University of Groningen Bacillus Mycoides

University of Groningen Bacillus mycoides: novel tools for studying the mechanisms of its interaction with plants Yi, Yanglei IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2018 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Yi, Y. (2018). Bacillus mycoides: novel tools for studying the mechanisms of its interaction with plants. University of Groningen. Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne- amendment. Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 07-10-2021 1 Introduction PLANT-MICROBE INTERACTION 1 Plants naturally harbor diverse species of microorganisms, because they offer a wide range of habitats, supporting microbial growth. These microorganisms form a complex biological community interacting with the plant host, e.g. being pathogenic, or employing mutualism (symbi- Introduction onts), and commensalism (Pini et al., 2012). Bacteria that associate with plants are diverse in their ability to affect plant health, their genotypes, and their phenotypic characteristics. Although the majority of research on plant-associated microorganisms has focused on phytopathogens and diazotrophic (nitrogen-fixing) phytosymbionts, it is clear that many plant-associated microbes, even those that comprise only a small pro- portion of a community, have functions that are of agricultural or environmental importance (Beattie, 2006). Bacteria could reside in/on seeds, roots, leaves, and fruits of plants. The rhizosphere, the narrow zone of soil influenced by the root, is much richer in bacteria than the surround- ing bulk soil and even more densely populated than other parts of a plant (Lugtenberg and Kamilova, 2009) (Figure 1). The rhizosphere contains an enormous range of compounds excreted by roots. The roots exudate a range of inorganic compounds like ions, Figure 1. Plant-associated microorganisms, plant-microbe and microbe-microbe interaction. Soil inhibiting bacteria are attracted by root secreted signals to become plant- associated bacteria. They may live in the rhizosphere, rhizoplane or endosphere. Some of them are aiding plant health by fighting against pathogens through niche competi- tion, antimicrobial production, and induced systematic resistance. 9 inorganic acids, oxygen and water. These compounds may directly affect has an important role in root colonization by Pseudomonas fluorescens Pf0-1 1 the biogeochemistry of the soil (Jones et al., 2009). However, the major- (Oku et al., 2012). In Azospirillum brasilense, the chemoreceptor- like pro- 1 ity of the root exudates are formed by organic materials, which can be di- tein Tlp1 serves as an energy taxis transducer and affects the coloniza- vided into low-molecular-weight compounds and high-molecular-weight tion on roots (Greer-Phillips et al., 2004). Chemotaxis towards A. thaliana compounds. The low-molecular-weight compounds include amino acids, root exudates was mediated by two well-characterized chemoreceptors, organic acids (citric, malic, succinic, oxalic and pyruvic), sugars (glucose, McpB and McpC, as well as by the orphan receptor TlpC in Bacillus subtilis Introduction xylose, fructose, maltose, sucrose, ribose), phenolics, fatty acids and an (Allard-Massicotte et al., 2016). Moreover, plant roots also secrete com- array of secondary metabolites. The high-molecular weight compounds pounds that mimic quorum-sensing (QS) signals of bacteria to stimulate Plant-microbe interaction Plant-microbe consist of mucilage and proteins (Badri and Vivanco, 2009; Rohrbacher QS-regulated responses of associated bacteria (Huang et al., 2014). The and St-Arnaud, 2016), and rhizosphere microorganisms can use some of most common QS system occurs via N-acyl homoserine lactones (AHLs) these compounds as an energy source for growth and development or as binding to members of LuxR-family transcriptional regulators. Thus, they signaling molecules (Carvalhais et al., 2015). The composition of root ex- regulate the expression of downstream genes with the lux box in the pro- udates varies by plant species, developmental stage and plant growth sub- moter region (Hartmann et al., 2014). However, the LuxR-family regu- strate (Doornbos et al., 2011). For example, the organic acids and sugars lator (Lux-R solo) found in plant-associated bacteria lacks the LuxI pro- in root exudates of tomato and cucumber increase during plant growth tein when compared with other LuxR families. These regulators do not on stone wool (Kamilova et al., 2006). A systematic proteomic analysis of bind AHLs but to plant-produced compounds (González et al., 2013; Ven- root exudates showed that the defense-related proteins such as chitinases, turi and Fuqua, 2013). For instance, a LuxR solo regulator of P. fluorescens, glucanases, and myrosinases showed more secretion during the flower- PsoR, was identified to have a function in responding to plant compounds ing stage of Arabidopsis thaliana (De-la-Peña et al., 2010), while the release and regulating genes involved in the biosynthesis of various antimicro- of amino acids and phenolics increased at later stages of life of Arabidopsis bial compounds including 2,4-diacetylphloroglucinol, which has antago- (Chaparro et al., 2013). nistic activity against the damping-off disease pathogen Pythium ultimum It is believed that the dynamic nature of root exudates is one of the driv- (Subramoni et al., 2011). ing forces for the plant to select associated microbial communities that are Following recognition and recruitment, bacteria physically interact favorable for the plant. The best-known plant-microbe symbiosis is the with different parts of the roots from the tip to the elongation zone to form nodulation of legumes by rhizobia. This interaction is very specific, allow- complex multicellular and often multispecies assemblies, including bio- ing certain rhizobial strains to nodulate with specific host legumes (Bais films and smaller aggregates (Danhorn and Fuqua, 2007). The rhizobac- et al., 2006). In soil, a Rhizobium spp. finds its host legume plant from a teria form biofilms in a heterogeneous way along the root surface, where distance by chemotaxis, being attracted to the root exudates due to the the root tips usually have the least bacterial biofilm formed (Rudrappa presence of flavonoids (Sugiyama and Yazaki, 2012). Flavonoids also reg- et al., 2008). In general, the zone immediately behind the root tip is con- ulate the expression of nod genes that play important roles in nodulation sidered to be a major site of colonization (Badri and Vivanco, 2009). This establishment (Abdel-Lateif et al., 2012). Another widely-occurring plant- is partially due to the pH difference from the root tip to basal regions associated microbiome part is formed by arbuscular mycorrhizal fungi ( Peters, 2004), which might affect the bacterial growth and biofilm devel- (AMF), which form a symbiotic relationship with more than 80% of terres- opment. The nutrient availability is also quite different since particular trial plants, from bryophytes to tracheophytes (Lee et al., 2013). Although cell types in the root system might be more important than others in the AMF have low host specificity in their symbiosis with plants, they may also secretion of particular compounds. The biofilm formation of rhizobacte- recognize their host by signals released by plant roots, similar to the rec- ria on root surfaces is a mutualistic interaction. In B. subtilis-A. thaliana ognition by rhizobia. It has been shown that mycorrhizal fungi are me- interaction, plant polysaccharides act as an environmental cue that trig- diated by root-secreted compounds, such as strigolactone 5-deoxystrigol gers biofilm formation by the bacterium (Beauregard et al., 2013). In turn, ( Yoneyama et al., 2008), sugars, and carbohydrates (Kiers et al., 2011). plants benefit from the biofilm of rhizobacteria. The inhibitory effect of Some specific root-released chemical signals have been identified, that Lysobacter sp. strain SB-K88 against pathogenic Aphanomyces cochlioides play a role in recruiting specific bacteria to build mutualistic interactions is due to a combination of antibiosis and biofilm formation at the rhizo- with the plant. For example, the chemotaxis to amino acids of root exudates plane of the host plant (Islam et al., 2005). 10 11 Although extensive studies have been performed to investigate plant- 1 associated bacteria, we are far from understanding the plant-microbe in- 1 teraction mechanisms, especially when indigenous

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