Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond

Insights into the panorama of multiple DNA viruses in municipal wastewater and recycled sludge in Tianjin, China

Environmental viruses in wastewater and sludge are widely recognized for their roles in waterborne diseases. However, previous studies mainly focused on RNA viruses, and little is known about the diversity of DNA viral communities and their driving factors in municipal wastewater treatment environments. Herein, we conducted a pilot study to explore DNA virus profiles in municipal wastewater and recycled sludge by metagenomics method, and track their temporal changes in northern China. Results showed that 467 viral species were co-shared among all the samples. We identified six families of human viruses with a prevalence of 0.1%, which were rare but relatively stable in wastewater and sludge for six months. Adenoviridae, Parvoviridae, and Herpersviridae were the most dominant human viral families in municipal wastewater and recycled sludge. A time series of samples revealed that the dynamic changes of human DNA viruses were stable based on qPCR results, particularly for high-risk fecal-oral transmission viruses of adenovirus, bocavirus, polyomavirus, human gamma herpesvirus, human papillomavirus, and hepatitis B virus. Concentrations of Adenovirus (5.39-7.48 log10 copies/L) and bocavirus (4.36-7.48 log10 copies/L) were observed to be the highest in these samples compared to other viruses. Our findings demonstrated the DNA viruses' high prevalence and persistence in municipal wastewater treatment environments, highlighting the value of enhancing public health responses based on wastewater-based epidemiology.

Fine-scale spatiotemporal variations in bacterial community diversity in agricultural pond water

Microbial communities in surface waters are affected by environmental conditions and can influence changes in water quality. To explore the hypothesis that the microbiome in agricultural waters associates with spatiotemporal variations in overall water quality and, in turn, has implications for resource monitoring and management, we characterized the relationships between the microbiota and physicochemical properties in a model irrigation pond as a factor of sampling time (i.e., 9:00, 12:00, 15:00) and location within the pond (i.e., bank vs. interior sites and cross-sectional depths at 0, 1, and 2 m). The microbial communities, which were defined by 16S rRNA gene sequencing analysis, significantly varied based on all sampling factors (PERMANOVA P < 0.05 for each). While the relative abundances of dominant phyla (e.g., Proteobacteria and Bacteroidetes) were relatively stable throughout the pond, subtle yet significant increases in α-diversity were observed as the day progressed (ANOVA P < 0.001). Key water quality properties that also increased between the morning and afternoon (i.e., pH, dissolved oxygen, and temperature) positively associated with relative abundances of Cyanobacteria, though were inversely proportional to Verrucomicrobia. These properties, among additional parameters such as bioavailable nutrients (e.g., NH3, NO3, PO4), chlorophyll, phycocyanin, conductivity, and colored dissolved organic matter, exhibited significant relationships with relative abundances of various bacterial genera as well. Further investigation of the microbiota in underlying sediments revealed significant differences between the bank and interior sites of the pond (P < 0.05 for α- and β-diversity). Overall, our findings emphasize the importance of accounting for time of day and water sampling location and depth when surveying the microbiomes of irrigation ponds and other small freshwater sources.

Comparison between the gut bacterial community of laboratory cultured and wild Daphnia

The fitness of an organism is often impacted by the composition and biological activity of its associated bacterial community. Many factors, including host genetics, diet, and temperature can influence the bacterial community composition. Furthermore, these factors can differ strongly between natural and laboratory environments. Consequently, several studies have highlighted results from laboratory experiments investigating host-associated bacterial communities to be conflicting with those obtained under field conditions. Here, we compared the Daphnia magna gut bacterial communities in natural host populations with those of laboratory cultured hosts. We further analyzed changes in the gut bacterial communities after transferring hosts from natural populations to the laboratory on the short- and long-term. Results show that, in general, the gut bacterial communities from natural populations differ from those of laboratory cultures and that their composition and diversity changed one hour after being transferred to the laboratory. Over the following 14 days, the composition and diversity changed gradually. On the longer term (after two years of rearing hosts in the laboratory) the composition and diversity of the gut bacterial communities was strongly altered compared to the initial state. Our findings indicate that the gut bacterial communities of Daphnia magna in laboratory experiments is not representative for natural field conditions, and that caution should be taken when interpreting results from laboratory experiments for natural settings.

Surveillance and mitigation of soil pollution through metagenomic approaches

Soil pollution is one of the serious global threats causing risk to environment and humans. The major cause of accumulation of pollutants in soil are anthropogenic activities and some natural processes. There are several types of soil pollutants which deteriorate the quality of human life and animal health. They are recalcitrant hydrocarbon compounds, metals, antibiotics, persistent organic compounds, pesticides and different kinds of plastics. Due to the detrimental properties of pollutants present in soil on human life and ecosystem such as carcinogenic, genotoxic and mutagenic effects, alternate and effective methods to degrade the pollutants are recommended. Bioremediation is an effective and inexpensive method of biological degradation of pollutants using plants, microorganisms and fungi. With the advent of new detection methods, the identification and degradation of soil pollutants in different ecosystems were made easy. Metagenomic approaches are a boon for the identification of unculturable microorganisms and to explore the vast bioremediation potential for different pollutants. Metagenomics is a power tool to study the microbial load in polluted or contaminated land and its role in bioremediation. In addition, the negative ecosystem and health effect of pathogens, antibiotic and metal resistant genes found in the polluted area can be studied. Also, the identification of novel compounds/genes/proteins involved in the biotechnology and sustainable agriculture practices can be performed with the integration of metagenomics.

Variations in Bacterial Communities and Antibiotic Resistance Genes Across Diverse Recycled and Surface Water Irrigation Sources in the Mid-Atlantic and Southwest United States: A CONSERVE Two-Year Field Study

Reduced availability of agricultural water has spurred increased interest in using recycled irrigation water for U.S. food crop production. However, there are significant knowledge gaps concerning the microbiological quality of these water sources. To address these gaps, we used 16S rRNA gene and metagenomic sequencing to characterize taxonomic and functional variations (e.g., antimicrobial resistance) in bacterial communities across diverse recycled and surface water irrigation sources. We collected 1 L water samples (n = 410) between 2016 and 2018 from the Mid-Atlantic (12 sites) and Southwest (10 sites) U.S. Samples were filtered, and DNA was extracted. The V3-V4 regions of the 16S rRNA gene were then PCR amplified and sequenced. Metagenomic sequencing was also performed to characterize antibiotic, metal, and biocide resistance genes. Bacterial alpha and beta diversities were significantly different (p < 0.001) across water types and seasons. Pathogenic bacteria, such as Salmonella enterica, Staphylococcus aureus, and Aeromonas hydrophilia were observed across sample types. The most common antibiotic resistance genes identified coded against macrolides/lincosamides/streptogramins, aminoglycosides, rifampin and elfamycins, and their read counts fluctuated across seasons. We also observed multi-metal and multi-biocide resistance across all water types. To our knowledge, this is the most comprehensive longitudinal study to date of U.S. recycled water and surface water used for irrigation. Our findings improve understanding of the potential differences in the risk of exposure to bacterial pathogens and antibiotic resistance genes originating from diverse irrigation water sources across seasons and U.S. regions.

BioMateriOME: To understand microbe-material interactions within sustainable, living architectures

BioMateriOME evolved from a prototyping process which was informed from discussions between a team of designers, architects and microbiologists, when considering constructing with biomaterials or human cohabitation with novel living materials in the built environment. The prototype has two elements (i) BioMateriOME-Public (BMP), an interactive public materials library, and (ii) BioMateriOME-eXperimental (BMX), a replicated materials library for rigorous microbiome experimentation. The prototype was installed into the OME, a unique experimental living house, in order to (1) gain insights into society's perceptions of living materials, and (2) perform a comparative analysis of indoor surface microbiome development on novel biomaterials in contrast to conventional indoor surfaces, respectively. This review summarizes the BioMateriOME prototype and its use as a tool in combining microbiology, design, architecture and social science. The use of microbiology and biological components in the fabrication of biomaterials is provided, together with an appreciation of the microbial communities common to conventional indoor surfaces, and how these communities may change in response to the implementation of living materials in our homes. Societal perceptions of microbiomes and biomaterials, are considered within the framework of healthy architecture. Finally, features of architectural design with microbes in mind are introduced, with the possibility of codifying microbial surveillance into design and construction benchmarks, standards and regulations toward healthier buildings and their occupants.