Pathogen Infection Influences a Distinct Microbial Community Composition in Sorghum Rils
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Plant Soil https://doi.org/10.1007/s11104-021-04875-3 REGULAR ARTICLE Pathogen infection influences a distinct microbial community composition in sorghum RILs K. Masenya & G. D. Thompson & M. Tekere & T. P. Makhalanyane & R. E. Pierneef & D. J. G. Rees Received: 10 May 2020 /Accepted: 2 February 2021 # The Author(s) 2021 Abstract Results We show that the foliar microbiome differs sub- Aims The rhizosphere microbiome substantially affects stantially in asymptomatic and symptomatic RILs subse- plant health, yet comparatively little is known regarding quent to natural infection by pathogens. A significant the foliar community dynamics. Here, we examine the association was found between plant health and micro- relationship between the microbiota and their response bial community structure. Our analyses revealed several to natural infection by pathogens. distinct fungal and bacterial pathogens. These pathogens Methods We established an experimental system using included Gibberella and Pantoea genera, which were a set of sorghum recombinant inbred lines (RILS). associated with the highly susceptible group. In addition These RILS included four models denoted as resistant, to these pathogens, we also found signatures for moderately resistant, susceptible and highly susceptible. Ascochyta, a known plant pathogenic genus. Members A combination of 16S rRNA and ITS gene amplicon of the bacterial genus Methylorubrum and the fungal approaches was used to assess bacteria and fungi, re- genus Hannaella, both known to exhibit plant growth- spectively, in foliar samples. promoting (PGP) traits, were associated with the resistant and moderately resistant groups. These data also reveal numerous highly diverse fungal and bacterial taxa in Responsible Editor: Anna Maria Pirttila RILs that did not show symptoms. We also found taxo- nomic differences between the microbiota hosted by the K. Masenya : G. D. Thompson : R. E. Pierneef : D. J. G. Rees symptomatic and asymptomatic RILs. Biotechnology Platform, Agricultural Research Council, Private Conclusions Together, these data suggest that pathogen Bag X5, Onderstepoort, Pretoria 0110, South Africa infection may result in distinct microbiota. These results suggest that highly diverse microbiome may promote K. Masenya (*) : M. Tekere : D. J. G. Rees the plants ability to resist the effects of pathogens po- University of South Africa, 28 Pioneer Ave, Florida Park, tentially contributing to plant health. Roodepoort 1709, South Africa e-mail: [email protected] Keywords Bacteria . Fungi .Sorghum .Leaf .Plant .RILs T. P. Makhalanyane Centre for Microbial Ecology and Genetics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa Introduction The past three decades of research using model systems D. J. G. Rees Botswana University of Agriculture and Natural Resources, (Nicotiana tabacum and Arabidopsis thaliana) have Private Bag, 0027 Gaborone, Botswana revealed a variety of plant adaptations (Chang et al. Plant Soil 2016; Ritpitakphong et al. 2016;Xuetal.2017). These major food production constraint, with global crop losses studies have provided clear evidence that these traits estimatedtobe20%– 30%, principally in areas with food have evolved in response to both biotic and abiotic shortages (Bandara et al. 2017). environmental stressors (Lundberg et al. 2012; While the vast majority of microorganisms are ben- Ritpitakphong et al. 2016; Ryu et al. 2007). There is eficial to plants, pathogens may colonize leaves and also evidence that healthy and asymptomatic plants co- overwhelm the innate defence mechanisms causing exist with diverse assemblages of microorganisms, in- plant diseases (Bandara et al. 2017; Chala et al. 2019; cluding protists, archaea, bacteria and fungi (Hassani Kelly et al. 2017). The colonization by bacterial and et al. 2018; Lebreton et al. 2019). These microorganisms fungal pathogens is a direct threat to the productivity have collectively been shown to influence plant growth and sustainability of sorghum production (Mihajlovski and productivity (Almario et al. 2017;Buéeetal.2009; et al. 2015; Sanmartín et al. 2018; Tripathi et al. 2018). Lindow and Brandl 2003; Stone et al. 2018). Plant- Currently, little is known regarding the diversity of associated microorganisms positively influence plant microbiomes in sorghum crops and the interplay be- health by increasing nutrient acquisition, stress tolerance tween associated bacteria and fungi remains unexam- and pathogen resistance (del Carmen Orozco-Mosqueda ined. Additionally, there are no reported microbial com- et al. 2020;Finkeletal.2019; Jones et al. 2019;Mia munity studies on sorghum recombinant inbred lines et al. 2014; Schirawski and Perlin 2018, Tsolakidou (RILs) in response to biotic stressors. Elucidating the et al. 2019). However, our understanding of the inter- composition of the sorghum microbiome and relating play between microbiomes and plants remains rudimen- this to its effects on plant health may provide important tary and has largely focused on model plant species cues on pathogen management. The limited studies (Aleklett et al. 2014; Berendsen et al. 2018; Edwards available on the sorghum microbiome have been based et al. 2015). Understanding the interaction between on culture-dependent methodologies, which are known microbiomes and plants is central to the elucidation of to miss 99% of microbial communities (Naylor et al. the response to biotic and abiotic stress in agriculturally 2017; Oberholster et al. 2018; Schlemper et al. 2017). important crops (Jones et al. 2019). To ensure food Recent reports, using metagenomic analysis, have re- security, it is essential to optimize the reliability of vealed potential key taxa associated with the rhizo- production pipelines by minimizing environmental im- sphere and seed of sorghum (Guo 2016; Hara et al. pacts (Saad et al. 2020; Wille et al. 2019). Integrating 2019; Kinge et al. 2019; Kuramae et al. 2020;Xu insights regarding beneficial plant microbiomes to en- et al. 2018). However, none of these studies assessed hance plant growth and disease resistance will contrib- the aerial region of the plant, which is suggested to be ute to increased agricultural production which will ulti- one of the primary entry sites for pathogens (Cernava mately contribute to food security (Busby et al. 2017; et al. 2019). This knowledge deficit is broadly true for Mounde 2015; Pascale et al. 2020; Sivakumar et al. plants where, in contrast to the rhizosphere, substantially 2020). less is known regarding the effects of plant-microbe Sorghum (Sorghum bicolor) is a robust species with a associations on foliar diseases. high tolerance to drought, altitude and a wide range of The phyllosphere, the leaf-dominated aerial part of temperatures (Medraoui et al. 2007). This species is a plants, represents one of the most abundant habitats for versatile crop which may be grown as a grain or sweet- microbiota colonization (Bodenhausen et al. 2013; stem. Sweet-stem sorghum is similar to grain (same spe- Bulgarelli et al. 2013; Carlström et al. 2019; Vorholt cies), however, it has a higher concentration of sugar in 2012). Commensals or beneficial symbionts which af- the stalks (Vanamala et al. 2018). Grain sorghum is an fect plant fitness by providing pathogen protection are important staple food crop grown globally and sweet-stem ubiquitous in the phyllosphere (Busby et al. 2017; sorghum is considered a promising biofuel feedstock Helfrich et al. 2018;Innerebneretal.2011). Despite (Mengistu et al. 2016). Yet, the full potential of sorghum the short life span nature of the phyllosphere, bacterial productivity has not been realised due in part to an array of communities dominated by the phyla Proteobacteria, biotic and abiotic constraints (Savary et al. 2019). Biotic Actinobacteria, Bacteroidetes and Firmicutes are found constraints may include weeds, animal pests, biological on leaves (Knief et al. 2010;Mülleretal.2016). Mo- interactions and plant pathogens (Donatelli et al. 2017; lecular studies suggest that yeast and fungal genera such Ghersa 2012). Plant pathogens represent a constant and as Cryptococcus, Sporobolomyces, Rhodotorula and Plant Soil associated species largely inhabit plant leaves mapped for quantitative traits such as grain yield and (Glushakova and Chernov 2004;Thompsonetal. stem sugar-related traits for biofuel yield of sorghum. 1993). Genera such as Cladosporium, Alternaria, Pen- The F9 generation seeds used in this study were collect- icillium, Acremonium, Mucor,andAspergillus are the ed from the Agricultural Research Council (ARC) - filamentous fungi frequently colonizing the Grain Crops Institute, Potchefstroom, South Africa phyllosphere as epiphytes and endophytes (Arnold (Table S1). et al. 2000;Inácioetal.2002;Ranaetal.2019). How- ever, such a phylogenetic conservation of community Cultivation of sorghum RILs composition suggests that community assembly is not a random process but is instead governed by structuring The sorghum RIL seeds were cultivated in a mixture of principles, which are currently only poorly understood autoclaved vermiculite and perlite medium in pots (Laforest-Lapointe and Whitaker 2019; Vorholt et al. disinfected at the ARC - Biotechnology Platform 2017). Additionally, in contrast to the intensively stud- (ARC-BTP), Onderstepoort, South Africa. A pot exper- ied roles of root-colonizing microbiota in plant health iment was carried out in a net-house which was used to (Durán et al. 2018; Finkel et al. 2017;