Real-time quantitative polymerase chain reaction (qPCR) and digital PCR (dPCR) methods have revolutionized environmental microbiology, yielding quantitative organism-specific data of nucleic acid targets in the environment. Such data are essential for characterizing interactions and processes of microbial communities, assessing microbial contaminants in the environment (water, air, fomites), and developing interventions (water treatment, surface disinfection, air purification) to curb infectious disease transmission. However, our review of recent qPCR and dPCR literature in our field of health-related environmental microbiology showed that many researchers are not reporting necessary and sufficient controls and methods, which would serve to strengthen their study results and conclusions. Here, we describe the application, utility, and interpretation of the suite of controls needed to make high quality qPCR and dPCR measurements of microorganisms in the environment. Our presentation is organized by the discrete steps and operations typical of this measurement process. We propose systematic terminology to minimize ambiguity and aid comparisons among studies. Example schemes for batching and combining controls for efficient work flow are demonstrated. We describe critical reporting elements for enhancing data credibility, and we provide an element checklist in the Supporting Information. Additionally, we present several key principles in metrology as context for laboratories to devise their own quality assurance and quality control reporting framework. Following the EMMI guidelines will improve comparability and reproducibility among qPCR and dPCR studies in environmental microbiology, better inform engineering and public health actions for preventing disease transmission through environmental pathways, and for the most pressing issues in the discipline, focus the weight of evidence in the direction toward solutions.

The Environmental Microbiology Minimum Information (EMMI) Guidelines: qPCR and dPCR Quality and Reporting for Environmental Microbiology.

Non-point source fecal contamination from aging wastewater infrastructure is a primary driver of antibiotic resistance in surface waters.

Microbially influenced concrete corrosion (MICC) causes substantial financial losses to modern societies. Concrete corrosion with various environmental factors has been studied extensively over several decades. With the enhancement of public awareness on the environmental and economic impacts of microbial corrosion, MICC draws increasingly public attention. In this review, the roles of various microbial communities on MICC and corresponding protective measures against MICC are described. Also, the current status and research methodology of MICC are discussed. Thus, this review aims at providing insight into MICC and its mechanisms as well as the development of protection possibilities. 

Review on Microbially Influenced Concrete Corrosion

Abstract Fecal contamination threatens human health and contributes to the eutrophication of water resources. In Oklahoma, approximately 75% of assessed stream miles in the state are listed as impaired for fecal indicator bacteria (FIB). We tested the performance of seven microbial source tracking (MST) markers in six Northeast Oklahoma streams. All samples were tested with human (HF183), bovine (COWM2, COWM3), porcine (Pig-2-Bac), avian (Av4143), Escherichia coli , and Enterococcus markers using digital PCR (dPCR), as well as culturable assays for E. coli (Colisure) and Enterococcus (Enterolert). Rural and agricultural land uses were characterized by bovine sources of bacterial contamination. Human fecal contamination was found to be prominent in developed landscapes with several indicators for chronic human fecal pollution in an urban stream. All the streams met the criterion for Enterococcus impairment in 2019 and 2020; however, we found no relationships between culturable Enterococcus and the MST markers except in the urban stream, which had chronic human fecal pollution issues. The urban stream met the criterion for E. coli impairment, and E. coli was significantly correlated with the dominant MST markers in both rural and urban streams. We find that the culturable Enterococcus assay is not specific enough to be used for FIB water quality standards. We support the continued use of culturable E. coli assays to monitor for fecal contamination, and we recommend following-up with MST to verify fecal sources so informed mitigative actions can be taken to improve stream water quality. 

/pdf/validating-microbial-source-tracking-markers-and-assessing-19gq7xd8.pdf

Validating Microbial Source Tracking Markers and Assessing the Efficacy of Culturable E. coli and Enterococcus Assays in Ozark Streams, USA

Land use and rainfall influences on bacterial levels and sources in stormwater ponds.

Collection system investigation microbial source tracking (CSI-MST): Applying molecular markers to identify sewer infrastructure failures.

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Collection system investigation microbial source tracking (CSI-MST): Applying molecular markers to identify sewer infrastructure failures.