Your search found 5 records
1 Acharya, K.; Blackburn, A.; Mohammed, Jemila; Haile, Alemseged Tamiru; Hiruy, A. M.; Werner, D. 2020. Metagenomic water quality monitoring with a portable laboratory. Water Research, 184:116112. [doi: https://doi.org/10.1016/j.watres.2020.116112]
Water quality ; Water analysis ; Monitoring ; Wastewater treatment plants ; Microbiological analysis ; Waterborne diseases ; Faecal coliforms ; Chemicophysical properties ; Portable equipment ; Costs ; Case studies / Ethiopia / United Kingdom / Addis Ababa / Birtley / Akaki River
(Location: IWMI HQ Call no: e-copy only Record No: H049934)
https://www.sciencedirect.com/science/article/pii/S0043135420306497/pdfft?md5=3d548784ecadc5dc3734e797551d099c&pid=1-s2.0-S0043135420306497-main.pdf
https://vlibrary.iwmi.org/pdf/H049934.pdf
https://vlibrary.iwmi.org/pdf/H049934.pdf
(1.54 MB) (1.54 MB)
We describe the technical feasibility of metagenomic water quality analysis using only portable equipment, for example mini-vacuum pumps and filtration units, mini-centrifuges, mini-PCR machines and the memory-stick sized MinION of Oxford Nanopore Technologies, for the library preparation and sequencing of 16S rRNA gene amplicons. Using this portable toolbox on site, we successfully characterized the microbiome of water samples collected from Birtley Sewage Treatment Plant, UK, and its environs. We also demonstrated the applicability of the portable metagenomics toolbox in a low-income country by surveying water samples from the Akaki River around Addis Ababa, Ethiopia. The 16S rRNA gene sequencing workflow, including DNA extraction, PCR amplification, sequencing library preparation, and sequencing was accomplished within one working day. The metagenomic data became available within 24e72 h, depending on internet speed. Metagenomic analysis clearly distinguished the microbiome of pristine samples from sewage influenced water samples. Metagenomic analysis identified the potential role of two bacterial genera not conventionally monitored, Arcobacter and Aeromonas, as predominant faecal pollution indicators/waterborne hazards. Subsequent quantitative PCR analysis validated the high Arcobacter butzleri abundances observed in the urban influenced Akaki River water samples by portable next generation sequencing with the MinION device. Overall, our field deployable metagenomics toolbox advances the capability of scientists to comprehensively monitor microbiomes anywhere in the world, including in the water, food and drinks industries, the health services, agriculture and beyond.
2 Pantha, K.; Acharya, K.; Mohapatra, S.; Khanal, S.; Amatya, N.; Ospina-Betancourth, C.; Butte, G.; Shrestha, S. D.; Rajbhandari, P.; Werner, D. 2021. Faecal pollution source tracking in the holy Bagmati River by portable 16S rRNA gene sequencing. npj Clean Water, 4:12. [doi: https://doi.org/10.1038/s41545-021-00099-1]
Water pollution ; Faecal pollution ; Coliform bacteria ; Faecal coliforms ; Biological contamination ; Rivers ; Water quality ; Sewage ; Wastewater treatment plants ; Sanitation ; Public health ; Indicators ; Monsoons / Nepal / Kathmandu Valley / Bagmati River
(Location: IWMI HQ Call no: e-copy only Record No: H050276)
(2.02 MB) (2.02 MB)
A suitcase laboratory was used for 16S rRNA amplicon sequencing to assess microbial water quality in the holy Bagmati River, Kathmandu, Nepal. SourceTracker analysis and Volcano plots revealed that microbial communities in the downstream part of the river were mainly contributed by untreated sewage. Seasonal variability in the sewage microbiome was reflected in the downstream river water quality. The bacterial genera Acidovorax, Geobacillus and Caulobacter predominated in the upstream sites, while genera containing putative human pathogens and gut bacteria, such as Clostridium, Prevotella, Arcobacter, Lactobacillus, Enterococcus and Streptococcus become prominent in the downstream sites. Marker gene qPCR assays for total bacteria, total coliforms, Human E. coli, Arcobacter butzleri and Vibrio cholerae confirmed the sequencing data trends. Even though basic sanitation provision is nowadays near universal in Nepal, our findings show how inadequate wastewater management may turn an urban river into an open sewer, which poses a public health risk.
3 Hiruy, A. M.; Mohammed, J.; Haileselassie, M. M.; Acharya, K.; Butte, G.; Haile, Alemseged Tamiru; Walsh, C.; Werner, D. 2022. Spatiotemporal variation in urban wastewater pollution impacts on river microbiomes and associated hazards in the Akaki Catchment, Addis Ababa, Ethiopia. Science of the Total Environment, 826:153912. [doi: https://doi.org/10.1016/j.scitotenv.2022.153912]
Municipal wastewater ; Water pollution ; River water ; Biological contamination ; Bacteria ; Faecal pollution ; Faecal coliforms ; Water quality standards ; Antimicrobial resistance ; Microbiological risk assessment ; Extended spectrum beta-lactamases ; Real time PCR ; Surface water ; Catchment areas ; Irrigation ; Effluents ; Health hazards / Ethiopia / Addis Ababa / Akaki River / Akaki Catchment
(Location: IWMI HQ Call no: e-copy only Record No: H051034)
https://www.sciencedirect.com/science/article/pii/S004896972201004X/pdfft?md5=e4136acb70d545e2d44e8f9069c0a381&pid=1-s2.0-S004896972201004X-main.pdf
https://vlibrary.iwmi.org/pdf/H051034.pdf
https://vlibrary.iwmi.org/pdf/H051034.pdf
(2.34 MB) (2.34 MB)
In Addis Ababa and its environs, most urban wastewater is discharged into rivers without treatment. This study related urban wastewater characteristics to the prevalence of faecal, antibiotic resistant, and potentially pathogenic bacteria in rivers of the Akaki catchment across six locations, for the dry and wet season. Spatiotemporal variation in bacterial hazards across the catchment was up to 6 log10 units. Cooccurrence of sewage pollution marker gene HF183 in all river samples testing positive for the Vibrio cholerae marker gene ompW, and high levels of these two genes in untreated wastewater, identified human sewage as the likely source of Vibrio cholerae hazards in the catchment. Levels of the marker genes rodA for E. coli, HF183 for human host associated Bacteroides, ciaB for Arcobacter, and ompW for Vibrio cholerae were all higher in the dry season than in the wet season. Marker gene gyrB for Pseudomonas aeruginosa was not detected in the samples. From the sequencing data, notable bacterial genera in the dry season included wastewater pollution indicators Arcobacter and Aeromonas, whereas soil erosion may explain the greater prominence of Legionella, Vicinamibacter, and Sphingomonas during the wet season. Except for the most upstream location, all faecal coliform (FC) counts exceeded WHO standards of 1000 CFU/100 mL for unrestricted irrigation. Concerningly, 0.6–20% of FC had ESBL producing antimicrobial resistance traits. In conclusion, multiple bacterial hazards were of concern for river water users in the Akaki catchment, and elevated in the dry season, when the river water is being used for irrigation of vegetable fields that supply the markets of Addis Ababa. This reflects inadequate treatment and limited dilution of urban wastewater by the natural river flows during periods of low rainfall.
4 Werner, D.; Acharya, K.; Blackburn, A.; Zan, R.; Plaimart, J.; Allen, B.; Mgana, S. M.; Sabai, S. M.; Halla, F. F.; Massawa, S. M.; Haile, Alemseged Tamiru; Hiruy, A. M.; Mohammed, J.; Vinitnantharat, S.; Thongsamer, T.; Pantha, K.; Filho, C. R. M.; Lopes, B. C. 2022. MinION nanopore sequencing accelerates progress towards ubiquitous genetics in water research. Water, 14(16):2491. (Special issue: Field Methods for Water Quality Surveying) [doi: https://doi.org/10.3390/w14162491]
Water ; Research ; Biomass ; Bioinformatics ; Sustainable Development Goals ; Goal 6 Clean water and sanitation
(Location: IWMI HQ Call no: e-copy only Record No: H051555)
https://www.mdpi.com/2073-4441/14/16/2491/pdf?version=1660812648
https://vlibrary.iwmi.org/pdf/H051555.pdf
https://vlibrary.iwmi.org/pdf/H051555.pdf
(1.66 MB) (1.66 MB)
In 2014, Oxford Nanopore Technologies (ONT) introduced an affordable and portable sequencer called MinION. We reviewed emerging applications in water research and assessed progress made with this platform towards ubiquitous genetics. With >99% savings in upfront costs as compared to conventional platforms, the MinION put sequencing capacity into the hands of many researchers and enabled novel applications with diverse remits, including in countries without universal access to safe water and sanitation. However, to realize the MinION’s fabled portability, all the auxiliary equipment items for biomass concentration, genetic material extraction, cleanup, quantification, and sequencing library preparation also need to be lightweight and affordable. Only a few studies demonstrated fully portable workflows by using the MinION onboard a diving vessel, an oceanographic research ship, and at sewage treatment works. Lower nanopore sequencing read accuracy as compared to alternative platforms currently hinders MinION applications beyond research, and inclusion of positive and negative controls should become standard practice. ONT’s EPI2ME platform is a major step towards user-friendly bioinformatics. However, no consensus has yet emerged regarding the most appropriate bioinformatic pipeline, which hinders intercomparison of study results. Processing, storing, and interpreting large data sets remains a major challenge for ubiquitous genetics and democratizing sequencing applications.
5 Babiso, W. Z.; Ayano, K. K.; Haile, Alemseged Tamiru; Keche, D. D.; Acharya, K.; Werner, D. 2023. Citizen science for water quality monitoring in the Meki River, Ethiopia: quality assurance and comparison with conventional methods. Water, 15(2):238. (Special issue: Field Methods for Water Quality Surveying) [doi: https://doi.org/10.3390/w15020238]
Water quality ; Monitoring ; Citizen science ; Scientists ; Quality assurance ; Pollution ; Physicochemical properties ; Parameters ; Rivers ; Irrigation / Ethiopia / Meki River
(Location: IWMI HQ Call no: e-copy only Record No: H052097)
https://www.mdpi.com/2073-4441/15/2/238/pdf?version=1673577779
https://vlibrary.iwmi.org/pdf/H052097.pdf
https://vlibrary.iwmi.org/pdf/H052097.pdf
(2.26 MB) (2.26 MB)
A lack of water quality information for many water bodies around the world makes it difficult to identify global change and discover early signs of myriad threats to freshwater resources. This problem is widely seen in Ethiopia due to absence of regular monitoring. Citizen science has a great potential to fill these gaps in water quality data, but there is concern about the accuracy of data collected by citizen scientists. Moreover, there is a gap to engage citizen scientists in water quality monitoring, and there is still insufficient awareness of how citizen scientists can become part of a collaborative scheme. This study aimed to evaluate the accuracy of water quality collected by citizen scientists and characterize the water quality of the Meki River with the involvement of citizen scientists. The suitability of the river water for irrigation was evaluated using a combination of citizen science and conventional water quality data collection methods. Water temperature, turbidity, ammonia, phosphate, nitrate, nitrite, total alkalinity, total hardness, and pH were analyzed by both citizen scientists and in a conventional laboratory. The citizen scientists’ data, expressed as percent of synthetic standard solution concentrations, indicated good agreement for selected water quality parameters: 123.8 ± 24.7% for PO4 3-, 115.6 ± 6.3% for NO3 -, 105.8 ± 7.4% for pH, and 133.3 ± 23.6% for NH4 + . Thus, citizen scientists can monitor and collect water quality data accurately. From the results, the Meki River water can be used for irrigation, but pollution sources should be controlled to reduce further quality deterioration as the population increases.
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