A census of the soil microbiome

Many people have experienced the mysterious death of a houseplant. Despite the abundance of water and sunlight, something invisible appears to be happening beneath the soil surface to sabotage the plant’s health. Just as communities of microbes live in the human gut and affect human health, the so-called soil microbiome of bacteria and fungi intimately affects plant health starting from the root.

In our changing climate, a thorough understanding of healthy soil microbiomes will lead to more resilient crops and thus more sustainable food sources. Now, a team led by Caltech researchers has developed a new computational technique to analyze the DNA present within a soil sample in order to detect the microbial species present. The technique revealed new knowledge on bacterial species that protect plants from pathogenic fungi.

The work was carried out in the laboratory of Dianne Newman, Gordon M. Binder / Amgen Professor of Biology and Geobiology and Executive Officer for Molecular Biology. Newman is the head of the Ecology and Biosphere Engineering Initiative at Caltech’s Resnick Sustainability Institute.

“While great strides have been made in understanding the human microbiome over the past decade, our comparative understanding of the soil microbiome is lagging behind,” says Newman. “Yet soil is a critically important microbial reservoir, given its direct link to food security, water and nutrient retention and the global carbon balance.”

Led by postdoctoral scholar Daniel Dar, the new study presents a computational algorithm for analyzing DNA from soil and root samples to quantify the abundance of bacteria with specific functional characteristics. The soil microbiome is often referred to as “microbial dark matter” because many of these species cannot be grown easily in the laboratory. Therefore, taking a soil sample and attempting to grow bacteria from it is not a reliable way to determine which species are present. Dar’s computation method, combined with techniques for sequencing DNA in an environment, allows microbiologists to examine complex populations of bacteria and fungi in a sample and accurately quantify the abundance of members carrying specific genes, such as genes for antibiotics.

Specifically, the team was interested in using the method to measure the abundance of certain types of bacteria that produce antibiotic and antifungal molecules called phenazines. These bacteria occupy the rhizosphere, a nutrient-rich habitat in the soil surrounding a plant’s roots, and phenazines act as a line of defense against pathogenic microbes, to prevent them from invading this space too. The plant also benefits from phenazine-producing bacteria, as the roots are protected from infectious and harmful fungi.

To test the accuracy of his computational algorithm, Dar collaborated with collaborators Linda Thomashow and David Weller of the USDA Agricultural Research Service. Thomashow and Weller carefully maintain and monitor experimental wheat plots located near commercial wheat fields in Washington state and have found that phenazine-producing species called fluorescent pseudomonads are often found in soil that grows healthy plants. The researchers sequenced environmental DNA from these grain batches and found that Dar’s algorithm correctly quantified the abundance of fluorescent pseudomonads, validating the effectiveness of this new computation method in the field. But surprisingly, the algorithm also revealed an abundance of several phenazine-producing bacteria, from a group called Streptomyces. This suggests that the protective effects of phenazines in the field could be mediated by multiple species; these species can now be the subject of targeted laboratory experiments.

Next, the team turned to publicly deposited DNA sequence data sets that had been obtained from hundreds of different soil and plant environments around the world. These environments included natural and agricultural soils as well as the root microbiomes of staple crops such as wheat, corn and sugar cane. The team ran these datasets through their own algorithm and found that phenazine-producing bacteria are abundant in many environments and, in particular, enriched in crop-associated microbiomes. The algorithm also revealed another surprise: a certain previously unknown phenazine-producing species called Dyella japonica is abundant among crops, particularly corn.

The team examined Dyella in the laboratory with genomic, genetic and other experimental techniques to define the type of phenazine it produces, the conditions under which the compound is produced, and the genes involved. Using advanced microscopy, the researchers discovered an intimate relationship between Dyella and corn; the microorganism is found inside the roots of plants rather than on the surface, as is more common among phenazine producing organisms, and also along the tips of the root hairs where many nutrients for the microorganisms are found.

“Understanding the species that make up a healthy soil microbiome could one day help naturally ‘engineer’ crop environments to improve crop yield, as a kind of soil probiotic,” says Dar. “These findings reinforce the theory that phenazines are important molecules for crop health.”

The paper is titled “The global panorama of phenazine biosynthesis and biodegradation reveals species-specific colonization patterns in agricultural soils and crop microbiomes”. Dar is the first author of the document. Thomashow, Weller and Newman are co-authors. Newman is the senior corresponding author of the study. Funding was provided by the National Institutes of Health, the Army Research Office, the Rothschild Foundation, EMBO, the Helen Hay Whitney Foundation, and Caltech’s Division of Geological and Planetary Sciences.