Biology subjects

Cha, G.

Publications and source records attributed to Cha, G..

4 recordsLinked to original sources

bioRxiv2025

Viral adsorption to Moore swabs in passive wastewater sampling

Moore swabs have been used extensively for passive sampling in wastewater surveillance, typically yielding presence/absence information for targets of interest. Quantitative analysis of Moore swab data is only possible if target uptake is well characterized, specifically the relationship between quantity of the target in the liquid sample matrix and the quantity of target sorbing to the Moore swab as a function of time. The mechanism of Moore swab absorption remains unclear and is important to understand toward using them more quantitatively. We conducted viral adsorption and desorption experiments using nonpathogenic SARS-CoV-2 surrogates: {Phi}6, MHV, and BCoV as well as heat-inactivated Zika virus (ZIKV). We fit empirical adsorption data from batch experiments to Langmuir, Freundlich and Redlich-Peterson isotherm models. We observed the adsorption behavior of viral targets onto Moore swabs is best characterized by the Redlich-Peterson isotherm model. Moore swabs retained the highest viral RNA concentrations after exposure durations between 9-12 hours in the presence of target microbes during kinetic viral adsorption experiments. The results inform current and future use of Moore swabs to produce quantitative data during wastewater surveillance, especially in settings where composite sampling remains infeasible. ImportanceThis paper describes the adsorption behavior of viruses and bacteriophages to Moore swabs. Passive sampling via Moore swabs is among the most scalable form of passive wastewater sampling, considered critical to advance wastewater surveillance globally. But key unknowns constrain the utility of Moore swabs and all passive sampling approaches, including the quantitative relationship between targets in wastewater and recovery via Moore swabs. Practical questions such as how long they should be deployed and whether they can be interpreted quantitatively really depend on a characterization of viral target loading behaviors on Moore swab material as a function of time and concentration in the wastewater. Here, we use an approach that is seldom applied to microbial targets to examine adsorption behavior of viruses to Moore swabs, deriving isotherms that describe the relationships between concentration of the viral targets in wastewater and time on attachment to swab material. This is a critical step in advancing the application of Moore swab passive sampling for wastewater surveillance, with potential relevance to other microbial targets of interest.

microbiology↗

bioRxiv2025

Decay and Solid-Liquid Partitioning of Mpox and Vaccinia Viruses in Primary Influent and Settled Solids to Guide Wastewater-Based Epidemiology Practices

Wastewater-based epidemiology (WBE) has proven to be a powerful tool for tracking the spread of viral pathogens, such as SARS-CoV-2, but as WBE has expanded to include new pathogens, such as mpox virus, more data is needed to guide practitioners on how to design WBE campaigns. Here, we investigated the decay rates of heat-inactivated mpox (HI-MPXV) and attenuated vaccinia virus (VV) in primary influent and settled solids collected from a local POTW at 4{degrees}C, 22{degrees}C, or 35{degrees}C using digital PCR. Subsequently, we studied the solid-liquid partitioning of the viruses in primary influent. Over the 30-day study period, we observed no significant difference in log-linear decay rates between viruses (p=0.5258), with significantly higher decay rates in primary influent (0.109-0.144/day) compared to settled solids (0.019-0.040/day) at both 22{degrees}C (p=0.0030) and 35{degrees}C (p=0.0166). Furthermore, as part of the partitioning experiment, we found that HI-MPXV and VV adsorb to the solids fraction of primary influent at higher intensities than previously studied enveloped viruses (KF = 1,000-31,800 mL/g, n = 1.01-1.41). Likewise, it was determined in the partitioning experiment that a concentration of greater than 103 gc/mL in raw influent was needed for the viable quantification of mpox and vaccinia viruses in the clarified liquid fraction of raw primarily influent. Our study provides essential insights into informative sample collection and storage conditions for the analysis of wastewater and for transport modeling studies. Due to the slow decay observed in settled solids at all tested temperatures in the persistence experiment, this matrix may be most suitable for retrospective analyses of community infection of the mpox virus.

microbiology↗

bioRxiv2023

pH selects for distinct N2O-reducing microbiomes in tropical soil microcosms

Nitrous oxide (N2O), a greenhouse gas with ozone destruction potential, is mitigated by the microbial reduction to dinitrogen catalyzed by N2O reductase (NosZ). Bacteria with NosZ activity have been studied at circumneutral pH but the microbiology of low pH N2O reduction has remained elusive. Acidic (pH<5) tropical forest soils were collected in the Luquillo Experimental Forest in Puerto Rico, and microcosms maintained with low (0.02mM) and high (2mM) N2O assessed N2O reduction at pH 4.5 and 7.3. All microcosms consumed N2O, but long lag times of up to 7 months were observed in microcosms with 2 mM N2O. Comparative metagenome analysis revealed that Rhodocyclaceae dominated in circumneutral microcosms under both N2O feeding regimes. In acidic microcosms, Peptococcaceae dominated in high-N2O, and Hyphomicrobiaceae in low-N2O microcosms. Seventeen metagenome-assembled genomes (MAGs) recovered from these microcosms harbored nos operons, with all eight MAGs derived from acidic microcosms carrying the clade II type nosZ, lacking nitrite reductase genes (nirS, nirK). Five of these MAGs represented novel taxa indicating an unexplored N2O-reducing diversity exists in acidic tropical soils. A survey of pH 3.5-5.7 soil metagenome datasets revealed that nosZ genes commonly occur, suggesting broad distribution of N2O reduction potential in acidic soils.

microbiology↗

bioRxiv2023

Sustained bacterial (N2O) reduction at acidic pH

Nitrous oxide (N2O) is a climate-active gas and emissions from terrestrial ecosystems are concerning. Microbial reduction of N2O to dinitrogen (N2) is the only known consumption process and has been studied extensively at circumneutral pH; however, N2O reduction under acidic conditions is thought to be limited. Global soil acidification, accelerated by anthropogenic practices, introduces high uncertainty into N2O emission budgets. We obtained an enrichment culture from an acidic tropical forest soil that robustly reduces N2O to N2 at pH 4.5 with the addition of pyruvate and hydrogen. Consecutive transfers at pH 4.5 yielded a co-culture and temporal analyses revealed a bimodal growth pattern with a Serratia sp. growing during the initial pyruvate fermentation phase followed by growth of a novel Desulfosporosinus sp. via hydrogenotrophic N2O reduction. The Desulfosporosinus sp. produced (3.1 {+/-} 0.11) x 108 cells per mmol of N2O consumed, on par with growth yields reported for clade II N2O reducers at circumneutral pH. Genome analysis identified a clade II nos gene cluster, but an incomplete pathway for sulfate reduction, a hallmark feature of the genus Desulfosporosinus. Physiological and metabogenomic characterization revealed interspecies nutritional interactions, with the pyruvate fermenting Serratia sp. supplying amino acids as essential growth factors to the Desulfosporosinus sp. The co-culture reduced N2O between pH 4.5 and 6 but not at or above pH 7, contradicting the paradigm that sustained microbial N2O reduction ceases under acidic pH conditions, thus confirming a previously unrecognized N2O reduction potential in acidic soils. Significance StatementProcesses generating N2O occur over a broad pH range spanning pH 3 to 12; however, the current paradigm assumes that microbial N2O consumption is limited to circumneutral pH (6 to 8). The imbalance between N2O production versus consumption has increased the atmospheric concentration of this climate active gas by 17 % over the last 100 years, and accelerated emissions due to global soil acidification are a major climate concern. From acidic soil, we obtained a bacterial culture harboring a novel Desulfosporosinus species that effectively reduces N2O at pH 4.5, but not at or above pH 7. The discovery of an N2O reducer adapted to acidic pH conditions has far-reaching implications for predicting, modeling, and potentially managing N2O emissions from low pH ecosystems. Note for publisher (this text will be removed prior to publication)This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan).

microbiology↗