Despite the ubiquity and importance of microbial eukaryotes (protists) in terrestrial and aquatic habitats, and animal and human microbiomes, population studies of protists in those environments are still scarce. In my lab researchers are attempting to redress this imbalance, and one step in this direction is our paper "Patterns of protist diversity associated with raw sewage in New York City" just published. This paper is the culmination of several years' work by Julia Maritz for her PhD (see Fig. 1) and was funded by a Grand Challenge grant from New York University (you can see a movie about the project here https://www.nyu.edu/about/news-publications/news/2013/september/nyu-announces-winners-of-grand-challenge-science-competition.html) as well as the Alfred P. Sloan Foundation.
Sewage! It’s a rich broth of urban microbes from a variety of sources, including human and animal waste, leftovers from restaurants, industrial processes, and green spaces. To study it we took advantage of New York City’s 14 wastewater treatment plants located in the five boroughs -- Manhattan, Brooklyn, Staten Island, the Bronx, and Queens – through the generosity of the city's Department of Environmental Protection (NYCDEP). With the help of the wonderful employees of the NYCDEP and especially the team at the Newton Creek plant in Brooklyn, we were able to collect composite samples from each plant quarterly over a 12 month period, and compare them to samples from soil, storm water, and sediment. Using a combination of amplicon sequencing of the 18S rDNA marker gene and shotgun metagenomics, we identified the weird and wonderful protist communities in each of the boroughs, how they changed over time, and their functional and network interactions. Our findings underscore the value of sewage as a biomarker for monitoring patterns in urban microbes, and provide a baseline protist metagenome of NYC.
When I was first contacted about writing a blog post for the "Behind the Paper" section of the Nature Research Microbiology Community, I leapt at the chance, not so much because we have published the coolest paper ever about the protist communities in NYC sewage (in my humble opinion), but because it gives me the opportunity to sing the virtues of collaboration between academics and local government organizations. We could not have undertaken such an extensive study without access to all the wastewater treatment plants of the NYCDEP. And though establishing a relationship of trust and mutual understanding with city officials required multiple treks from Greenwich Village to Newton Creek and several presentations describing our project and its goals, the knowledge exchanged and collaborative bonds forged were well worth the effort.
So, what next? While our study examined the protist populations of sewage collected from a variety of sources, it didn't tell us how those protists might be moving around the city. Our latest study will track protists in the pets (cats and dogs) and pests (cockroaches, rats, and pigeons) of New York, collected from all five NYC boroughs. Watch this space!
Fig. 1. Collecting samples of storm water (left) and sewage (right) from a private residential apartment complex in Manhattan.