National Microbiome InitiativeBlack-band disease appears on a coral colony of Montastraea cavernosa in the Florida Keys. AOML researchers hope to identify genetic variants to understand why some corals are more resistant to the disease than others.On May 13th, the White House Office of Science and Technology Policy introduced the National Microbiome Initiative, an effort to support multi-agency research to sample and better understand communities of micro-organisms that are critical to both human health and the world's ecosystems. As the nation's premier ocean science agency, NOAA is leading interdisciplinary research to improve the observation and assessment of marine microbiomes. In support of this national initiative, AOML received nearly $2 million in funding this year to conduct a number of projects that integrate genetic sampling techniques and technologies to advance understanding of the ocean's microbiomes.

Microbiomes are communities of diverse microscopic organisms that include plants, animals, fungi, viruses, bacteria, and other organisms that live on and inside of people, plants, animals, soil, the oceans, and the atmosphere. These microbiomes can influence human health, climate change, and food security, as well as many other aspects of our lives and the environment.

By sampling DNA, RNA, and proteins from single cells to whole organisms to entire communities, scientists hope to better understand where these organisms are, what they are doing, how they are affected by changing environmental conditions, and how they, in turn, affect the environment. The multi-disciplinary research conducted at AOML leverages existing resources and partnerships to enhance ecosystem observations and establish new approaches to assessing these communities.

At research sites in Florida and the Caribbean, AOML scientists and their partners will sample coral reefs, seawater, and marine sediments to identify genetic variations that may explain why some corals are more susceptible or resilient to bleaching and coral diseases than others. With a focus on two species of rare and endangered corals, scientists will collect and study coral tissue to identify the genetic makeup and diversity of the microbiome, which currently consists of poorly understood communities of micro-organisms living in close association with the corals.

Researchers hope to identify the genetic traits of the most resilient corals and their microbial communities by using next-generation-sequencing of the DNA and RNA associated with these microbiome communities before, during, and after bleaching or coral disease events. Experiments aim to identify communities associated with the corals that are resistant to warming waters and disease to advise coral restoration efforts across the region. 

Another collaborative project will test the potential benefit of a state-of-the-art autonomous underwater vehicle (AUV) to conduct marine microbiome analysis. Successful development and transition of genomic analysis using AUV technology could reduce sample processing time, ship time needs and costs, and reliance on tissue sample collection. This work will test instrumentation from the Monterey Bay Research Institute in partnership with the J. Craig Venter Institute, NOAA's National Marine Fisheries Service, and the Scripps Institution of Oceanography.

In addition to assessing the microbiome to improve the understanding of food web dynamics, the project will also include field-testing of a new technique known as environmental DNA (eDNA), which can be used to detect the genetic signature of macro-organisms such as invertebrates or fish by analyzing cells that have been shed into the water column. Understanding the connection between the marine microbiome and fisheries holds the potential to improve the ability to monitor and predict ecosystem responses to environmental change.

NOAA is also working to enhance an existing ecosystem observation program by adding genetic sampling technology. The multi-agency California Cooperative Oceanic Fisheries Investigations (CalCOFI) program is one of the longest-running ocean observing projects in the US and seeks to gain a more comprehensive understanding of the dynamics of the California Current ecosystem to foster stewardship, resilience, and sustainable resource management.

By including genetic sampling technologies as part of CalCOFI, scientists hope to improve their understanding of the diversity and function of microbes in the ecosystem, enabling better prediction of ecosystem response to environmental pressures, including climate change. This project is a pilot for potentially broader applications to other regions and to NOAA's fleet of research ships.

New projects at AOML will focus on increasing computing capacity and enhancing bioinformatic capabilities. Bioinformatics is the application of computer science to analyze and integrate biological and genetic information. This new field has developed in response to the massive amounts of sequencing data generated by the types of studies described above, all of which rely on bioinformatics. AOML's bioinformatic capabilities will be used to better understand and predict ecosystem responses to changing environmental conditions.