Managing Plant-parasitic Nematodes and Promoting Beneficial Soil Organisms Through Sod-based Crop Rotation

Research Objective 1 (Assess the impacts of sod-based crop rotation on plant-parasitic nematodes, beneficial nematodes, and soil microbial communities at different depths in the soil profile compared to a conventional peanut-cotton-cotton crop rotation.)

Our hypotheses for this objective were: (1) Sod-based rotation will better manage plant-parasitic nematodes and soil-borne plant pathogens throughout the soil profile than conventional rotation; (2) Beneficial nematode and microbe populations will be more robust in sod-based rotation, particularly deep in the soil profile. 

Results relating to hypothesis 1 of objective 1 (sod-based rotation will better manage plant-parasitic nematodes and soil-borne plant pathogens throughout the soil profile than conventional rotation):

Across all seasons, reniform nematode abundances have been highest in the upper soil profile (0-1 foot) and decreased incrementally as depth in the soil profile increases (Figure 1 from Preplant 2017 shown as an example).  Even at 3-4 feet deep in the soil profile, relatively substantial reniform nematode populations reside, suggesting that the most effective management strategies will be effective deep in the soil profile.  Reniform nematode depth distribution did not change substantially across seasons, suggesting vertical movement of this nematode in this system may be minimal. 

In preplant and winter samples, crop effects have been similar at all soil profile depths and reniform nematode abundances have been greater in conventional rotation, particularly cotton, than sod-based rotation (Figure 2).  In fall, the impact of cropping system on reniform nematode varied by depth in the soil profile (Figure 3, Fall 2018 shown as example). At shallow depths (0-1 feet), trends were similar to preplant/winter except that populations increased in sod-based cotton and were similar to conventional phases. At 1-2 feet, reniform nematode soil populations were still lower for sod-based than conventional rotation. At deeper depths, reniform nematode populations were low and there were not meaningful differences among crop phases.

            Crop rotation impacts and vertical distribution in the soil profile vary by particular plant-parasitic nematode.  For example, ring nematodes are present in this study and are considered a minor pest, particularly of peanut, and have a wide host range.  Across seasons, ring nematode abundances were consistently greater in SBR peanut than most other crop phases, particularly conventional cotton, at 0-1 feet deep in the soil profile (Figure 4).  Ring nematodes abundances crashed below 1 foot deep in the soil profile.  This highlights that there is no perfect crop rotation for all nematodes.  Sod-based rotation works well for reniform nematode because peanut and bahiagrass are non-hosts.  Based on results of this study, cotton is a poor host of the ring nematode population at this site, so the 2 years of cotton in conventional rotation work better than SBR for reducing its abundances.  In practical terms, ring nematode is not an important pest, so sod-based rotation is still a better choice in this scenario. However, these trends highlight the importance of knowing the nematodes in a field and how a particular rotation may affect them.  It also suggests ring nematode will easier to manage than reniform nematode with management strategies that affect shallow layers (such as nematicide application). Continuing to explore depth distribution for various important plant-parasitic nematodes has the potential to improve management of these pests.

       To conclude, our hypothesis that SBR will help manage plant-parasitic nematodes better than conventional rotation was generally supported. Sod-based rotation helped manage reniform nematode, the major plant-parasitic nematode at the site, but was not effective for ring nematode, a minor plant-parsitic nematode. Monitoring for plant-parasitic nematodes will continue to be important for growers that employ SBR. The results from this section of objective 1 are being prepared as a manuscript for peer-review publication.

Hypothesis 2 of objective 1 (Beneficial nematode and microbe populations will be more robust in sod-based rotation, particularly deep in the soil profile), here are the preliminary results for two groups of beneficial nematodes (fungal-feeding nematodes and bacteria-feeding nematodes):

            For fungal-feeding nematodes (beneficial nematodes that feed on fungi, which plays a role in nutrient mineralization), the results support our hypothesis that abundances will be more robust in SBR, but do not support the clause of the hypothesis that differences will be more apparent deeper in the soil profile.  Figure 5 shows fungal-feeding nematode results, which are similar to other seasons assessed. Consistently across seasons, at the 0-1 foot soil depth, fungal-feeding nematode abundances were greater in bahiagrass, particularly 2^nd-year bahiagrass, than any other crop phase (Figure 5).  Deeper than 1 foot deep in the soil profile, there were no differences among crop phases and nematode abundances were much lower than in the 0-1 foot depth. The relatively high C:N ratio found in bahiagrass is likely the driver for greater fungal-feeding nematode populations in SBR.

            In general, trends for bacteria-feeding nematodes (beneficial nematodes that feed on bacteria and also play a role in nutrient mineralization) did not match with our hypothesis either.  Similar to fungal-feeding nematode abundances, bacteria-feeding nematode abundances were greatest at 0-1 feet deep in the soil profile and were insubstantial below 1 foot deep in the soil profile (Figure 6).   Crop effects on bacteria-feeding nematodes were not biologically meaningful as they generally occurred deep in the soil profile where populations were very low.   

     Omnivores (nematodes that may feed on fungi or other nematodes) had perhaps the most intriguing results of any beneficial nematodes. Omnivore soil populations tended to be greater in cotton phases and, less consistently, bahiagrass phases (Figure 7). Differences were more pronounced at the 1-2 and 2-3 foot soil depths, unlike other beneficial nematodes that had low abundances below the plow layer (0-1 foot). This raises the possibility that the omnivores present are feeding on reniform nematode, which is why populations are high in cotton, even deeper in the soil profile.

    Assessment of the microbial community from deep soil profiles (1-4 feet) has not yet been successful due to challenges in extracting DNA from these layers with high clay content (and likely low microbial community population densities). For this reason, the microbial community was assessed only in the surface soil layer (0-1 feet) and roots. However, spurred in part by this project, the Liao lab has developed a published methodology for extracting microbial DNA from deep soil profiles (Guerra et al., 2020), which may be used for this project in the near future.

    Influence of crop rotation and irrigation on the microbial community in the soil plow layer for cotton has been published (Zhang et al., 2022) in Applied Soil Ecology. There were minimal differences in overall bacterial soil community diversity and structure among rotations (data not shown), but there were some differences among specific bacteria taxa. Certain groups of carbon-associated bacteria (Figure 8A) varied by rotation phase, with abundances lowest in 1st-year cotton conventional rotation. Nitrogen-associated bacteria taxa also varied by rotation phase, sometimes interacting with irrigation status (Figure 8B).

     Results for microbial communities in cotton roots are also under review for peer-reviewed publication. Bacterial community diversity in cotton roots was not affected by crop rotation or irrigation, but did vary by year (Figure 9A), which is similar to bacteria-feeding nematode results. In contrast, fungal community diversity in cotton roots was greater in SBR than conventional rotation (Figure 9C). An on-going question is how much beneficial soil communities (nematodes and microbes) contribute to crop production. In this system, increasing abundances of a number of fungal families was correlated with increased cotton yield in SBR, but not conventional rotation (Figure 10). This suggests a positive link between fungal soil communities and cotton production in diverse rotation.

     In summary, our second hypothesis for objective 1 was partially supported. Among benefical soil organisms assessed, fungi and fungal-feeding nematodes seemed to stimulated by SBR, but bacteria and bacterial feeding nematodes were less affected. Most groups of beneficial organisms are scarce below the plow layer and do not vary by rotation system. Omnivorous nematodes were the exception, and were more affected below the plow layer (1-3 feet), which supported our hypothesis, but increased with cotton phases, which did not support our hypothesis that SBR would increase beneficial nematodes.

Research Objective 2 (Assess the impact of nematicide application on non-target, beneficial organisms and determine if growers can eliminate nematicide application in sod-based rotation while maintaining plant-parasitic nematode management and crop yield.)

Our hypotheses for this objective were: (1) Sod-based rotation will manage plant-parasitic nematodes sufficiently without nematicide application; (2) Nematicide application will reduce populations of non-target, beneficial nematodes and microbes.  

Results for hypothesis 1 (SBR will manage nematodes without nematicide):

            No major plant-parasitic nematodes were found in peanut phases, so this objective focuses on cotton production. Results have been published in Schumacher et al. (2020) and are summarized here. Sod-based rotation consistently reduced reniform nematode abundances in soil and roots (Figure 11) compared with conventional rotation.  In some seasons, reniform nematode populations were also lower for 1st-year than 2nd-year conventional cotton. Nematicide application did not reduce reniform nematode populations in any season (data not shown), but nematode abundances should be viewed as only a portion of the picture when it comes to nematode management.  Early season nematode control may lead to greater root growth and ultimately higher nematode abundances despite nematicides protecting from nematode damage. 

In both 2017 and 2018, cotton yield was greater in sod-based than conventional cotton (1644 vs 1372 lb/acre lint in 2017 and 1815 vs 1708 lb/acre lint in 2018), but yield response to nematicide application varied by crop rotation.  In 2017, there was not a significant yield response to nematicide application in the higher-yield treatments with less nematode pressure, namely cotton following bahiagrass and 1^st-year cotton in the conventional rotation.  In 2^nd-year conventional cotton, there was a significant yield increase with nematicide application which would have resulted in an economic return of approximately $120/acre (Figure 12).  In 2018, there was no positive yield response to nematicide application in any rotation phase and nematicide application decreased cotton yield in sod-based rotation (Figure 12). 

The cotton yield results from this study, particularly 2017, provide evidence to support our hypothesis that sod-based rotation adequately manages reniform nematode without nematicide application.  Namely, in this study, nematicide application did not provide any value for increasing cotton yield or managing reniform nematode in sod-based rotation.  Reniform nematode abundances were low in sod-based rotation and yields were high, suggesting that reniform nematode was already adequately managed by rotation and that nematicide application may not be needed in sod-based rotation.  In conventional rotation, nematicide application with fluopyram increased yield in one season under high reniform nematode pressure, but was otherwise ineffective. As new management techniques that may be more effective (new resistant varieties, new chemistries) become available, it may shift calculations about whether additional nematode management is beneficial in SBR.

Results for hypothesis 2 (nematicide will affect non-target, beneficial organisms):

      Fluopyram nematicide application had minimal effects on non-target, beneficial nematodes. Fungal-feeding and bacteria-feeding nematodes were not affected by fluopyram nematicide application (data not shown). In cotton production, fluopyram application decreased ominvore populations in 2018, but not 2017 (Table 1). In peanut production, fluopyram did not affect omnivores in either year.      

            In summary, our results suggest that impacts of this particular nematicide on non-target nematodes is relatively minimal, in contrast to our initial hypothesis.  Further analysis does need to be done to assess if different genera of nematodes (even of the same feeding habit) were more sensitive to nematicide that overall feeding groups. It also worth noting that nematicide application was not particular effective in reducing abundances of target, plant-parasitic nematodes either, so lack of non-target effects may just reflect that the nematicide used was not effective in this soil type.