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New York City Drinking Water Microbiome Study Reveals Variety of Bacterial Species

NEW YORK (GenomeWeb) – New York City drinking water harbors hundreds of types of bacteria that differ somewhat in composition depending on where samples are taken on the water's way from reservoirs to city buildings, according to early results from an ongoing microbiome study conducted by the New York City Department of Health and Mental Hygiene.

Overall, the study found almost 700 different bacterial species, of which about 560 were detected in samples of distributed water that had undergone treatment, according to Enoma Omoregie, chief of environmental services at the NYC DOHMH's Public Health Laboratory. He presented preliminary results from the study at a meeting about metagenomics in urban settings at New York University last week.

It is well known that drinking water contains a variety of microorganisms — most of them harmless — that can influence the water's properties such as odor and taste, he explained, and several drinking water microbiome studies have already been conducted in other cities. Also, drinking water is already tested daily for potential pathogens, such as enteric bacteria.

However, the microbial composition of NYC's drinking water has not been explored yet, and given its potential significance for consumers' health, Omoregie and his team set out to characterize the water's microbiome, including archaea, bacteria, and eukaryotes. 

New York City's 8.5 million plus residents get their water from reservoirs upstate that are part of the Catskill/Delaware Watersheds area, west of the Hudson River, and the Croton Watershed area east of the Hudson.

The water flows through aqueducts to one of two treatment plants, where UV light is used to kill germs and where chemicals such as chlorine and fluoride are added. From there, it is distributed to the city through several major tunnels.

In the City, almost 1,000 water sampling stations are used to monitor the water daily, and about 600,000 microbial or chemical tests are conducted each year to ensure that residents can enjoy what NYC says is among "the best drinking water in the nation."

For their study, Omoregie and his team took samples from several dozen sites across the five boroughs and beyond — including untreated water and treated water — at regular intervals between November 2017 and now, with the last sampling still to come.

So far, they have collected more than 250 samples, he reported, in which they measured a variety of both physico-chemical and microbial parameters. To study the water's microbiome, they opted for 16S rRNA sequencing with Illumina instrumentation, which he pointed out only covers bacteria but not eukaryotic microbes, such as amoebae or fungi.

For their initial analysis, the researchers focused on 70 untreated and treated water samples, collected in December of 2017 and in February, April, and June of this year. They also included five samples from New York City cooling towers.

In total, they detected 695 different bacterial species, of which 595 were found in treated water samples. Many of those species are very common to water systems, Omoregie said, and known to be part of environmental processes such as the carbon, nitrogen, iron, and sulfur cycle.

In good news for NYC residents, his team discovered very few enteric bacteria, such as E. coli and Salmonella, which he said may be due in part to the fact that the city owns many of the reservoirs and does not allow animal farms nearby that could serve as a sources for intestinal bacteria.

The analysis did pick up a few types of bacteria, though, such as Legionella and Mycobacterium, that count pathogenic species among them. However, other species that are part of these genera are common in freshwater aquatic systems, he said, and the sequence data was unable to determine whether the bacteria identified in the samples were pathogenic.

When the researchers compared the bacterial communities in the three sample types — untreated water, treated water, and cooling tower water — they discovered that some bacteria were more common in one type than the others. For example, about 70 percent of the bacteria in the untreated samples were actinobacteria, which are common degraders of organic matter, whereas only about 5 percent of bacteria in the other two sample types were actinobacteria. Conversely, up to 30 percent of the bacteria in the treated or the cooling tower samples were alphaproteobacteria, but they only made up about 5 percent of the bacteria in the untreated samples.

The next step of the analysis will be to correlate bacterial composition with a variety of environmental variables that were measured in the samples, he said. The researchers also plan to extend their analysis to ribosomal RNA from archaea and eukaryotes going forward.

Finally, in a collaboration with Arc Bio, a startup that is developing next-generation sequencing for pathogen detection, the team plans to conduct shotgun metagenomic sequencing and make functional predictions from the sequences found.