Reconstructing Soil Microbiomes in High Tunnel Agricultural Systems Focus of Study

UNIVERSITY PARK, Pa .– The presence of high concentrations of salt and nitrogen in high tunnel soils may make it more difficult to rebuild a healthy soil microbiome after a soil cleaning event, according to microbial ecologists at Penn State . College of Agricultural Sciences.

The results of their research have important implications for soil fertility and, by extension, crop health and yields, explained Laura Kaminsky, doctoral student in plant pathology, who conducted the investigation under the direction of Terrence Bell, assistant professor of phytobiomes.

“Plants generally grow best with an active and diverse community of bacteria, fungi and other microbes in the soil,” she said. “If these microbes are eliminated by a soil cleaning event, we want to know how quickly the soil microbiome is rebounding and which microbes are most successful in recovering. Our study lays the groundwork for the future development of guidelines that will help farmers rebuild soils with microbial additives. “

The researchers focused on farming systems that use tall tunnels, which are greenhouse-like plastic structures placed on a section of field soil. These structures are used to extend the growing season and to grow high value crops such as tomatoes in a more protected setting.

However, the quality of the soil under high tunnels tends to deteriorate over time. “If the same crop is grown in a high tunnel year after year, the pathogens specific to that crop will accumulate to higher and higher levels in the soil and cause increasing amounts of crop disease,” Kaminsky said. .

One way to deal with this growing disease pressure is to reduce the pathogen population by removing the entire microbial community from the soil, which is done through chemical fumigation or through less harsh practices such as anaerobic soil disinfestation and soil solarization.

The problem, Kaminsky pointed out, is that these land clearing practices indiscriminately remove microbes from the soil, including microbes that benefit crop plants and microbes that perform general soil functions like cycling nutrients.

Kaminsky and Bell’s experiments, which took place at Buckhout’s lab in 2018 and 2019, specifically investigated whether high soil salinity and high soil nitrogen concentrations – two soil properties that often develop under high tunnels over time – altered the development of the soil microbiome.

To do this, the researchers buried small nylon mesh bags containing unsterilized “source” soil in sterilized “recipient” soil and allowed them to incubate for seven weeks. This allowed microbes to colonize in the recipient soil, simulating how microbes from the soil surrounding an area of ​​cleared soil would recolonize the cleared soil over time. Recipient soils were amended with salt, nitrogen, both, or neither to determine if these properties impacted the composition of microbial communities in the recipient soil.

The team sampled the recipient soil at two times: one week and seven weeks of incubation. At each point in time, researchers have characterized the microbial community by measuring microbial biomass and cataloging the bacterial species present using gene sequencing techniques.

After the first week, the microbial communities had a relatively low biomass and were dominated by a very limited set of species from the genera Bacillus and Paenibacillus. At seven weeks, there was a much larger and more diverse microbial community.

Lana T. Arthur