Lisa Fultz, Adam Bigott and Jeff Hoy

In Louisiana, sugarcane has been grown on some of the same soils for more than 200 years. Yield decline, a phenomenon wherein long-term sugarcane cropping produces decreased yields compared with fields recently converted for sugarcane cultivation (what the farmers call “new ground”), has been documented in multiple regions. Alternative cropping practices, such as planting pasture or other crops and fallow periods, have been used to alleviate declines in sugarcane production. Because these approaches may not be practical or economical, there is a need to better understand the cause of yield decline associated with sugarcane monoculture. Previous research using biocides or sterilized soils has resulted in improved yields, suggesting the importance of soil microbiology in maintaining sugarcane productivity.

Soil microbiology plays a significant role in agricultural production. Microbes are responsible for the breakdown of crop residue, the release of nutrients and increased soil stability, and they can cause or suppress plant disease. However, the study of soil microbiology — specifically microbial communities — has been limited in the past due to highly variable soil properties. Of the billions of soil microbes found in less soil than would fill a thimble, scientists had been able to identify only about five percent of the species present. Previous methods were limited by researchers’ ability to culture organisms in the lab. Now, improvements in next generation sequencing technologies have enabled the production of millions of genetic sequences that can be used to identify most of the organisms in soil samples. This has dramatically improved scientists’ ability to identify and then compare biological communities associated with plant roots. For this reason, genomic sequencing is now being used to better understand changes in microbial communities following changes in farming systems.

A current study selected six sites with paired fields, one new ground in the first year of sugarcane production and one under long-term sugarcane production. To limit variation, fields were paired based on the same or similar soil types and were planted with the same sugarcane variety. Of the six new-ground fields, two had been forested and four had been in pasture. Soil samples were collected from both the soil in direct contact with the sugarcane roots and the soil within the sugarcane row. These samples were analyzed for macronutrients, micronutrients, organic matter, enzyme activity (responsible for the breakdown and release of carbon and nitrogen) and populations of bacteria and fungi.

Louisiana farmers have long observed improved plant growth that resulted in higher yields when sugarcane was planted on new ground. Yield results from paired fields in each of the six sites revealed sugarcane in new-ground fields generally out-yielded the long-term counterparts. New-ground sites averaged 50.2 tons of cane per acre compared with long-term fields, which averaged 36.1 tons of cane per acre.

Organic matter, macronutrients, micronutrients and soil extracellular enzymes were generally higher in new-ground soils. While differences were observed based on cropping history, results varied greatly among the six sites. Therefore, nutrient differences alone did not provide a consistent explanation for the new-ground effect.

Staining sugarcane roots from paired fields at three sites revealed greater fungal endophyte colonization in long-term cultivation soils. Fungal endophytes are organisms that live within plant tissue. Their effects can range from beneficial — increasing nutrient uptake and resistance to pests — to detrimental — acting as pathogens themselves.

Sequencing of extracted microbial DNA from soils produces extensive data sets for identifying organisms and the makeup of the microbial community. These data sets can be evaluated to determine if system management differences have any relationship to shifts in the composition of microbial communities. Bacterial population analysis revealed that differences in the structure of microbial communities associated with roots were based primarily on site or location, while the crop production history of a field had no consistent effect on changes in the bacterial community.

Differences in fungal communities, however, were related to cropping history, or how long the site had been in sugarcane production. For example, relative to all other identified organisms, populations of Basidiomycota fungi were generally greater in fields under long-term cultivation. Some of these fungi form long, branching structures that can increase the overall surface area of the plant root system. When these fungi form symbiotic relationships with plants, they can increase their access to plant nutrients and soil moisture, promoting overall plant growth. However, plant pathogens are also found in this group of fungi necessitating further investigation into the distribution of beneficial and harmful organisms within the soil.

Overall, 58 potentially detrimental fungi were identified in greater quantities in soils under long-term sugarcane cultivation while 37 potentially beneficial fungi were greater in new-ground sugarcane cultivation. This suggests that fungi are major contributors to decreased yields associated with long-term sugarcane production. Further exploration of these distinct differences in the fungal community is the next step in understanding and developing management strategies to counter the yield decline associated with sugarcane monoculture.

Lisa Fultz is an assistant professor in the School of Plant, Environmental, and Soil Sciences; and Adam Bigott is a graduate student and Jeff Hoy is a professor in the Department of Plant Pathology and Crop Physiology.

(This article appears in the winter 2018 issue of Louisiana Agriculture.)