD and TSS are correlated, as well as ammoniacal nitrogen. Sample C3 presented the highest values of COD, AN and solids (SS, SD and TSS). The highest COD, AN, and solids values are correlated to the high frequency of the phylum Armatimonadota in C3.
Molecular responses to influenza A virus (IAV) infections vary between mammalian species. To identify conserved and species-specific molecular responses, we perform a comparative study of ...transcriptomic data derived from blood cells, primary epithelial cells, and lung tissues collected from IAV-infected humans, ferrets, and mice. The molecular responses in the human host have unique functions such as antigen processing that are not observed in mice or ferrets. Highly conserved gene coexpression modules across the three species are enriched for IAV infection-induced pathways including cell cycle and interferon (IFN) signaling.
is predicted as an IFN-inducible host factor that is up-regulated upon IAV infection in the three species.
is required for antiviral IFN response, potentially modulating IFN signaling via the JAK/STAT/IRF9 pathway. Identification of the common and species-specific molecular signatures, networks, and regulators of IAV infection provides insights into host-defense mechanisms and will facilitate the development of novel therapeutic interventions against IAV infection.
Losses of microbial diversity in degraded ecosystems still have obscure consequences, especially when considering the interaction between arbuscular mycorrhizal fungi (AMF) and soil bacteria. This ...study investigates the effect of decreasing microbial biomass on mycorrhizal attributes and soil quality indicators. The dilution-to-extinction approach was applied in microcosms to search for associations among bacterial diversity, mycorrhizal attributes, and soil quality indicators. The experiment was conducted with four soil treatments (undiluted control 100 = D0, 10−3 = D3, 10−6 = D6, and 10−9 = D9) from a short-term (two years = 2Y) and a long-term (15 years = 15Y) coal mine revegetation area. Microcosms were inoculated with 300 spores of Acaulospora colombiana, Gigaspora albida, and Claroideoglomus etunicatum with millet as the host plant. Results included the total number of AMF spores, mycorrhizal colonization, soil aggregation, glomalin, fluorescein diacetate hydrolysis (FDA), basal soil respiration, microbial biomass, and soil bacterial microbiome. Larger differences were observed between areas than between dilution treatments within the sampling area. Attributes that presented differences in the dilutions compared to D0 2Y samples were mycorrhizal colonization (D0 = 85% and D9 = 43.3%), FDA (D0 = 77.2% and D9 = 55.5%), extractable glomalin-related soil protein (D0 = 0.09 and D9 = 0.11) and bacterial diversity (D0 = 7.3 and D6 = 5.3). D0 15Y samples presented differences in microbial biomass nitrogen (D0: 232.0) and bacterial diversity (D0: 7.9, D9: 5.6) compared to the dilutions. Bacterial microbiome present in the D0 samples formed distinct clusters as to other samples and correlated with soil aggregation and basal respiration attributes. Results suggest that AMF inoculation and dilution-to-extinction did not affect soil quality indicators preeminently, but the bacterial community is affected and can influence the process of environmental revegetation. A long-term revegetation period is substantial to improve quality indicators and establish the diversity of microorganisms and consequently revegetation in areas impacted by coal mining.
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•Inoculation with AMF did not affect broadly the soil quality indicators.•Soil quality indicators were not affected by the dilution-for-extinction approach.•Bacterial OTUs were correlated with AMF spore number and mycorrhizal colonization.•Long-term revegetation improves soil quality indicators and bacterial diversity.•Richness and diversity of microorganisms increased with revegetation time.
Periphyton communities in freshwater systems play an essential role in biogeochemical processes, but knowledge of their structure and dynamics lags far behind other environments. We used eDNA ...metabarcoding of 16S and 18S rRNA markers to investigate the formation and establishment of a periphytic community, in addition to a morphology-based approach for peritrich ciliate determinations, its most abundant group. We sampled two nearby sites within a large Neotropical lake at four time points, aiming to assess whether periphyton establishment can be replicated on this local scale. Producers and denitrifiers were abundant in the community, illustrating the relevant role of biofilms in freshwater nutrient recycling. Among microeukaryotes, peritrich ciliates dominated the community, with genera
Epistylis
and
Vorticella
being the most abundant and showing a clear succession at both sites. Other ciliates were morphologically identified and, in some cases, their occurrence was strongly related to bacterial abundance. The structure of both prokaryotic and eukaryotic components of periphyton was not different, while the turnover dynamics differed between the two sites, in spite of their adjacent locations and similar abiotic properties. This indicates that the establishment of these communities can vary even on a local scale within a lake ecosystem.
The Pampa biome is a rich and fertile area of grassland in Brazil, South America, which has been considered ecologically important owing to its enriched biodiversity. However, this landscape has ...undergone serious fragmentation, with half of its original vegetation being removed due to continuous agricultural activities and its widespread use for livestock production. The excessive cattle farming has generated a significant grazing load on the area, which is reflected in the diminishing soil microbial diversity. With an aim to study the impact of increasing grazing load on microbial diversity of soil of pampas, the present study compared the bacterial communities of grassland-controlled soils of the Pampa biome under different grazing pressures: high (HG), moderate (MG), low (LG), and a control area (CG) in a long-term experiment using high-throughput sequencing. The soil microbial community was not significantly affected by the presence or absence of bacterial taxonomic groups; however, significant changes were detected in each different grazing pasture sample. This observation was especially notable in MG pressure that, when compared to other grazing pressures and control grazing (CG), was found to be associated with an increased prevalence of some specific groups of microorganisms. These include those belonging to the following families: Nitrospirae, DA052, Syntrophobacteraceae, Methylocystaceae, Syntrophaceae, Mycobacteriaceae, and Koribacteraceae. Moreover, the grazing pressure disturbance created by MG was believed to enhance the diversity of a bacterial community, thereby maintaining the stability of soil and indicating that stressed bio-systems might be more stable than those not experiencing stress. Thus, the results of the current study imply that quantitative and qualitative changes in the composition of the soil bacterial community could serve as an important indicator of both short- and long-term changes in soil health.
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•Effect of different grazing pressures loads on the soil bacterial community assessed.•Statistically significant changes were observed in different grazing pastures samples.•Moderate grazing pressure differed in relation to the other grazing pressures.•Moderate grazing pressure disturbance adds diversity to a bacterial community - Intermediate Disturbance Hypothesis.
The scope of this study was to establish the genomic diversity existing between
Escherichia coli isolates obtained from water samples retrieved from Arroio Feijó, southern Brazil, using the ...repetitive extragenic palindromic elements-polymerase chain reaction protocol. Ninety-eight different isolates were identified from samples obtained from five sites. Eleven different clusters presenting identical fingerprinting patterns were detected. The dendrogram contained 28 clusters for 70% similarity cut-off. These clusters enabled the observation of 16 single patterns. The results enabled the observation of genetic diversity between isolates obtained in one sampling site, and those from other sampling sites. Site 5 showed the highest diversity (Shannon–Weaver,
H′=2.92) and site 3 exhibited the lowest diversity degree (Shannon–Weaver,
H′=2.16).
•We evaluated five commercial rapid tests for potential use in the Brazilian national HIV testing algorithm.•We compared rapid tests results with those obtained by reference tests.•Performance ...against seroconversion and performance panels was accessed.•Three out of five HIV rapid tests performed as well as the reference assays and fulfilled the requirements for use in the national algorithm.
Since 2005, the Department of Sexually Transmitted Diseases (STDs), Acquired Immunodeficiency Syndrome (AIDS) and Viral Hepatitis under the Health Surveillance Secretariat in Brazil's Ministry of Health has approved a testing algorithm for using rapid human immunodeficiency virus (HIV) tests in the country. Given the constant emergence of new rapid HIV tests in the market, it is necessary to maintain an evaluation program for them. Conscious of this need, this multicenter study was conducted to evaluate five commercially available rapid HIV tests used to detect anti-HIV antibodies in Brazil.
The five commercial rapid tests under assessment were the VIKIA HIV-1/2 (bioMérieux, Rio de Janeiro, Brazil), the Rapid Check HIV 1 & 2 (Center of Infectious Diseases, Federal University of Espírito Santo, Vitória, Brazil), the HIV-1/2 3.0 Strip Test Bioeasy (S.D., Kyonggi-do, South Korea), the Labtest HIV (Labtest Diagnóstica, Lagoa Santa, Brazil) and the HIV-1/2 Rapid Test Bio-Manguinhos (Oswaldo Cruz Foundation, Rio de Janeiro, Brazil). A total of 972 whole-blood samples were collected from HIV-infected patients, pregnant women and individuals seeking voluntary counselling and testing who were recruited from five centers in different regions of the country. Informed consent was obtained from the study participants. The results were compared with those obtained using the HIV algorithm used currently in Brazil, which includes two enzyme immunoassays and one Western blot test. The operational performance of each assay was also compared to the defined criteria.
A total of 972 samples were tested using reference assays, and the results indicated 143 (14.7%) reactive samples and 829 (85.3%) nonreactive samples. Sensitivity values ranged from 99.3 to 100%, and specificity was 100% for all five rapid tests. All of the rapid tests performed well, were easy to perform and yielded high scores in the operational performance analysis. Three tests, however, fulfilled all of the prerequisites established previously by the Department of STDs, AIDS and Viral Hepatitis: the HIV-1/2 3.0 Strip Test Bioeasy, the Rapid Check HIV 1 & 2 and the VIKIA HIV-1/2.
Three of the five tests evaluated (the HIV-1/2 3.0 Strip Test Bioeasy, the Rapid Check HIV 1 and 2 and the VIKIA HIV-1/2) performed as well as the reference assays and fulfilled the requirements for use in the Brazilian national algorithm.
Glycerol is a by-product generated in the biodiesel industry and can be converted by biological processes into products such as hydrogen, alcohols and acids. This study aimed at comparing two sources ...of inoculum in dark fermentation using raw glycerol and at identifying the microorganisms present by high-performance sequencing. Granular sludge obtained from a vegetable oil industry (VOI) and anaerobic sludge from a wine industry (WI) were evaluated in batch reactors with raw glycerol. The highest hydrogen yield was obtained for VOI (1.12 mol H
2
/ mol glycerol
consumed
). The WI was more efficient in producing soluble metabolites, with 6.2 g / L of 1,3 – propanediol, ethanol (2.5 g / L) and acids (122 mg / g glycerol
consumed
). Both assays consumed more than 60% of the glycerol. A significant variation in microbial diversity was observed between the beginning and the end of the fermentation. The microbial community showed a predominance of Firmicutes and the
Clostridiaceae
and
Peptostreptococcaceae
families in different abundances among the inocula, which could lead to an increase in hydrogen production or a higher concentration of metabolites.
Clostridium bifermentans
was the only species isolated, showing a yield of H
2
(0.135 mol H
2
/ mol glycerol
consumed
) and the main metabolite produced was ethanol (670 mg / L). These results showed that two different kinds of seed sludge can lead to different metabolic profiles from the same substrate, highlighting the importance of choosing the inoculum and, consequently, that the knowledge regarding microorganisms can direct the process towards products of industrial interest and contribute to the generation of sustainable energy.
Graphical abstract
Human Immunodeficiency Virus Type 1 and 2 antibodies detection was performed in 457 dried whole blood spots samples (S&S 903). Q-Preven HIV 1+2 was the screening test used. The results were compared ...with the gold standard serum tests by ELISA (Cobas Core e Axsym HIV1/2 gO) and immunofluorescence was the definitive confirmatory test. The samples were obtained from the Hospital Nossa Senhora da Conceição in Porto Alegre, RS - Brazil, through whole blood transfer to filter paper card and sent to Caxias do Sul, RS-Brazil where the tests were performed. The dried whole blood spot stability was evaluated with two different panels. The first one was composed of five negative and five positive samples stored at room temperature, 4 degrees C, -20 degrees C and -70 degrees C, while the second was composed of two negative and three positive samples stored at 37 degrees C (humidity <50%). Each sample was screened every week for six weeks. These measurement results didn't show variation during the study period. The detected sensibility was 100%, specificity was 99.6%, the positive predictive value was 99.5% and negative predictive values were 100%. The results demonstrated high performance characteristics, opening a new perspective of dried whole blood spot utilization in HIV screening diagnosis.
The scope of this study was to establish the genomic diversity existing between Escherichia coli isolates obtained from water samples retrieved from Arroio Feijó, southern Brazil, using the ...repetitive extragenic palindromic elements-polymerase chain reaction protocol. Ninety-eight different isolates were identified from samples obtained from five sites. Eleven different clusters presenting identical fingerprinting patterns were detected. The dendrogram contained 28 clusters for 70% similarity cut-off. These clusters enabled the observation of 16 single patterns. The results enabled the observation of genetic diversity between isolates obtained in one sampling site, and those from other sampling sites. Site 5 showed the highest diversity (Shannon–Weaver, H′=2.92) and site 3 exhibited the lowest diversity degree (Shannon–Weaver, H′=2.16).
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