Influence of seasonality on the aerosol microbiome of the Amazon rainforest

Antibiotic resistance genes in the coastal atmosphere under varied weather conditions: Distribution, influencing factors, and transmission mechanisms

Antibiotic resistance genes (ARGs) have escalated to levels of concern worldwide as emerging environmental pollutants. Increasing evidence suggests that non-antibiotic antimicrobial substances expedite the spread of ARGs. However, the drivers and mechanisms involved in the generation and spread of ARGs in the atmosphere remain inadequately elucidated. Co-occurrence networks, mantel test analysis, and partial least squares path modeling were used to analyze the symbiotic relationships of ARGs with meteorological conditions, atmospheric pollutants, water-soluble inorganic ions, bacteria, mobile genetic elements (MGEs), antibacterial biocide and metal resistance genes, and to identify the direct drivers of ARGs. The types and abundance of ARGs exhibited different seasonal distribution. Specifically, the types exhibited a strong alignment with the diversity of air masses terrestrial sources, while the abundance displayed a significant positive correlation with both biocide resistance genes (BRGs) and metal resistance genes (MRGs). The contribution of bacterial communities and MGEs to the generation and spread of ARGs was constrained by the low levels of antibiotics in the atmosphere and the existence of "viral intermediates". Conversely, antibacterial biocides and metals influenced mutation rates, cellular SOS responses, and oxidative stress of bacteria, consequently facilitating the generation and spread of ARGs. Moreover, the co-selection among their derivatives, resistance genes, ensured a stable presence of ARGs. The research highlighted the significant impact of residual antimicrobial substances on both the generation and spread of ARGs. Elucidating the sources of aerosols and the co-selection mechanism linking with ARGs, BRGs, and MRGs were crucial for preserving the stability of ARGs in the atmosphere.

Antibiotic-resistant bacteria aerosol in a Caribbean coastal city: Pre- and post- COVID-19 lockdown

This study assessed the prevalence and spatial distribution of viable ultrafine and fine antibiotic-resistant bacteria aerosols (ARB) in the Metropolitan Area of Barranquilla, Colombia, pre- and post-lockdown (September 2019 to December 2020). Samples were systematically collected from urban, suburban, and rural sites using a six-stage viable cascade impactor. We employed logistic regression and Bayesian Neural Network Classifiers to analyze meteorological variables' influence on antibiotic resistance persistence. The lockdown led to a significant decrease (76 %) in overall bacterial aerosol concentrations, likely due to reduced human activity. The most significant reduction (82 %) was observed at Peace Square. Bacillus cereus was the most prevalent species, showing high concentrations at all sampling sites. Other species, like Leifsonia aquatica and Staphylococcus lentus, were linked to wastewater effluents and agricultural activities. Despite the overall decrease in bacterial aerosols, antibiotic-resistant bacteria remained high, particularly in highly impacted urban areas like the Barranquilla Riverwalk. Bacillus cereus exhibited resistance to multiple antibiotics, including commonly used ones like Ampicillin and Penicillin G. Resistance to newer antibiotics like Vancomycin was rare. Peace Square, a high-traffic urban area, showed elevated resistance rates in the deeper respiratory regions compared to other locations. Our findings indicate that while overall concentration levels decreased, the threat of antibiotic resistance in bacterial bioaerosols persists, emphasizing the need for continuous monitoring and targeted public health interventions in urban areas.

Air quality in a small city: criteria pollutants, volatile organic compounds, metals, and microbes

This work presents a year-long integral study of air quality parameters in Ciudad Real, a small city in the center of Spain, and its influence on the nearby national park, Las Tablas de Daimiel. The study covers meteorological parameters and criteria pollutants such as O3, NO, NO2, SO2, and PM10. Additionally, for each month, a 1-week campaign was performed sampling air in sorbent tubes with 8-h time resolution to analyze anthropogenic volatile organic compounds and the effects of seasons, daytime, and working-weekend days. During these campaigns, 24-h PM2.5 samples were also collected to measure the load of bacteria and fungi, as well as the trace concentrations of elements.The city and the national park NOx profiles showed that emissions from the town had a non-perceivable effect on the protected area. PM10 levels in Ciudad Real were influenced by Saharan intrusions, as was the national park; however, Ciudad Real had a higher contribution from anthropogenic sources. Ozone levels were lower in the city during the cold season due to the higher concentration of NOx and have not changed significantly in the last decade.The VOCs with higher average concentrations were toluene, m,p-xylene, benzene, methylene chloride, and o-xylene, with traffic being the main source of these pollutants in the city. For benzene and carbon tetrachloride levels, weak carcinogenic risks were estimated. In PM2.5, the most abundant metals were Na, Zn, Mg, Ca, Al, Fe, and K. The carcinogenic and non-carcinogenic risks estimated from the levels of the studied metals were negligible. Bacterial and fungal counts positively correlated with the concentration of PM2.5. Microbial community composition showed seasonal variability, with the dominance of human pathogenic bacteria which correlated with certain pollutants such as SO2. Bacillus and Cutibacterium were the most abundant genera.

Indoor/Outdoor airborne microbiome characteristics in residential areas across four seasons and its indoor purification

Bioaerosols are more likely to accumulate in the residential environment, and long-term inhalation may lead to a variety of diseases and allergies. Here, we studied the distribution, influencing factors and diffusion characteristics of indoor and outdoor microbiota pollution in six residential buildings in Guangzhou, southern China over a period of one year. The results showed that the particle sizes of bioaerosol were mainly in the range of inhalable particle size (<4.7 μm) with a small difference among four seasons (74.61 % ± 2.17 %). The microbial communities showed obvious seasonal differences with high abundance in summer, but no obvious geographical differences. Among them, the bacteria were more abundant than the fungi. The dominant microbes in indoor and outdoor environments were similar, with Anoxybacillu, Brevibacillus and Acinetobacter as the dominant bacteria, and Cladosporium, Penicillium and Alternaria as the dominant fungi. The airborne microbiomes were more sensitive to temperature and particulate matter (PM2.5, PM10) concentrations. Based on the Sloan neutral model, bacteria were more prone to random diffusion than fungi, and the airborne microbiome can be randomly distributed in indoor and outdoor environments and between the two environments in each season. Bioaerosol in indoor was mainly from outdoor. The health risk evaluation showed that the indoor inhalation risks were higher than those outdoor. The air purifier had a better removal efficiency on 1.1-4.7 μm microorganisms, and the removal efficiency on Gram-negative bacteria was better than that on Gram-positive bacteria. This study is of great significance for the risk assessment and control of residential indoor bioaerosol exposure.

Accessing the specialized metabolome of actinobacteria from the bulk soil of Paullinia cupana Mart. on the Brazilian Amazon: a promising source of bioactive compounds against soybean phytopathogens

The Amazon rainforest, an incredibly biodiverse ecosystem, has been increasingly vulnerable to deforestation. Despite its undeniable importance and potential, the Amazonian microbiome has historically received limited study, particularly in relation to its unique arsenal of specialized metabolites. Therefore, in this study our aim was to assess the metabolic diversity and the antifungal activity of actinobacterial strains isolated from the bulk soil of Paullinia cupana, a native crop, in the Brazilian Amazon Rainforest. Extracts from 24 strains were subjected to UPLC-MS/MS analysis using an integrative approach that relied on the Chemical Structural and Compositional Similarity (CSCS) metric, GNPS molecular networking, and in silico dereplication tools. This procedure allowed the comprehensive understanding of the chemical space encompassed by these actinobacteria, which consists of features belonging to known bioactive metabolite classes and several unannotated molecular families. Among the evaluated strains, five isolates exhibited bioactivity against a panel of soybean fungal phytopathogens (Rhizoctonia solani, Macrophomina phaseolina, and Sclerotinia sclerotiorum). A focused inspection led to the annotation of pepstatins, oligomycins, hydroxamate siderophores and dorrigocins as metabolites produced by these bioactive strains, with potentially unknown compounds also comprising their metabolomes. This study introduces a pragmatic protocol grounded in established and readily available tools for the annotation of metabolites and the prioritization of strains to optimize further isolation of specialized metabolites. Conclusively, we demonstrate the relevance of the Amazonian actinobacteria as sources for bioactive metabolites useful for agriculture. We also emphasize the importance of preserving this biome and conducting more in-depth studies on its microbiota.

Seasonal discrepancy of airborne fungal diversity and community structure in Lentinula edodes factory

Understanding the composition and community of airborne mycobiota associated with fungal diseases was critical for mushroom production and disease control. In this study, we first investigated airborne fungi concentrations in different function areas of a Chinese shiitake factory. Then, high-throughput sequencing was employed to characterise the airborne fungal compositions and communities of this factory during high and low incidence seasons of shiitake artificial log rot disease (SLRD). The lowest concentration of culturable airborne fungi was observed in spawn-running greenhouse (250-450 CFU/m3), while the airborne fungi concentrations in cultivation greenhouses were up to 7,000-8,500 CFU/m3. The airborne fungal communities across distinct function areas showed convergence. The four major mushroom contaminants, Trichoderma, Penicillium, Cladosporium, and Aspergillus were the stable core fungi. Seasonal shifts in compositions, abundances, and communities of airborne fungi were systematically analysed and found to be associated with SLRD. Compared with the SLRD low incidence season, the airborne fungal communities were rich but uneven in the SLRD high incidence season, in which Trichoderma was dominant. Further analysis indicated that the favourable temperature and humidity caused the proliferation of Trichoderma and then affected the fungal communities, which presented an SLRD-seasonal variation. SLRD incidence could be significantly reduced by reasonably increasing the ambient temperature. For the first time, we comprehensively characterised the dynamics of airborne fungal communities across the SLRD occurrence in the shiitake factory. Findings here also provided valuable information for fungal exposures in the mushroom industry.

Evaluation of the safety and quality of Brazil nuts (Bertholletia excelsa) using the tools of dna sequencing technology and aflatoxin profile

Introduction

Brazil nuts (BNs) result from sustainable extraction and are widely exploited in the Amazon region. Due to the production characteristics in the forest and the nutritional characteristics of these nuts, the occurrence of fungal contamination and the presence of aflatoxins are extensively discussed in the literature as a great aspect of interest and concern. This study aims to evaluate the microbial profile through DNA sequencing and amplification of 16S and ITS genes for bacterial and fungal analysis, respectively, and the presence of mycotoxins using high-performance liquid chromatography with fluorescence detection (HPLC-FD) from different fractions of the nuts processed.

Methods

The BN samples, harvest A (HA) and harvest B (HB), from two different harvests were collected in an extractive cooperative in the Amazon region for microbiological analysis (from DNA extraction and amplification of 16S genes, bacteria analysis, and ITS for fungi) and mycotoxins (aflatoxins AFB1, AFB2, AFG1, and AFG2) using HPLC-FD/KobraCell®.

Results and discussion

The samples showed a very different microbiome and aflatoxin profile. Genera such as Rothia (HA) and Cronobacter (HB) were abundant during the analysis of bacteria; as for fungi, the genera Aspergillus, Fusarium, Penicillium, and Alternaria were also considered prevalent in these samples. Soil microorganisms, including those pathogenic and related to inadequate hygienic-sanitary production practices, as well as aflatoxins, were found in the samples. However, they were within the established limits permitted by Brazilian legislation. Nuts have a diverse microbiota and are not restricted to fungi of the genus Aspergillus. The microbiological and toxicological profile can vary significantly within the same nut in the same extraction region and can be exacerbated by global climate changes. Therefore, it is necessary to advance sanitary educational actions by applying good production practices and inspection programs to ensure the sustainability and quality of the BN production chain.

Microbiology of the built environment: harnessing human-associated built environment research to inform the study and design of animal nests and enclosures

SUMMARYOver the past decade, hundreds of studies have characterized the microbial communities found in human-associated built environments (BEs). These have focused primarily on how the design and use of our built spaces have shaped human-microbe interactions and how the differential selection of certain taxa or genetic traits has influenced health outcomes. It is now known that the more removed humans are from the natural environment, the greater the risk for the development of autoimmune and allergic diseases, and that indoor spaces can be harsh, selective environments that can increase the emergence of antimicrobial-resistant and virulent phenotypes in surface-bound communities. However, despite the abundance of research that now points to the importance of BEs in determining human-microbe interactions, only a fraction of non-human animal structures have been comparatively explored. It is here, in the context of human-associated BE research, that we consider the microbial ecology of animal-built natural nests and burrows, as well as artificial enclosures, and point to areas of primary interest for future research.

Understanding the ecological effects of the fungicide difenoconazole on soil and Enchytraeus crypticus gut microbiome

Increasing knowledge of the impacts of pesticides on soil ecological communities is fundamental to a comprehensive understanding of the functional changes in the global agroecosystem industry. In this study, we examined microbial community shifts in the gut of the soil-dwelling organism Enchytraeus crypticus and functional shifts in the soil microbiome (bacteria and viruses) after 21 d of exposure to difenoconazole, one of the main fungicides in intensified agriculture. Our results demonstrated reduced body weight and increased oxidative stress levels of E. crypticus under difenoconazole treatment. Meanwhile, difenoconazole not only altered the composition and structure of the gut microbial community, but also interfered with the soil-soil fauna microecology stability by impairing the abundance of beneficial bacteria. Using soil metagenomics, we revealed that bacterial genes encoding detoxification and viruses encoding carbon cycle genes exhibited a dependent enrichment in the toxicity of pesticides via metabolism. Taken together, these findings advance the understanding of the ecotoxicological impact of residual difenoconazole on the soil-soil fauna micro-ecology, and the ecological importance of virus-encoded auxiliary metabolic genes under pesticide stress.

Diversity and compositional differences of the airborne microbiome in a biophilic indoor environment

Biophilic design based on indoor planting plays an important role in human physical and mental well-being. To investigate and assess the effects of indoor planting on air quality, we sequenced 16S rRNA gene amplicons to compare the airborne bacterial microbiomes of three planting rooms before and after installing natural materials (plants, soil, water, etc.) with distinct biophilic attributes. Incorporation of indoor plantings significantly increased the taxonomic diversity of the airborne microbiome in each room, and we observed different microbiome compositions in each room. The proportional contribution of each bacterial source to the airborne microbiome in the indoor planting rooms was estimated by SourceTracker2. This analysis revealed that the proportion of airborne microbial sources (e.g., plants and soil) varied depending on the natural materials installed. Our results have important implications for indoor planting with biophilic design to control the indoor airborne microbiome.

Perspectives on Sampling and New Generation Sequencing Methods for Low-Biomass Bioaerosols in Atmospheric Environments

Bioaerosols play essential roles in the atmospheric environment and can affect human health. With a few exceptions (e.g., farm or rainforest environments), bioaerosol samples from wide-ranging environments typically have a low biomass, including bioaerosols from indoor environments (e.g., residential homes, offices, or hospitals), outdoor environments (e.g., urban or rural air). Some specialized environments (e.g., clean rooms, the Earth's upper atmosphere, or the international space station) have an ultra-low-biomass. This review discusses the primary sources of bioaerosols and influencing factors, the recent advances in air sampling techniques and the new generation sequencing (NGS) methods used for the characterization of low-biomass bioaerosol communities, and challenges in terms of the bias introduced by different air samplers when samples are subjected to NGS analysis with a focus on ultra-low biomass. High-volume filter-based or liquid-based air samplers compatible with NGS analysis are required to improve the bioaerosol detection limits for microorganisms. A thorough understanding of the performance and outcomes of bioaerosol sampling using NGS methods and a robust protocol for aerosol sample treatment for NGS analysis are needed. Advances in NGS techniques and bioinformatic tools will contribute toward the precise high-throughput identification of the taxonomic profiles of bioaerosol communities and the determination of their functional and ecological attributes in the atmospheric environment. In particular, long-read amplicon sequencing, viability PCR, and meta-transcriptomics are promising techniques for discriminating and detecting pathogenic microorganisms that may be active and infectious in bioaerosols and, therefore, pose a threat to human health.

Supplementary Information

The online version contains supplementary material available at 10.1007/s41745-023-00380-x.

Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data

Dimensionality reduction techniques are a key component of most microbiome studies, providing both the ability to tractably visualize complex microbiome datasets and the starting point for additional, more formal, statistical analyses. In this review, we discuss the motivation for applying dimensionality reduction techniques, the special characteristics of microbiome data such as sparsity and compositionality that make this difficult, the different categories of strategies that are available for dimensionality reduction, and examples from the literature of how they have been successfully applied (together with pitfalls to avoid). We conclude by describing the need for further development in the field, in particular combining the power of phylogenetic analysis with the ability to handle sparsity, compositionality, and non-normality, as well as discussing current techniques that should be applied more widely in future analyses.

Multi-antibiotic resistant bacteria in landfill bioaerosols: Environmental conditions and biological risk assessment

Landfills, as well as other waste management facilities are well-known bioaerosols sources. These places may foment antibiotic-resistance in bacterial bioaerosol (A.R.B.) due to inadequate pharmaceutical waste disposal. This issue may foster the necessity of using last-generation antibiotics with extra costs in the health care system, and deaths. The aim of this study was to reveal the multi-antibiotic resistant bacterial bioaerosol emitted by a sanitary landfill and the surrounding area. We evaluated the influence of environmental conditions in the occurrence of A.R.B. and biological risk assessment. Antibiotic resistance found in the bacteria aerosols was compared with the AWaRE consumption classification. We used the BIOGAVAL method to assess the workers' occupational exposure to antibiotic-resistant bacterial bioaerosols in the landfill. This study confirmed the multi-antibiotic resistant in bacterial bioaerosol in a landfill and in the surrounding area. Obtained mean concentrations of bacterial bioaerosols, as well as antibiotic-resistant in bacterial bioaerosol (A.R.B.), were high, especially for fine particles that may be a threat for human health. Results suggest the possible risk of antibiotic-resistance interchange between pathogenic and non-pathogenic species in the landfill facilities, thus promoting antibiotic multi-resistance genes spreading into the environment.