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Title: Contribution of biocontrol agents to sustainable agriculture: do insights from microbiome research and BCA “omics” pay off

item Weller, David
item Thomashow, Linda

Submitted to: Proceedings, IOBC
Publication Type: Abstract Only
Publication Acceptance Date: 6/21/2016
Publication Date: 9/19/2016
Citation: Weller, D.M., Thomashow, L.S. 2016. Contribution of biocontrol agents to sustainable agriculture: do insights from microbiome research and BCA “omics” pay off. Proceedings, IOBC. O KL 1.

Interpretive Summary:

Technical Abstract: By the year 2050 there will be 9 to 11 billion people on earth to feed using the same amount or less land and water as is currently available for agricultural production. The United Nations estimated that global food production will need to increase by 70% by 2050. Currently, about one-third of all potential agricultural commodities grown worldwide are lost to diseases and other pests. Farmers are challenged to grow more, but with less fertilizer, pesticides and fumigants and more sustainable practices such as reduced tillage, precision farming and biological control. In addition, greater numbers of consumers are demanding pesticide-free food. Biocontrol via introduced or indigenous microbes is considered an essential component of sustainable agriculture. Biocontrol of plant pathogens has been studied since the early 1900s, and research on microbial inoculants during the last 40 years has yielded a growing list of commercially available products based on organisms from several different microbial groups (Fravel, 2005; Junaid et al., 2013; McSpadden Gardener & Fravel, 2002; Pal et al., 2006; Stockwell & Stack, 2007). However, Bacillus and Trichoderma spp. have been the microbes of choice for development into commercial biocontrol agents (BCAs) of plant diseases (Harman et al., 2010; Kloepper et al., 2004). These microorganisms are appealing because they are easily mass produced and formulated. On the other hand, Pseudomonas spp. have been preferred for fundamental studies of biocontrol mechanisms because they are more amenable to genetic analysis than Bacillus and Trichoderma, and they are aggressive colonists of roots and leaves. Although Gram negative bacteria like pseudomonads are easily mass produced, they have been harder to formulate because they do not produce dormant spores like Bacillus spp. do. Spores of bacilli can remain viable for years. On the other hand, the non-spore forming Agrobacterium radiobacter strain K84 and its transfer deficient mutant K1026 have been used successfully worldwide for crown gall control for decades. The most successful BCAs often possess multiple mechanisms of action that potentially can be active in either biocontrol or direct plant growth promotion. For example, most Pseudomonas, Bacillus and Trichoderma BCAs, besides having mechanisms that directly attack the target pathogen also can induce systemic resistance in the plant, and many BCAs can directly improve plant growth (Kloepper et al., 2004; Loper et al., 2012; Lorito & Woo, 2015; Lugtenberg & Kamilova, 2009; Pieterse et al., 2014; Raaijmakers & Mazzola, 2012). For example, it has been known for 25 years that P. protegens (formerly P. fluorescens) Pf-5 produces a wide spectrum of antibiotics inhibitory to oomycetes and fungi, but surprisingly, genome sequencing revealed that approximately 6% of the Pf-5 genome is devoted to the production of secondary metabolites, many of which could contribute to biocontrol activity (Loper et al., 2007). Trichoderma spp. (e.g., T. harzianum strain T22) have the amazing ability to: control root and foliar pathogens by directly attacking the pathogen or by inducing resistance; change the microfloral composition on the roots; enhance nutrient uptake, including uptake of nitrogen; enhance the solubilization of soil nutrients; and enhance root development and root hair formation (Lorito & Woo, 2015). The availability of inexpensive whole-genome sequencing of biocontrol strains is revealing both a “treasure trove” of previously unknown potential biocontrol genes and traits, and perhaps more importantly, the tremendous genetic diversity among strains of the same species that appear to be morphologically and physiologically identical. Enhancing the biocontrol activity of indigenous microbes that are part of the phytobiome is also critical to the success of 21st century sustainable agricultu