Biocontrol agents enhance plant disease resistance by altering plant microbiomes

Plants provide a habitat for a tremendous diversity of microbes, including bacteria and fungi, with the relationship ranging from mutualism to parasitism. The assemblages of microbes hosted on the stem and leaf surfaces and in internal tissues of plants are defined as plant microbiomes (Gilbert & Parker, 2023). Plant microbiomes play a critical role in promoting host plant fitness through enhanced nutrition acquisition, stress tolerance, and also resistance to herbivores and pathogens (Trivedi et al., 2020). Specifically, antagonistic phyllosphere microbes can regulate plant resistance substances and signaling pathways, and influence the outcome of plant–pathogen interactions (i.e., diseases) (Agrios, 2005). In fact, the process of pathogens infecting host plants can be seen as the colonization by “invasive” species of plant microbiomes, in which environmental filtering and competitive exclusion processes play important roles (Liu et al., 2021). The process of infection by plant disease agents is also regulated by biocontrol agents (BCAs), including Trichoderma and plant growth-promoting rhizobacteria (PGPR). To better understand the relationship between plants and their microbiome, we need to go beyond the previous studies on how A affects B and clarify the interaction among all players through more rigorous and complex field and greenhouse manipulative experiments.

Although the interactions between plant microbiomes and pathogens have been the subject of active research in recent years (e.g., Carrión et al., 2019; Kwak et al., 2018; Yin et al., 2021), the influence and modifying role of BCAs in these interactions are still unclear. The reason for this knowledge gap is that the analysis of the complex interactions among plant microbiomes, BCAs, and pathogens requires controlled experiments, and sequencing is essential for analyzing the plant microbiome. A recently published paper in Grassland Research by Zhu et al. (doi:10.1002/glr2.12081) used greenhouse manipulative experiments, combined with high-throughput sequencing, to provide novel insights into these complex interactions. Based on their findings, the authors suggest that the BCAs can induce plant defense by shifting the community composition of plant microbiomes toward favorable phyllosphere bacteria.

Both Trichoderma and plant PGPR are used as BCAs for common vetch (Vicia sativa L.), while anthracnose caused by Colletotrichum spinaciae usually reduces the yield of common vetch. In their study, Zhu et al. manipulated the presence or absence of two PGPRs, Bacillus subtilis and Bacillus licheniformis, and also Trichoderma longibrachiatum, and evaluated the anthracnose disease index 7 days after C. spinaciae inoculation. They found that common vetch with PGPR and T. longibrachiatum showed significant reduction in both disease incidence and disease index. As BCAs, PGPR and Trichoderma performed well in promoting disease resistance. As also found in other research systems, these results confirmed the critical role of PGPR and Trichoderma in enhancing plant disease resistance. Anthracnose is a widespread and insidious disease that causes yield reduction in common vetch and significant and often underestimated economic losses. Along with previous empirical evidence, these studies indicate the potential of PGPR and Trichoderma for use in biocontrol programs. The next step will be to conduct experiments to confirm the efficacy of PGPR and Trichoderma in field production of common vetch.

With respect to elucidation of the response mechanism, Zhu et al. found that the activities of defense enzymes, including peroxidase (POD) and polyphenol oxidase (PPO), showed positive responses to both C. spinaciae and PGPR inoculation. Meanwhile, simultaneous inoculation of PGPR and T. longibrachiatum lowered the salicylic acid (SA) content, and the jasmonic acid (JA) content was the highest in the treatment with PGPR inoculation only. Further, by using high-throughput sequencing to identify 16S rRNA genes from the phyllosphere bacteria, the authors confirmed that the community composition of the phyllosphere bacteria varied significantly between host plants inoculated or uninoculated with C. spinaciae. By using linear discriminant effect size analyses, the authors found that C. spinaciae, PGPRs, and T. longibrachiatum inoculation all significantly shifted the phyllosphere bacterial community composition at both family and genus levels. Finally, based on structural equation modeling, the authors confirmed that PGPRs strongly positively associated with increased enzyme activity, while JA and SA levels were associated with specific components of the phyllosphere bacterial community. The positive coupling between the plant microbiome and the production of defense enzymes helps to improve the overall disease resistance of host plants, highlighting the important role of the plant microbiome in regulating fungal diseases. In subsequent studies, isolation and inoculation of potentially important functional bacteria and fungi may facilitate a more mechanistic understanding of the results, although the function of defense enzymes often depends on the microbial community.

Overall, by combining data on plant disease severity, enzyme activity, hormone, and phyllosphere bacterial community membership, their study found that (1) plant defense for anthracnose (C. spinaciae) in common vetch can be induced by both PGPR and Trichoderma and (2) PGPR and Trichoderma inoculation were linked to a significant increase in the relative abundance of favorable phyllosphere bacteria, which can enhance host plant defense against anthracnose. In summary, the study by Zhu et al. provides empirical evidence that BCAs have a significant preventative effect against anthracnose and reveals something of the mechanisms behind this inhibitory effect. Considering that the common and diverse BCAs interact with both host plants and pathogens in both agro-ecosystems and natural ecosystems (Andrews & Harris, 2000), better understanding of these interactions can improve our ability to predict disease outbreak progression to develop adaptive management measures for grassland and animal husbandry. Such knowledge is especially relevant against the background of global changes (Trivedi et al., 2022).

While Zhu et al. focused on effects of BCAs on plant disease, the other side of this interaction, that is, potential effects of pathogens on BCA–plant associations, remains unknown. Moreover, there is no reason to expect that interactions between BCAs and the plant microbiome are limited to pathogens only. Mammalian and insect herbivores can also potentially regulate plant fitness and growth in terrestrial ecosystems. Given the diverse spectrum of primary consumer groups in natural ecosystems, it is important to consider the potential linkages among all of these groups in future research. Specifically, little is known about how the plant microbiome responds to the presence of insects and herbivores or about plant microbiome responses when plants are eaten by insects or livestock. The complex interactions among herbivores (i.e., insects and grazers) and their ecological consequences require more field and greenhouse manipulation experiments in the near future, combined with use of sequencing technology to identify shifts in plant microbiome composition, to reveal the underlying mechanisms of these complex interactions between plant hosts and their microbiomes.