Press Release

Scientists Identify Genome-Wide Traits Associated with Microbial Growth Strategy and Ecosystem Nutrient Status

New Methods Developed May Shed Light on Evolution in the World’s Oceans

(La Jolla, California)—February 18, 2020—Scientists from the J. Craig Venter Institute (JCVI), Arizona State University (ASU), Flathead Lake Biological Station, United States Department of Agriculture (USDA), and Universidad Nacional Autónoma de México, Mexico published results in the journal eLife, identifying key genomic traits indicative of an ecosystem’s nutrient status with respect to nitrogen and phosphorus, key ingredients in fertilizer.

The study, focused on a low-nutrient (oligotrophic), phosphorus-deficient oasis in Cuatro Ciénegas, Mexico, is one of the first ever whole-ecosystem experiments involving replicated metagenomic assessments. After putting in place a grid that subdivided a pond into numerous mesocosms (an outdoor experimental system), scientists then fertilized a subset of these mesocosms in order to observe how the now nutrient-rich (copiotrophic) environments would cause the communities of organisms to respond.

Whole mixed microbial communities from the both fertilized and unfertilized mesocosms were collected and their DNA sequenced. Typically, scientists would then catalog the genes in the samples, predict what organisms they came from, and what they do. This type of analysis can suffer from database bias and other issues. Here, a novel approach was taken by cataloging fundamental phylogeny-agnostic genome “traits” instead.

Scientists working at Lagunita, site of the experimental pond. It was subdivided, allowing researchers to fertilize some areas with nitrogen and phosphorus. The platforms allowed samples to be taken from both fertilized and unfertilized sections without disturbing sediments. The pond is located in the valley of Cuatro Cienegas, Coahuila, Mexico. Photos courtesy Jim Elser / School of Sustainability, Arizona State University.

JCVI associate professor and a senior author on the study, Christopher Dupont, Ph.D. stated, “We hypothesized that microorganisms found in oligotrophic environments would, out of necessity, rely on low-resource strategies for replication of DNA, transcription of RNA, and translation of protein. Conversely, a copiotrophic environment favors resource-intensive strategies. The question is whether these basic traits could be turned into a metric for ecosystem nutrient status.”

The experiment confirmed the hypothesized genomic traits affecting the rates and costs of biochemical information processing within cells reflected the copiotrophic and oligotrophic mesocosms.

“This study is unique and powerful because it takes ideas from ecological study of large organisms and applies them to microbial communities in a whole-ecosystem experiment. By doing so, we were able, perhaps for the first time, to identify and confirm that there are fundamental genome-wide traits associated with systematic microbial responses to ecosystem nutrient status, without regard to the species identity of those microbes,” said Jim Elser, Ph.D., senior author on the study and research professor at the School of Sustainability, Arizona State University.

This metric provides an assessment of ecosystem productivity, something currently not possible using canonical metagenomic analyses. JCVI scientists, with funding from the NASA Astrobiology Institute, are now applying these methods to large-scale metagenomic surveys, including JCVI’s Global Ocean Sampling Expedition and Tara Ocean projects. These modern profiles of ecosystem growth will then be extrapolated into geological history using biogeochemical modeling. Ultimately, the hope is to map growth back in space and time.

Additional study participants include researchers from Rice University and University of Montana.

The full study, Genomic adaptations in information processing underpin trophic strategy in a whole-ecosystem nutrient enrichment experiment, can be found in the journal eLife at https://doi.org/10.7554/eLife.49816.

Background on JCVI’s Environmental Metagenomics Program

J. Craig Venter Institute’s Global Ocean Sampling Expedition used large-scale shotgun metagenomics sequencing to catalogue the microbial diversity of the world’s oceans and beyond. The program’s first study was conducted in 2003 in the Sargasso Sea. Following this successful endeavor, JCVI circumnavigated the globe for more than two years (2004-2006), covering a staggering 32,000 nautical miles, visiting 23 different countries and island groups on four continents. Subsequent voyages ensued. From 2007-2008 the Institute set its focus on diverse, and in some cases, extreme environments, including surface waters, deep sea thermal vents, high saline ponds, and polar ice. JCVI scientists again set out from 2009-2010 to sample the waters of the Baltic, Mediterranean, and Black Seas. JCVI’s environmental metagenomics expertise has been applied to other areas as well, such as studying the community of organisms living in the human gut, publishing the first human microbiome paper cataloging these organisms in 2006.

About J. Craig Venter Institute

The J. Craig Venter Institute (JCVI) is a not-for-profit research institute in Rockville, Maryland and La Jolla, California. dedicated to the advancement of the science of genomics; the understanding of its implications for society; and communication of those results to the scientific community, the public, and policymakers. Founded by J. Craig Venter, Ph.D., the JCVI is home to approximately 200 scientists and staff with expertise in human and evolutionary biology, genetics, bioinformatics/informatics, information technology, high-throughput DNA sequencing, genomic and environmental policy research, and public education in science and science policy. The JCVI is a 501(c)(3) organization. For additional information, please visit www.JCVI.org.

Media Contact

Matthew LaPointe, mlapointe@jcvi.org, 301-795-7918