Microbes Eat the Same in Labs and the Desert

Analyses of natural communities forming soil crusts agree with laboratory studies of isolated microbe-metabolite relationships.

The Science

Far from barren, arid lands host diverse communities of bacteria and other microbes. The biocrust these communities form affects local and global resources. The residents of these communities are dormant through long, dry spells, but are active when it rains. While it’s obvious that the community consumes more when it’s active, scientists need more details. Previous research used simplified tests to identify which community members thrived and which didn’t during wet and dry seasons. Now, a team examined microbes in their more complex native setting. They found the same patterns.

The Impact

This study sheds new light on the microbial communities that make up the biocrust. While that might seem like a small detail, 40 percent of the world’s land is arid. These communities affect the soil chemistry. That chemistry affects water availability, soil fertility, and the movement of nutrients and energy. This study gets us closer to understanding the complex microbial food webs and their impact on the global carbon cycle.


Scientists can determine the structure and metabolic potential of microbial communities by established metagenomic approaches. However, linking microbial species data to exogenous metabolites that microbes process and produce (the exometabolome) is still a challenge. A group of scientists at Lawrence Berkeley National Laboratory examined microbe-metabolite relationships in native biological arid soil crusts (biocrusts) upon changes in water availability. The water levels are a critical factor affecting metabolic activity in these ecosystems. The researchers discovered that those relationships are consistent with previous laboratory tests using bacterial isolates from the same ecosystems. Overall, most soil metabolites displayed the expected correlation with four dominant bacteria over time, after it rained. The results show that scientists can successfully combine metabolite profiling, shotgun sequencing, and exometabolomics to link microbial community structure with environmental chemistry. Such research techniques can shed light on biological carbon cycling processes in arid environments.

Principal Investigator(s)

Trent Northen
Lawrence Berkeley National Laboratory


The Office of Science Early Career Research Program, Office of Biological and Environmental Research, Office of Science, Department of Energy funded this research. DNA was sequenced using the Vincent J. Coates Genomics Sequencing Laboratory at the University of California, Berkeley, supported by a grant from the National Institutes of Health.


T.L. Swenson, U. Karaoz, J.M. Swenson, B.P. Bowen, and T.R. Northen, “Linking soil biology and chemistry in biological soil crust using isolate exometabolomics.” Nature Communications 9, 19 (2018). [DOI: 10.1038/s41467-017-02356-9]