The Use of Ribosomal RNA as a Microbial Source Tracking Target Highlights the Assay Host-Specificity Requirement in Water Quality Assessments

Funding Information: We thank Tiina Heiskanen, Tarja Rahkonen, and Tarja Yli-Tuomi for their technical assistance and local health and environment authorities, and communal water supply personnel Jukka Meriluoto, Salla Leppänen, Anu Väänänen, Päivi Rissanen, Katja Ylönen, Hanna Jääskeläinen, and especially Ville Soininen and Inkeri Eronen, who received funding for the work from the North Ostrobothnia Centre for Economic Development, Transport, and the Environment (grant number POPELY/2687/2017), for organizing sample collection. Funding. This research was supported in part by the cities of Kalajoki, Tampere, Kuopio, and the municipal wastewater treatment plants Hämeenlinnan Seudun Vesi Ltd., Nokian Vesi Ltd., and Oulun Vesi Ltd., who provided samples for the study. Further, the work was partially funded by the Regional Council of Häme, grant number 518 HL/106/04.01.01/2018. We acknowledge all of the project partners and collaborators, especially the personnel of HAMK University of Applied Sciences, Hämeenlinnan Seudun Vesi Ltd., the Lammi Biological Station, and Ilkka Hirvonen of Led Future Ltd. Funding Information: This research was supported in part by the cities of Kalajoki, Tampere, Kuopio, and the municipal wastewater treatment plants Hämeenlinnan Seudun Vesi Ltd., Nokian Vesi Ltd., and Oulun Vesi Ltd., who provided samples for the study. Further, the work was partially funded by the Regional Council of Häme, grant number 518 HL/106/04.01.01/2018. We acknowledge all of the project partners and collaborators, especially the personnel of HAMK University of Applied Sciences, Hämeenlinnan Seudun Vesi Ltd., the Lammi Biological Station, and Ilkka Hirvonen of Led Future Ltd. Publisher Copyright: © Copyright © 2021 Rytkönen, Tiwari, Hokajärvi, Uusheimo, Vepsäläinen, Tulonen and Pitkänen.For microbial source tracking (MST), the 16S ribosomal RNA genes (rDNA) of host-specific bacteria and mitochondrial DNA (mtDNA) of animal species, known to cause fecal contamination of water, have been commonly used as molecular targets. However, low levels of contamination might remain undetected by using these DNA-based qPCR assays. The high copy numbers of ribosomal RNA (rRNA) could offer a solution for such applications of MST. This study compared the performance of eight MST assays: GenBac3 (general Bacteroidales), HF183 (human), BacCan (dog), Rum-2-Bac (ruminant), Pig-2-Bac (swine), Gull4 (gull), GFD, and Av4143 (birds) between rRNA-based and rDNA-based approaches. Three mtDNA-based approaches were tested: DogND5, SheepCytB, and HorseCytB. A total of 151 animal fecal samples and eight municipal sewage samples from four regions of Finland were collected for the marker evaluation. The usability of these markers was tested by using a total of 95 surface water samples with an unknown pollution load. Overall, the performance (specificity, sensitivity, and accuracy) of mtDNA-based assays was excellent (95-100%), but these markers were very seldom detected from the tested surface water samples. The rRNA template increased the sensitivity of assays in comparison to the rDNA template. All rRNA-based assays (except Av4143) had more than 80% sensitivity. In contrast, only half (HF183, Rum-2-Bac, Pig-2-Bac, and Gull4) of rDNA-based assays reached this value. For markers targeted to bird feces, the use of the rRNA-based assay increased or at least did not change the performance. Regarding specificity, all the assays had >95% specificity with a DNA template, except the BacCan assay (71%). While using the RNA template for the assays, HF183 and BacCan exhibited only a low level of specificity (54 and 55%, respectively). Further, the HF183 assay amplified from multiple non-targeted animal fecal samples with the RNA template and the marker showed cross-amplification with the DNA template as well. This study recommends using the rRNA-based approach for MST assays targeting bird fecal contamination. In the case of mammal-specific MST assays, the use of the rRNA template increases the sensitivity but may reduce the specificity and accuracy of the assay. The finding of increased sensitivity calls for a further need to develop better rRNA-based approaches to reach the required assay performance.peerReviewe

Colilert-menetelmän verifiointi sosiaali- ja terveysministeriön asetuksen 461/2000 mukaisiin koliformisten bakteerien ja Escherichia coli -bakteerin tutkimuksiin Suomessa

Colilert -18 Quanti-Tray -menetelmä (IDEXX Laboratories

Haihtuvat orgaaniset yhdisteet asunnoissa : Pitoisuustasot, yleisimmät yhdisteet ja terveysvaikutukset

Haihtuvat orgaaniset yhdisteet ovat yleisiä sisäilman yhdisteitä. Niitä vapautuu asuntojen sisäilmaan esimerkiksi rakennus- ja sisustusmateriaaleista, kuluttajatuotteista sekä tilan käyttäjistä ja heidän toiminnastaan. Haihtuvia orgaanisia yhdisteitä tutkitaan, koska suurina pitoisuuksina ne voivat aiheuttaa terveysvaikutuksia, kuten ärsytysoireita. Tässä katsauksessa tarkastellaan VOC-alueella esiintyvien haihtuvien orgaanisten yhdisteiden sekä formaldehydin esiintymistä, pitoisuuksia ja muutostrendejä Suomessa sijaitsevissa asunnoissa vuosina 2010 2019. Lisäksi selvitetään, ovatko terveysvaikutukset todennäköisiä asunnoissa esiintyvillä pitoisuuksilla. Tuloksia verrataan asumisterveysasetuksen ja sen soveltamisohjeen toimenpiderajoihin sekä kansainvälisiin terveysperusteisiin ohjearvoihin

Determination of Removal Efficiencies for Escherichia coli, Clostridial Spores, and F-Specific Coliphages in Unit Processes of Surface Waterworks for QMRA Applications

The removal efficiencies of bacteria, bacterial spores, and viruses after a change in source water and water pH in coagulation were studied at pilot scale in coagulation with flotation, rapid sand filtration, and disinfection with UV and chlorine. The results were compared to the treatment efficiencies of full-scale waterworks and data from literature. A quantitative microbial risk assessment (QMRA)-method was applied to estimate the numbers of illness cases caused by Campylobacter and norovirus after simulation of six operational malfunction scenarios. Coagulation with flotation and disinfection were more efficient in removing Clostridium spp. spores and MS2 coliphages than sand filtration in the pilot scale experiments (p View Full-Text</a

Bacterial diversity and predicted enzymatic function in a multipurpose surface water system – from wastewater effluent discharges to drinking water production

Funding Information: The authors would like to express special acknowledgment to the CONPAT research team at the Finnish Institute for Health and Welfare, Finnish Environment Institute, and VATT Institute for Economic Research. Special thanks go to Tiina Heiskanen and Laura Wessels for extracting the nucleic acids. The Water Protection Association of the River Kokem?enjoki (KVVY) is acknowledged for surface water and wastewater sampling. Funding Information: Academy of Finland (grant number 263451) and Kaute Foundation (grant number 20190366) are acknowledged for providing funds for the project establishment and manuscript writing, respectively. Funding Information: The authors declare that they have no competing interests. This work was in part supported by the U.S. Environmental Protection Agency (EPA), and any opinions expressed do not reflect the views of the agency; therefore, no official endorsement should be inferred. Any mention of trade names or commercial products does not constitute endorsement or recommendation for use. Publisher Copyright: © 2021, The Author(s).Background Rivers and lakes are used for multiple purposes such as for drinking water (DW) production, recreation, and as recipients of wastewater from various sources. The deterioration of surface water quality with wastewater is well-known, but less is known about the bacterial community dynamics in the affected surface waters. Understanding the bacterial community characteristics -from the source of contamination, through the watershed to the DW production process-may help safeguard human health and the environment. Results The spatial and seasonal dynamics of bacterial communities, their predicted functions, and potential health-related bacterial (PHRB) reads within the Kokemaenjoki River watershed in southwest Finland were analyzed with the 16S rRNA-gene amplicon sequencing method. Water samples were collected from various sampling points of the watershed, from its major pollution sources (sewage influent and effluent, industrial effluent, mine runoff) and different stages of the DW treatment process (pre-treatment, groundwater observation well, DW production well) by using the river water as raw water with an artificial groundwater recharge (AGR). The beta-diversity analysis revealed that bacterial communities were highly varied among sample groups (R = 0.92, p = 13%) than in other groups (= 13%) than in others (Peer reviewe