First-ever one-day, island-wide soil microbiome study completed on Crete

It was nothing short of "groundbreaking" research—literally. Scientists conducted the first-ever study of an island's soil microbiome—on Crete—all in one day—a major challenge since the Greek island is about 160-miles long and rises more than 8,000 feet above sea level.

The genomic sequencing and analysis of more than 435 samples taken that day have just been published in Environmental Microbiome.

A microbiome is the community of organisms—bacteria, fungi, viruses—that live together in one space, such as in the gut, on the skin, or in water or soil. A healthy soil microbiome is critical for maintaining a thriving ecosystem, including mitigating climate change, sustaining plant health, and balancing carbon dioxide in the atmosphere.

"It was a history-making day—the first large-scale, island-wide sampling ever conducted on Crete, and the first comprehensive survey of its soil microbiome. From coastal beaches to mountain peaks, the Island Sampling Day captured a snapshot in time," said the study's lead author Johanna Holm, Ph.D., a researcher at the Center for Advanced Microbiome Research and Innovation (CAMRI) and Assistant Professor at the University of Maryland School of Medicine (UMSOM).

"Most importantly, by collecting the soil samples all on the same day, we minimized variation from weather fluctuations, seasons, and land usage."

During the annual meeting of the Genomic Standards Consortium (GSC) on June 15, 2016, scientists and citizen volunteers sampled soil across 72 locations throughout Crete.

The GSC is an international group of scientists whose mission is to develop metadata standards for reporting genomic data so that it is easily discoverable and interoperable to researchers across different countries. The GSC developed strict sampling protocols, ensuring the collection was standardized and scientifically rigorous.

Some of the results surprised the researchers. For example, they discovered that microbes in the Crete soil remained highly diverse throughout the island.

"We thought that perhaps the elevation might reduce the microbial diversity due to more extreme conditions," said Lynn Schriml, Ph.D., the study leader, Professor, and scientist at UMSOM's Institute for Genome Sciences (IGS) and GSC President. "We found that it was a combination of environmental factors, soil moisture, and nitrogen that drove microbial diversity across ecozones."

In addition to creating a new framework for comparing ecosystems by collecting all samples in one day, the GSC has made this data openly available for reuse, encouraging future studies. Data can be accessed on GitHub.