Environmental surface surveillance during a COVID-19 outbreak in a school community: implications for controlling indirect transmission.

Environmental surface surveillance is a valuable tool for detecting and controlling infectious diseases. During the COVID-19 pandemic, concerns have been raised regarding the potential for indirect transmission of SARS-CoV-2 via contaminated surfaces. However, few studies have evaluated environmental contamination in non-clinical settings during outbreaks. We conducted a study in a school community during a major outbreak, collecting 35 surface samples from high-traffic areas and testing them for SARS-CoV-2 RNA using RT-qPCR. Our results showed that 31.4% of samples were positive, including high-touch surfaces such as drinking fountains and washbasins. These findings emphasize the importance of environmental monitoring to identify and address specific areas for attention, and implementing such strategies can help prevent the indirect transmission of COVID-19 in various settings.

Decoding the chromosome-scale genome of the nutrient-rich Agaricus subrufescens: a resource for fungal biology and biotechnology.

Agaricus subrufescens, also known as the "sun mushroom," has significant nutritional and medicinal value. However, its short shelf life due to the browning process results in post-harvest losses unless it's quickly dehydrated. This restricts its availability to consumers in the form of capsules. A genome sequence of A. subrufescens may lead to new cultivation alternatives or the application of gene editing strategies to delay the browning process. We assembled a chromosome-scale genome using a hybrid approach combining Illumina and Nanopore sequencing. The genome was assembled into 13 chromosomes and 31 unplaced scaffolds, totaling 44.5 Mb with 96.5% completeness and 47.24% GC content. 14,332 protein-coding genes were identified, with 64.6% of the genome covered by genes and 23.41% transposable elements. The mitogenome was circularized and encoded fourteen typical mitochondrial genes. Four polyphenol oxidase (PPO) genes and the Mating-type locus were identified. Phylogenomic analysis supports the placement of A. subrufescens in the Agaricomycetes clade. This is the first available genome sequence of a strain of the "sun mushroom." Results are available through a Genome Browser (https://plantgenomics.ncc.unesp.br/gen.php?id=Asub) and can support further fungal biological and genomic studies.

The impact of early-life exposure to three agrochemicals on survival, behavior, and gut microbiota of stingless bees (Partamona helleri).

Over the last few decades, agrochemicals have been partially associated with a global reduction in bees' population. Toxicological assessment is therefore crucial for understanding the overall agrochemical risks to stingless bees. Therefore, the lethal and sublethal effects of agrochemicals commonly used in crops (copper sulfate, glyphosate, and spinosad) on the behavior and gut microbiota of the stingless bee, Partamona helleri, were assessed using chronic exposure during the larval stage. When used at the field-recommended rates, both copper sulfate (200 µg of active ingredient/bee; a.i µg bee-1) and spinosad (8.16 a.i µg bee-1) caused a decrease in bee survival, while glyphosate (148 a.i µg bee-1) did not show any significant effects. No significant adverse effects on bee development were observed in any treatment with CuSO4 or glyphosate, but spinosad (0.08 or 0.03 a.i µg bee -1) increased the number of deformed bees and reduced their body mass. Agrochemicals changed the behavior of bees and composition of the gut microbiota of adult bees, and metals such as copper accumulated in the bees' bodies. The response of bees to agrochemicals depends on the class or dose of the ingested compound. In vitro rearing of stingless bees' larvae is a useful tool to elucidate the sublethal effects of agrochemicals.

Methanogenic communities and methane emissions from enrichments of Brazilian Amazonia soils under land-use change.

Amazonian forest conversion into agricultural and livestock areas is considered one of the activities that contribute most to the emission of greenhouse gases, including methane. Biogenic methane production is mainly performed by methanogenic Archaea, which underscores the importance of understanding the drivers shaping microbial communities involved in the methane cycling and changes in methane metabolism. Here, we aimed to investigate the composition and structure of bacterial and archaeal communities in tropical soils in response to land-use changes, emphasizing the methanogenic communities. We collected soil samples from primary forest, pasture, and secondary forest of the Amazonian region and used a strategy based on the enrichment of the methanogenic community with three different methanogenic substrates followed by measurements of methane emission, quantification of mcrA gene copies by qPCR, and total 16 S rRNA gene sequencing (metataxonomics). We observed variations in the structure of bacterial and archaeal communities of soils under different uses. The richness of methanogenic communities was higher in pasture than forest soils and this richness remained during the incubation period, and as a consequence, the enrichment induced earlier methane emission in pastures-derived samples. Furthermore, pastures enrichments exhibited methanogenic archaea networks more complex than primary and secondary forests. In conclusion, pastures harbor a richer and more responsive methanogenic community than forest samples, suggesting that conversion of forest areas to pasture may boost methane emission.

Dominant microbial communities and biochemical profile of pulped natural fermented coffees growing in different altitudes.

Altitude changes the coffee fruits and beans composition before and after harvesting. We aimed to evaluate the effect of altitude on the microbial community structure associated with pulped coffee fruits under self-induced anaerobic fermentation (SIAF) and their acids, volatiles, and antioxidants biochemical profiles. The most abundant bacterial genera were Gluconobacter (800 m), Weissella (1,000 m), and Leclercia (1,200 and 1,400 m). Yeasts dominated the pulped natural fermentations within the fungal species, containing high abundances of Cystofilobasidium infirmominiatum, Wickerhamomyces anomalus, and Meyerozyma caribbica. Citric, alcohols, and caffeine were the most dominant compounds in SIAF among acids, volatiles, chemical groups, and antioxidants. High altitude coffees favor alcohols, aldehydes, and esters groups, while low altitude coffees favor phenols.

Ecological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood.

The bacterial genus Sodalis is represented by insect endosymbionts as well as free-living species. While the former have been studied frequently, the distribution of the latter is not yet clear. Here, we present a description of a free-living strain, Sodalis ligni sp. nov., originating from decomposing deadwood. The favored occurrence of S. ligni in deadwood is confirmed by both 16S rRNA gene distribution and metagenome data. Pangenome analysis of available Sodalis genomes shows at least three groups within the Sodalis genus: deadwood-associated strains, tsetse fly endosymbionts and endosymbionts of other insects. This differentiation is consistent in terms of the gene frequency level, genome similarity and carbohydrate-active enzyme composition of the genomes. Deadwood-associated strains contain genes for active decomposition of biopolymers of plant and fungal origin and can utilize more diverse carbon sources than their symbiotic relatives. Deadwood-associated strains, but not other Sodalis strains, have the genetic potential to fix N2, and the corresponding genes are expressed in deadwood. Nitrogenase genes are located within the genomes of Sodalis, including S. ligni, at multiple loci represented by more gene variants. We show decomposing wood to be a previously undescribed habitat of the genus Sodalis that appears to show striking ecological divergence.

The Altitude of Coffee Cultivation Causes Shifts in the Microbial Community Assembly and Biochemical Compounds in Natural Induced Anaerobic Fermentations.

Coffee harvested in the Caparaó region (Minas Gerais, Brazil) is associated with high-quality coffee beans resulting in high-quality beverages. We characterize, microbiologically and chemically, fermented coffees from different altitudes through target NGS, chromatography, and conventional chemical assays. The genera Gluconobacter and Weissella were dominant in coffee's fruits from altitudes 800 and 1,000 m. Among the Eukaryotic community, yeasts were the most dominant in all altitudes. The most dominant fungal genus was Cystofilobasidium, which inhabits cold environments and resists low temperatures. The content of acetic acid was higher at altitudes 1,200 and 1,400 m. Lactic acid and the genus Leuconostoc (Pearson: 0.93) were positively correlated. The relative concentration of volatile alcohols, especially of 2-heptanol, was high at all altitudes. Bacteria population was higher in coffees from 800 m, while at 1,000 m, fungi richness was favored. The altitude is an important variable that caused shifts in the microbial community and biochemical compounds content, even in coffees belonging to the same variety and cultivated in the same region under SIAF (self-induced anaerobic fermentation) conditions. Coffee from lower altitudes has higher volatile alcohols content, while high altitudes have esters, aldehydes, and total phenolics contents.

Genomic analysis reveals the potential for hydrocarbon degradation of Rhodopirellula sp. MGV isolated from a polluted Brazilian mangrove.

Planctomycetes are bacteria found in several environments, such as mangroves. In the coastline of the State of Sao Paulo (Brazilian Southeast), mangroves occur in different stages of environmental contamination, promoted by the proximity to the city and industrial activities. One of these mangroves (located in the city of Bertioga) is characterized by the high impact due to past petroleum and ongoing urban contamination. We isolated five bacteria affiliated to Planctomycetes from this mangrove and further subjected them to phenotypical and genetic analysis. The tolerance for salinity was demonstrated by the cultivation under distinct concentrations of NaCl. The ability of this bacterium to use diverse carbon sources was revealed by the use of 30 C-sources from a total of 31 tests. We found the isolate Rhodopirellula sp. MGV very closely affiliated to species of the genus Rhodopirellula, harboring a genome with 7.16 Mbp and 55.3% of GC. The annotation of the 77 contigs resulted in 6.284 CDS, with a remarkable occurrence of sequences associated with aromatic carbon metabolism. In conclusion, we present the isolation and characterization of a Planctomycetes from mangroves, suggesting its participation in the degradation of hydrocarbons present in the contaminated mangroves studied.

Genome-Resolved Metagenomics Is Essential for Unlocking the Microbial Black Box of the Soil.

Despite several efforts to unravel the microbial diversity of soil, most microbes are still unknown. A recent large-scale effort based on genome-resolved metagenomics by Nayfach et al. has demonstrated how this approach can expand our understanding of novel bacterial lineages, including those from soils. Genomic catalogs of soil microbiomes are now enabling a deeper investigation of the evolutionary and functional role of high-complex soil microbiomes, promoting new knowledge from the reuse and sharing of multi-omics data.

Soil Microbial Diversity Affects the Plant-Root Colonization by Arbuscular Mycorrhizal Fungi.

Terrestrial plants establish symbiosis with arbuscular mycorrhizal fungi (AMF) to exchange water and nutrients. However, the extent to which soil biodiversity influences such association remains still unclear. Here, we manipulated the soil microbial diversity using a "dilution-to-extinction" approach in a controlled pot microcosm system and quantified the root length colonization of maize plants by the AMF Rhizophagus clarus. The experiment was performed by manipulating the soil microbiome within a native and foreign soil having distinct physicochemical properties. Overall, our data revealed significant positive correlations between the soil microbial diversity and AMF colonization. Most importantly, this finding opposes the diversity-invasibility hypothesis and highlights for a potential overall helper effect of the soil biodiversity on plant-AMF symbiosis.

16S rRNA Gene Copy Number Normalization Does Not Provide More Reliable Conclusions in Metataxonomic Surveys.

Sequencing 16S rRNA gene amplicons is the gold standard to uncover the composition of prokaryotic communities. The presence of multiple copies of this gene makes the community abundance data distorted and gene copy normalization (GCN) necessary for correction. Even though GCN of 16S data provided a picture closer to the metagenome before, it should also be compared with communities of known composition due to the fact that library preparation is prone to methodological biases. Here, we process 16S rRNA gene amplicon data from eleven simple mock communities with DADA2 and estimate the impact of GCN. In all cases, the mock community composition derived from the 16S sequencing differs from those expected, and GCN fails to improve the classification for most of the analysed communities. Our approach provides empirical evidence that GCN does not improve the 16S target sequencing analyses in real scenarios. We therefore question the use of GCN for metataxonomic surveys until a more comprehensive catalogue of copy numbers becomes available.

Effects of winter and summer conditions on Cd fractionation and bioavailability, bacterial communities and Cd phytoextraction potential of Brachiaria decumbens and Panicum maximum grown in a tropical soil.

The interactions between soil properties, microorganisms, plant species and climate affect cadmium (Cd) availability in tropical soils. In this study, we investigated the effects of simulated summer and winter conditions on Cd fractionation and bacterial communities in Oxisols and on growth of two high biomass production-grasses (Brachiaria decumbens and Panicum maximum) that were evaluated for their Cd phytoextraction potential. We also assessed how these interactions could influence the availability of Cd and its possible phytoextraction by these grasses. The Cd fraction bound to carbonates was higher in the winter conditions, while Cd bound to Fe- and Mn oxides was higher in the summer conditions, which resulted in a higher Cd availability in winter compared to summer conditions. B. decumbens and P. maximum took up more Cd when grown in the winter conditions, but their biomasses were not affected by the higher Cd uptake. The occurrence and relative abundance of bacterial taxa in the bare soil differed from the soils cultivated with grasses, where the Gammaproteobacteria predominated. However, no positive correlations were observed between the rhizosphere bacterial community in the cultivated soils and Cd availability, irrespective of the season conditions.

Draft Genomic Sequences of Streptomyces misionensis ACT66 and Streptomyces albidoflavus ACT77, Bacteria with Potential Application for Phytopathogen Biocontrol.

Here, we report the draft genomic sequences and annotation of Streptomyces misionensis ACT66 and Streptomyces albidoflavus ACT77, which are two bacteria with potential application for phytopathogen biocontrol.

Bacterial communities associated with anthracnose symptomatic and asymptomatic leaves of guarana, an endogenous tropical crop, and their pathogen antagonistic effects.

Plants are colonized by diverse microorganisms that can substantially impact their health and growth. Understanding bacterial diversity and the relationships between bacteria and phytopathogens may be key to finding effective biocontrol agents. We evaluated the bacterial community associated with anthracnose symptomatic and asymptomatic leaves of guarana, a typical tropical crop. Bacterial communities were assessed through culture-independent techniques based on extensive 16S rRNA sequencing, and cultured bacterial strains were evaluated for their ability to inhibit the growth of Colletotrichum sp. as well as for enzyme and siderophore production. The culture-independent method revealed that Proteobacteria was the most abundant phylum, but many sequences were unclassified. The emergence of anthracnose disease did not significantly affect the bacterial community, but the abundance of the genera Acinetobacter, Pseudomonas and Klebsiella were significantly higher in the symptomatic leaves. In vitro growth of Colletotrichum sp. was inhibited by 11.38% of the cultured bacterial strains, and bacteria with the highest inhibition rates were isolated from symptomatic leaves, while asymptomatic leaves hosted significantly more bacteria that produced amylase and polygalacturonase. The bacterial isolate Bacillus sp. EpD2-5 demonstrated the highest inhibition rate against Colletotrichum sp., whereas the isolates EpD2-12 and FD5-12 from the same genus also had high inhibition rates. These isolates were also able to produce several hydrolytic enzymes and siderophores, indicating that they may be good candidates for the biocontrol of anthracnose. Our work demonstrated the importance of using a polyphasic approach to study microbial communities from plant diseases, and future work should focus on elucidating the roles of culture-independent bacterial communities in guarana anthracnose disease.

Closed Genome Sequence of Bacillus paralicheniformis Strain CBMAI 1303, a Bacterium Applied for Phytopathogen Biocontrol.

We report the complete genome sequence and annotation of Bacillus paralicheniformis strain CBMAI 1303, a bacterium applied for phytopathogen biocontrol.

Seasonal dynamics alter taxonomical and functional microbial profiles in Pampa biome soils under natural grasslands.

Soil microbial communities' assembly is strongly tied to changes in temperature and moisture. Although microbial functional redundancy seems to overcome taxonomical composition changes, the sensitivity and resilience of soil microbial communities from subtropical regions in response to seasonal variations are still poorly understood. Thus, the development of new strategies for biodiversity conservation and sustainable management require a complete understanding of the soil abiotic process involved in the selection of microbial taxa and functions. In this work, we used state of the art molecular methodologies (Next Generation Sequencing) to compare the taxonomic (metataxonomics) and functional (metatranscriptomics) profiles among soil samples from two subtropical natural grasslands located in the Pampa biome, Brazil, in response to short-term seasonal variations. Our data suggest that grasslands maintained a stable microbial community membership along the year with oscillation in abundance. Apparently soil microbial taxa are more susceptible to natural climatic disturbances while functions are more stable and change with less intensity along the year. Finally, our data allow us to conclude that the most abundant microbial groups and functions were shared between seasons and locations reflecting the existence of a stable taxonomical and functional core microbiota.

Closed Genome Sequence of Phytopathogen Biocontrol Agent Bacillus velezensis Strain AGVL-005, Isolated from Soybean.

We report here the closed and near-complete genome sequence and annotation of Bacillus velezensis strain AGVL-005, a bacterium isolated from soybean seeds in Brazil and used for phytopathogen biocontrol.

Differences in bacterial composition between men's and women's restrooms and other common areas within a public building.

Humans distribute a wide range of microorganisms around building interiors, and some of these are potentially pathogenic. Recent research established that humans are the main drivers of the indoor microbiome and up to now significant literature has been produced about this topic. Here we analyzed differences in bacterial composition between men's and women's restrooms and other common areas within the same public building. Bacterial DNA samples were collected from restrooms and halls of a three-floor building from the Federal University of Pampa, RS, Brazil. The bacterial community was characterized by amplification of the V4 region of the 16S rRNA gene and sequencing. Throughout all samples, the most abundant phylum was Proteobacteria, followed by Actinobacteria, Bacteroidetes and Firmicutes. Beta diversity metrics showed that the structure of the bacterial communities were different among the areas and floors tested, however, only 6-9% of the variation in bacterial communities was explained by the area and floors sampled. A few microorganisms showed significantly differential abundance between men's and women's restrooms, but in general, the bacterial communities from both places were very similar. Finally, significant differences among the microbial community profile from different floors were reported, suggesting that the type of use and occupant demographic within the building may directly influence bacterial dispersion and establishment.

Aliphatic Hydrocarbon Enhances Phenanthrene Degradation by Autochthonous Prokaryotic Communities from a Pristine Seawater.

The microbial diversity and functioning around oceanic islands is poorly described, despite its importance for ecosystem homeostasis. Here, we aimed to verify the occurrence of microbe-driven phenanthrene co-oxidation in the seawater surrounding the Trindade Island (Brazil). We also used Next-Generation Sequencing to evaluate the effects of aliphatic and polycyclic aromatic hydrocarbons (PAHs) on these microbial community assemblies. Microcosms containing seawater from the island enriched with either labelled (9-14C) or non-labelled phenanthrene together with hexadecane, weathered oil, fluoranthene or pyrene, and combinations of these compounds were incubated. Biodegradation of phenanthrene-9-14C was negatively affected in the presence of weathered oil and PAHs but increased in the presence of hexadecane. PAH contamination caused shifts in the seawater microbial community-from a highly diverse one dominated by Alphaproteobacteria to less diverse communities dominated by Gammaproteobacteria. Furthermore, the combination of PAHs exerted a compounded negative influence on the microbial community, reducing its diversity and thus functional capacity of the ecosystem. These results advance our understanding of bacterial community dynamics in response to contrasting qualities of hydrocarbon contamination. This understanding is fundamental in the application and monitoring of bioremediation strategies if accidents involving oil spillages occur near Trindade Island and similar ecosystems.

Compositional shifts in bacterial communities associated with the coral Palythoa caribaeorum due to anthropogenic effects.

Corals harbor abundant and diverse prokaryotic communities that may be strongly influenced by human activities, which in turn compromise the normal functioning of coral species and predispose them to opportunistic infections. In this study, we investigated the effect of sewage dumping on the bacterial communities associated with the soft coral Palythoa caribaeorum at two sites in the Brazilian coast. We observed a dominance of bacterial species classified as human pathogens at sites exposed to untreated sewage discharge. The microbial diversity of undisturbed sites was more homogeneous and diverse and showed greater abundance. In addition, bacterial communities differed substantially between the exposed and undisturbed areas. The microbial community associated with the samples collected from the exposed sites revealed the anthropogenic effect caused by organic matter from untreated sewage dumping, with an abundance of pathogenic bacterial species.