Advancing the science of freshwater research for more than 40 years

Fall 2011

Upstream

Newsletter

Stroud™ Scientists at Work

The Magic of Revealing the Mysteries of Metaecosystems

By Diane Huskinson

Abracadabra

“Any sufficiently advanced technology is indistinguishable from magic.” — Sir Arthur Charles Clarke, Author and Inventor

In a long white lab coat, wearing pale blue, translucent medical gloves, Jinjun Kan sits at what’s called a clean bench. The scene is stark, white, sterile. To prevent his samples from being contaminated, Kan has already disinfected the bench’s tabletop. Like a magician about to make his assistant disappear, he pulls down a screen over the opening of the work area. With the flip of a UV light switch, presto chango, the microorganisms inside are gone, or rather, dead. For his next trick, Kan gathers a set of 12 stream sediment samples containing microorganisms from which he will extract those mysterious double-stranded genetic coding materials of all life — DNA.

His work is part of a new study funded through a grant from the National Science Foundation (NSF).

The History Behind the Science

Using cutting-edge technologies, Center scientists Lou Kaplan and Jinjun Kan in collaboration with Robert Findlay of University of Alabama and Jen Mosher, who will join the Center staff when she leaves Oak Ridge National Laboratory in early 2012, are building on the scientific theories set forth in the River Continuum Concept (RCC), the idea that a river is not a static body of water but rather a dynamic flow of ecosystems that varies throughout a river’s course.

It was the RCC that initially brought worldwide attention to the work being done at Stroud™ Water Research Center.

Robin L. Vannote and some of his fellow researchers published the RCC in 1980, forming a new foundation for river studies that is still applicable today. Vannote, who was the director of the Center at the time, and his colleagues recognized that downstream aquatic communities are linked to those that exist upstream. Much like how the human digestive system breaks down food — first in the mouth through chewing, then through the esophagus to the stomach and then the intestines for further processing and absorption of nutrients — a river’s aquatic microbial communities in the headwaters begin to process dissolved organic matter (DOM), organic chemicals that dissolve out of leaves or algae or are excreted by organisms into stream water, using some of the molecules while other molecules “escape” downstream. According to the RCC, downstream aquatic communities are specially adapted to exploit inefficiencies in their upstream counterparts.

The model was ahead of its time, and in fact, until recently, its predictions concerning DOM molecules and species of bacteria couldn’t even be fully tested. The technology to do so was simply lacking.

But a little something — or perhaps more accurately, a big explosion of information centered around things so small they can’t be seen with the naked eye — called the molecular revolutions in microbiology and geochemistry have yielded new and improved tools like the simple molecule DNA sequencer and ultrahigh-resolution mass spectrometer. Kaplan says, “There’s very few of these mass spectrometers in the world. We’re talking a million-dollar instrument, but the National Science Foundation provides community access to one through Florida State University [at the National NSF High-Field FT-ICR Mass Spectrometry Facility].” And thanks to the University of Delaware Biotechnology Institute, they’ll also have access to a high-throughput DNA sequencer that will reveal the identity of bacterial species. Together they’ll work to detect the composition of a broad spectrum of DOM molecules and the communities of bacterial species that use the DOM as a food resource through entire river networks.

Magic in the Making

Detecting molecules will play an integral role in the research team’s study of the quality and quantity of DOM that serves as a food source for the quadrillions of microorganisms that live in streams and rivers. The scientists want to know what is the influence of DOM on the structure and function of the communities of microorganisms.

To find out, they’ll employ a natural tracer: ¹³C. Short for carbon 13, it’s one of only two stable carbon isotopes that exist in nature. Carbon 12 (¹²C) accounts for 99 percent of carbon in the atmosphere of Earth. The remaining 1 percent is ¹³C. Labeling DOM with the much less common ¹³C is like planting a tracking device: it can be traced to see which microorganisms process what and to what extent. The process is called stable isotope probing, and it’s another hot trend in the world of microbial ecology.

Microorganisms comprise most of the genetic biodiversity on Earth, so understanding microbial community structure is an important aspect of understanding how ecosystems function, and that’s why the Education Department at the Center is working closely with the scientists to interpret results to the general public and develop educational materials for K-12 teachers and students. Yet studies within freshwater habitats have lagged behind studies of marine and soil communities and have focused primarily on the plankton or seston suspended in the water in lakes or large rivers. Few studies have been done on the communities that make up the freshwater biofilms found on rocks and sand grains at the bottom of streams and rivers, and those that have done so have relied on technologies that were limited in their ability to detect rare or small populations.

Kan explains that the traditional method of identifying microorganisms through culture captures a small percentage, fewer than 1 percent, of the existing populations within a given stream, but advancements in both technology and knowledge now allow them to extract the DNA from the bacterial cells and characterize microorganisms at the species level.

“All the prior knowledge was based on the ability to grow organisms in culture. Some organisms are fastidious, and knowing how to culture them is an art,” says Kaplan.

Working from three forested headwater stream ecosystems — White Clay Creek (WCC) in the Pennsylvania Piedmont, Río Tempisquito in the Cordillera de Guanacaste of Costa Rica, and the Neversink River in the Catskill Mountains of New York — the research team will now be able to detect and analyze those rare populations, and more common ones too, as well as the DOM that they hypothesize is linked to the upstream-downstream variations in aquatic communities.

While recent advancements have opened the door for the researchers to explore new scientific territory, earlier studies at Stroud Water Research Center have led them to this point. Stroud scientists have worked in each of these waters before, and their experience continues to foster a deeper understanding of freshwater systems. So often it seems that a bright idea comes out of nowhere like a light switch that is suddenly flipped on; it’s easy to forget the electrical engineer who installed the wiring. Stroud Center science is all about the wires.

“The River Continuum Concept was based on decades of studying streams,” says Kaplan.

Hot on the trail that led to the RCC, the team expects to both challenge but mostly confirm its predictions. Chief among the challenges relates to the question of where diversity peaks in a stream. The RCC predicts that the diversity of soluble organic compounds is at its highest in first-order streams, the first and smallest in a stream hierarchy of 12 orders, and declines sharply thereafter, especially in third-order streams, but researchers now think that DOM diversity is high throughout an entire river network and perhaps doesn’t peak until midorder reaches.

Other key questions will be: Does the composition of DOM display longitudinal trends across stream orders throughout river networks? Do the spatial distributions of bacterial populations display longitudinal trends across stream orders throughout river networks? And does DOM molecular composition structure the composition and function of communities of heterotrophic bacteria, that is, bacteria that must take in and digest food to survive? The predicted answers: yes to all three.

“The invisible world in stream ecosystems that includes communities with thousands of different species of microorganisms which compete for food in the form of 10,000 different organic compounds is fascinating,” says Kaplan. “That invisible world profoundly affects our daily lives, and we are excited by this opportunity to explore its beauty and complexity.”

Links:

To read more about the River Continuum Concept, go to: http://www.stroudcenter.org/about/portrait/continuum.shtm

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