Biology subjects

Barich, D.

Publications and source records attributed to Barich, D..

4 recordsLinked to original sources

bioRxiv2025

Comparative Analysis of Denitrification and Other Nitrogen Cycle Genes in Diverse Environmental Microbiomes

The nitrogen cycle includes the microbial transformation of reactive nitrogenous molecules within a given ecosystem. Shotgun metagenomics, the unbiased sequencing of a microbial community, can reveal the unique gene profile and community composition of diverse microbiomes. We used NCycDB, an assembly-free, alignment-based pipeline, to determine and compare the potential nitrogen cycle processes in seven distinct microbiomes: wetland soils, agricultural soils, forest soils, compost, river water, and pond water from Knox County, Ohio, and lake water from the McMurdo Dry Valley Region in Antarctica. Soil metagenomes showed high levels of bacterial denitrifier genes, whereas freshwater metagenomes showed fewer denitrifiers. In wetland and agricultural soil cores, the relative abundance of norB, the marker gene for nitric oxide reductase, was a predictor of ambient N2O flux as measured by gas chromatography. Denitrifiers were predicted using the Kraken2/Bracken pipeline. In Ohio wetland soils, the relative abundance of Bradyrhizobium species were strongly associated with denitrification genes. We also explored how freshwater environmental factors select for or against nitrogen cycle genes. Denitrifier genes were positively correlated with phosphate concentration. Denitrifiers and denitrification genes were detected under microaerobic conditions, demonstrating that denitrification activity diminishes proportionally to oxygen concentration. An improved understanding of the denitrifier community in diverse microbiomes is necessary to mitigate excess N2O emissions from anthropogenic activities such as wetland drainage and crop production. IMPORTANCETerrestrial nitrogen limitations have historically reduced crop output. To fertilize crops, humans have developed synthetic N fixation methods, such as the Haber-Bosch process, which now account for half of global nitrogen uptake in biomass. The resulting nitrogen surplus in soils leads to eutrophication, harmful algal blooms in lakes and other aquatic ecosystems, and increased N2O emissions from denitrification via anaerobic respiration by soil bacteria. Considering that the nitrogen cycle is controlled by microbial communities, we need a better understanding of how nitrogen-cycling microbes control N runoff and N2O flux in each unique microbiome.

microbiology↗

bioRxiv2024

Pond Water Microbiome Taxa Profiles and Antibiotic Resistance Genes Associated with Acidity and Tannins

Microbial communities of small freshwater bodies are poorly understood. Four ponds in Knox County, Ohio, were sampled over two years to investigate the relationship between the microbial taxa profiles, antibiotic resistance genes (ARGs), and environmental factors such as pH and tannin concentrations. For each site, microbial communities were collected by filtration and metagenomes were analyzed by short-read sequencing. Taxa profiles were predicted by the Kraken2/Bracken pipelines. Bacterial taxa with high abundance in these ponds included Betaproteobacteria (Polynucleobacter and Methylopumilus) and Actinobacteria (Planktophila, Nanopelagicus, and Mycolicibacterium). One pond, a former quarry with elevated pH, showed high prevalence of Cyanobacteria with a seasonal shift from Synechococcus to Planktothrix in the fall. Planktothrix increase was associated with acidification. ARGs were quantified using the ShortBRED pipeline to detect and quantify hits to a marker set derived from the Comprehensive Antibiotic Resistance Database (CARD). The top two ARGs with the largest marker hits encode components of a Stenotrophomonas drug efflux pump powered by proton-motive force (smeABC) and a mycobacterial global regulator that activates a drug pump and other cell defenses (mtrA). Pump function and global activation of transcription incur large energy expenditures, whose fitness cost may increase at high external pH where the cells proton-motive force is diminished. The smeABC and mtrA prevalence showed a modest correlation with acidifying conditions (low pH and high tannins) which contribute a large transmembrane pH difference to the proton-motive force, thus increasing the cells energy available for pump function and global gene expression. IMPORTANCECompared to rivers and lakes, pond microbial ecosystems are understudied despite close contact with agriculture and recreation. Environmental microbes offer health benefits as well as hazards for human contact. Small water bodies may act as reservoirs for drug-resistant organisms and transfer of antibiotic resistance genes. Yet, the public is rarely aware of the potential for exposure to ARG-carrying organisms in recreational water bodies. Little is known about the capacity for freshwater microbial communities to remediate drug pollution and which biochemical factors may select against antibiotic resistance genes. This study analyzes the bacterial taxa composition and ARG prevalence including possible influence of factors such as pH and tannic acid levels.

microbiology↗

bioRxiv2021

Antibiotic Resistance Genes from Mat and Planktonic Microbiomes of Antarctic Lake Fryxell and Lake Bonney, and a Mat-forming Culture of Rhodoferax antarcticus

The perennial ice-covered lakes of the Antarctic McMurdo Dry Valleys harbor oligotrophic microbial communities that are separated geographically from other aquatic systems. Their microbiomes include planktonic microbes as well as lift-off mat communities that emerge from the ice. We used ShortBRED to quantify the antibiotic resistance genes (ARGs) from metagenomes of lift-off mats emerging from ice, and from filtered water samples of Lake Fryxell and Lake Bonney. The overall proportion of ARG hits was similar to that found in temperate-zone rural water bodies with moderate human inputs. Specific ARGs showed distinct distributions for the two lakes, and for mat versus planktonic sources. Metagenomic taxa distributions showed that mat phototrophs consisted mainly of cyanobacteria or betaproteobacteria, whereas the water column phototrophs were mainly protists. An enrichment culture of the betaproteobacterium Rhodoferax antarcticus from a Lake Fryxell mat sample showed an unusual mat-forming phenotype not previously reported for this species. Its genome showed no ARGs associated with betaproteobacteria, but had ARGs consistent with a minor Pseudomonas component. The Antarctic lake mats and water showed specific ARGs distinctive to the mat and water sources, but overall ARG levels were similar to those of temperate water bodies with moderate human inputs.

microbiology↗

bioRxiv2021

A Scenic River in Rural Ohio Shows Elevated Antibiotic Resistance Genes, Including Acinetobacter Tetracycline and Macrolide Resistance, Downstream of Wastewater Treatment Plant Effluent

The entry of antibiotic resistance genes (ARGs) into aquatic systems has been documented for large municipal wastewater treatment plants, but there is less study of the impact of smaller plants that are situated on small rural rivers. We sampled water metagenomes for ARG and taxa composition from the Kokosing River, a small rural river in Knox County, Ohio, which has been designated an Ohio State Scenic River for retention of natural character. Samples were obtained 1.0 km upstream, 120 m downstream, and 6.4 km downstream from the effluent release of the Mount Vernon wastewater treatment plant (WWTP). ARGS were identified in metagenomes using ShortBRED markers from the CARD database screened against UniPROT. Through all seasons, the metagenome just downstream of the WWTP effluent showed a substantial elevation of at least 15 different ARGs, including 6 ARGs commonly associated with Acinetobacter baumannii such as msrE, mphE (macrolide resistance) and tet(39) (tetracycline resistance). The ARGs most prevalent near the effluent pipe persisted 6.4 km downriver. Using MetaPhlAn2 clade-specific marker genes, the taxa distribution near the effluent showed elevation of reads annotated as Acinetobacter species as well as gut-associated taxa, Bacteroides and Firmicutes. The ARG levels and taxa prevalence showed little dependence on seasonal chlorination of the effluent. Nitrogen and phosphorus were elevated near the effluent pipe but had no consistent correlation with ARG levels. We show that in a rural river microbiome, year-round wastewater effluent substantially elevates ARGs including those associated with multidrug-resistant A. baumanii. IMPORTANCEAntibiotic resistance is a growing problem worldwide, with frequent transmission between pathogens and environmental organisms. Rural rivers can support high levels of recreational use by people unaware of inputs from treated wastewater, while WWTPs can generate a small but significant portion of flow volume into a river surrounded by forest and agriculture. There is little information on the rural impacts of WWTP effluent on the delivery and transport of antibiotic resistance genes. In our study, the river water proximal to wastewater effluent shows evidence for the influx of multidrug-resistant Acinetobacter baumanii, an opportunistic pathogen of concern for hospitals but also widespread in natural environments. Our work highlights the importance of wastewater effluent in management of environmental antibiotic resistance, even in high quality, rural river systems.

microbiology↗