Microbiologist’s work rides crest of technology

Paul Johnson_GSC
Paul Johnson

Imaging to sequencing, 45-year career spans field’s advances

As Paul Johnson, manager of the RI Genomics and Sequencing Center (GSC) at University of Rhode Island (URI), heads into retirement at the end of May, he leaves both a field vastly changed in his time and a promising legacy for the future of Ocean State research.

Sitting behind his office desk at the RI EPSCoR core facility, on the third floor of the Center for Biotechnology and Life Sciences (CBLS), Johnson smiles easily as he talks about starting at URI as an undergraduate in 1965, earning his BS degree in Bacteriology, the precursor to what would become the Department of Cell and Molecular Biology. He earned his master’s in Microbiology at the University of Massachusetts in 1972, and then returned to URI to conduct research on marine microorganisms for the late Professor John Sieburth at the Graduate School of Oceanography (GSO).

For the most part, Johnson says, the position involved culturing diverse microbes from a variety of marine sources as well as examining the native microorganisms from environments like Narragansett Bay, Narrow River, and the North Atlantic Ocean, and using light, transmission electron and scanning electron microscopy. In his 18 years at GSO, Johnson figures he probably acquired more than 60,000 images of microorganisms, many of which had never been seen before.

“On one occasion, we looked at water samples from Narragansett Bay during a bloom of a small alga in what was called a ‘brown tide,'” Johnson recalls from a summer 1985 event as he reflects on some of his memorable research events. “It was pretty significant. The state went on to close shellfishing in the Bay since another toxic bloom of the same species had occurred on Long Island, NY. In addition to publishing a description of the alga that caused the brown tide, in the same water samples we also found an extremely abundant testacean, an amoeba that makes its own shell, which was described in a second publication.”

In another study involving the chemistry and microbiota of the Narrow River and its upper basin, Johnson says the lab encountered a green ciliate, a single-celled organism that preys upon a single-cell alga, Euglena: “What was unique about that observation made by using light and electron microscopy was that the ciliate, Perispira, was found to sequester or retain and not digest the mitochondria and chloroplasts of its prey possibly using these foreign organelles in its own metabolism.”

The RI Genomics and Sequencing Center staff, from left, Janet Atoyan, genomics technician; Professor David Nelson, director; and Paul Johnson, manager.

These same water samples also led to the observation of a diverse population of bacterial cells, which contain chains of tiny magnets.  The phenomenon of magnetotactic bacteria had been described previously but never seen in Narrow River. These and other findings, says Johnson, add to the body of knowledge about Rhode Island’s coastal waters.

In July 1990, Johnson left GSO to manage the Microbiology Department’s electron microscopy facility, then housed in Morrill Hall, and shifted his attention away from basic research to training students and staff, and doing electron microscopy for facility users. He stayed in that position until 2002, when URI Professor David Nelson, Cell and Molecular Biology, secured a National Science Foundation (NSF) award to purchase DNA sequencing equipment.

“Instead of looking at organisms with microscopy alone, we’re now looking at genes and the genome,” Johnson explains, putting the technological evolution into context. “Now, when you want to know who is present in the Bay, you don’t just do imaging — you also look at the DNA and it tells you who is there. It may not tell you what they are doing, but it gives you a wider view of the spectrum of organisms.”

In 2006, an initial round of funding for Rhode Island NSF Experimental Program to Stimulate Competitive Research (EPSCoR) increased the GSC’s capabilities and opened up the facility’s sequencing services to more users across the state. As a shared center, the GSC provides capabilities that individual institutions otherwise could not afford on their own, with equipment that handles increased data loads at a much more rapid pace.

Nelson, GSC director, says he got to know Johnson in his position as manager of the electron microscopy facility and quickly realized his value.

“Here was a guy who enjoys work, pays very close attention to detail, and is fanatical about getting it done correctly,” Nelson says. “He’s incredibly responsible.”

When the time came to set up the sequencing facility, Nelson adds, “He could take my vision and turn it into reality; set up the facility to make it inviting and make sure the work got done on time and with good results. What scientists want is to go to a place, having spent a lot of time and maybe a fair amount of money collecting this sample, and say, ‘You guys take it and give me the information contained within.’ Paul can do that.”

The sequencing of a genome can reveal the cause of disease and offer clues to its vulnerability, possibly leading to a vaccine or another method of inhibiting the activity of a toxin. Johnson, along with genomics technician Janet Atoyan, has been dedicated to the vision of providing the services scientists need to gain a better understanding of how genes are regulated and how they function, according to Nelson.

Under Johnson’s management, the GSC continues to progress with scientific advancements. He has seen the facility evolve from one DNA sequencer that worked well, but slowly, conducting eight samples at a time, to two machines that can analyze two and three times the number of samples more quickly. And, a third machine, operating on different technology, rather than sequencing one piece of DNA, can read a few million bases at once for the sequencing of an entire genome to determine who or what exists in an environment.

Johnson marvels at the advances in technology and the dramatic shift from taking images with a microscope to unraveling the mysteries encoded in DNA: “I thought I’d be doing imaging for the rest of my career. The advances now are happening so quickly. They’re using DNA sequencing to diagnose the potential for future illnesses. If you want to find out where your ancestors came from, you can spend $100 and get that information. The electronics are just phenomenal — that’s what is going to push the science. Instead of $1,500 for a MiSeq (sequencing) run, in five years it could be a few hundred dollars.”

But, Johnson has other plans than keeping pace with technology. An avid and accomplished photographer, he says he aims to spend his retirement in the garden, traveling and with his family and grandchildren.

Story and photos by Amy Dunkle