Window Opens on the Secret Life of Microbes: Scientists Develop First Microbial Profiles of Ecosystems

Coral from Kingman atol (Northern Line Islands). Coral ecosystems were among those profiled by the researchers. Credit: Forest Rohwe, San Diego State University.

Nowhere is the principle of "strength in numbers" more apparent than in the collective power of microbes: despite their simplicity, these one-cell organisms--which number about 5 million trillion trillion strong (no, that is not a typo) on Earth--affect virtually every ecological process, from the decay of organic material to the production of oxygen.

But even though microbes essentially rule the Earth, scientists have never before been able to conduct comprehensive studies of microbes and their interactions with one another in their natural habitats. Now, a new study--funded by the National Science Foundation (NSF) and described in the March 12, 2008 online issue of Nature--provides the first inventories of microbial capabilities in nine very different types of ecosystems, ranging from coral reefs to deep mines.

"These new microbial inventories provide a new and important window into ecosystems and how they respond to stresses, such as pesticide runoff and invasive species," said Lita Proctor, an NSF program director.

Rather than identifying the kinds of microbes that live in each ecosystem, the study catalogued each ecosystem's microbial "know-how," captured in its DNA, for conducting metabolic processes, such as respiration, photosynthesis and cell division. These microbial catalogues are more distinctive than the identities of resident microbes. "Now microbes can be studied by what they can do not who they are," said Proctor.

This microbial study employed the principles of metagenomics, a powerful new method of analysis that characterizes the DNA content of entire communities of organisms rather than individual species. One of the main advantages of metagenomics is that it enables scientists to study microbes--most of which cannot be grown in the laboratory--in their natural habitats.

Specifically, the microbial study produced the following results:

• A unique, identifying microbial fingerprint for each of nine different types of ecosystems. Each ecosystem's fingerprint was based on its unique suite of microbial capabilities.
• Methods for early detection of ecological responses to environmental stresses. Such methods are based on the principle that "microbes grow faster and so respond to environmental stresses more quickly than do other types of organisms," said Forest Rohwer of San Diego State University, a member of the research team. Because microbes are an ecosystem's first-responders, by monitoring changes in an ecosystem's microbial capabilities, scientists can detect ecological responses to stresses earlier than would otherwise be possible--even before such responses might be visibly apparent in plants or animals, Rohwer said. <>·

NSF Co-Investigator:  Forest Rohwer,  San Diego State University

Contents thanks to the National Science Foundation: http://www.nsf.gov/ release of March 12, 2008 and Forest Rohwer, San Diego State University.

Note:  A related article that "more closely describes four of the metagenomes used in the Nature paper," according to Dr. Rohwer, appears in the PLoS ONE Open Access journal:

Microbial Ecology of Four Coral Atolls in the Northern Line Islands

by Elizabeth A. Dinsdale1,2.*, Olga Pantos1.¤, Steven Smriga3, Robert A. Edwards4,5, Florent Angly1, Linda Wegley1, Mark Hatay1, Dana Hall1, Elysa Brown1, Matthew Haynes1, Lutz Krause6, Enric Sala3, Stuart A. Sandin3, Rebecca Vega Thurber1, Bette L. Willis7, Farooq Azam3, Nancy Knowlton3, Forest Rohwer1,4*

Abstract:

Microbes are key players in both healthy and degraded coral reefs. A combination of metagenomics, microscopy, culturing, and water chemistry were used to characterize microbial communities on four coral atolls in the Northern Line Islands, central Pacific. Kingman, a small uninhabited atoll which lies most northerly in the chain, had microbial and water chemistry characteristic of an open ocean ecosystem. On this atoll the microbial community was equally divided between autotrophs (mostly Prochlorococcus spp.) and heterotrophs. In contrast, Kiritimati, a large and populated (,5500 people) atoll, which is most southerly in the chain, had microbial and water chemistry characteristic of a near-shore environment. On Kiritimati, there were 10 times more microbial cells and virus-like particles in the water column and these microbes were dominated by heterotrophs, including a large percentage of potential pathogens. Culturable Vibrios were common only on Kiritimati. The benthic community on Kiritimati had the highest prevalence of coral disease and lowest coral cover. The middle atolls, Palmyra and Tabuaeran, had intermediate densities of microbes and viruses and higher percentages of autotrophic microbes than either Kingman or Kiritimati. The differences in microbial communities across atolls could reflect variation in 1) oceanographic and/or hydrographic conditions or 2) human impacts associated with land-use and fishing. The fact that historically Kingman and Kiritimati did not differ strongly in their fish or benthic communities (both had large numbers of sharks and high coral cover) suggest an anthropogenic component in the differences in the microbial communities. Kingman is one of the world’s most pristine coral reefs, and this dataset should serve as a baseline for future studies of coral reef microbes. Obtaining the microbial data set, from atolls is particularly important given the association of microbes in the ongoing degradation of coral reef ecosystems worldwide.

     1 Department of Biology, San Diego State University, San Diego, California, United States of America, 2 School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia, 3 Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America, 4 Center for Microbial Sciences, San Diego State University, San Diego, California, United States of America, 5 Fellowship for Interpretation of Genomes, Burr Ridge, Illinois, United States of America, 6 Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany, 7 Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies, School of Marine and Tropical Biology, James Cook University, Townsville, Queensland, Australia

 PLoS ONB, www.plosone.org

February 2008/Volume 3/Issue 2/e1584