Defining the Core Citrus Leaf- and Root-Associated Microbiota: Factors Associated with Community Structure and Implications for Managing Huanglongbing (Citrus Greening) Disease

Abstract

Stable associations between plants and microbes are critical to promoting host health and productivity. The objective of this work was to test the hypothesis that restructuring of the core microbiota may be associated with the progression of huanglongbing (HLB), the devastating citrus disease caused by Liberibacter asiaticus, Liberibacter americanus, and Liberibacter africanus. The microbial communities of leaves (n ϭ 94) and roots (n ϭ 79) from citrus trees that varied by HLB symptom severity, cultivar, location, and season/time were characterized with Illumina sequencing of 16S rRNA genes. The taxonomically rich communities contained abundant core members (i.e., detected in at least 95% of the respective leaf or root samples), some overrepresented site-specific members, and a diverse community of lowabundance variable taxa. The composition and diversity of the leaf and root microbiota were strongly associated with HLB symptom severity and location; there was also an association with host cultivar. The relative abundance of Liberibacter spp. among leaf microbiota positively correlated with HLB symptom severity and negatively correlated with alpha diversity, suggesting that community diversity decreases as symptoms progress. Network analysis of the microbial community time series identified a mutually exclusive relationship between Liberibacter spp. and members of the Burkholderiaceae, Micromonosporaceae, and Xanthomonadaceae. This work confirmed several previously described plant disease-associated bacteria, as well as identified new potential implications for biological control. Our findings advance the understanding of (i) plant microbiota selection across multiple variables and (ii) changes in (core) community structure that may be a precondition to disease establishment and/or may be associated with symptom progression.IMPORTANCE This study provides a comprehensive overview of the core microbial community within the microbiomes of plant hosts that vary in extent of disease symptom progression. With 16S Illumina sequencing analyses, we not only confirmed previously described bacterial associations with plant health (e.g., potentially beneficial bacteria) but also identified new associations and potential interactions between certain bacteria and an economically important phytopathogen. The importance of core taxa within broader plant-associated microbial communities is discussed.KEYWORDS core microbiome, plant-associated microbiota, Liberibacter, pathogenmicrobe interactions

Apple endophyte community is shaped by tissue type, cultivar and site and has members with biocontrol potential againstNeonectria ditissima

“…This study is the first to show that endophyte communities in ‘Royal Gala’ were more diverse than those in ‘Braeburn’, suggesting that they were under tighter regulation in ‘Braeburn’. This supported several studies in other plant species such as cotton ( Gossypium hirsutum ) by culture‐dependent method (Adams and Kloepper ), rice ( Oryza sativa ) by PCR‐DGGE (Hardoim et al ) and citrus ( Citrus sinensis ) by Illumina sequencing (Blaustein et al ) that showed host is a major driver of endophyte recruitment. Although this is a new result for cultivars of apple, research into the structure and function of microbial members of the holobiont and the genetic determinants of host recruitment being relaxed or stringent remain unknown.…”

“…The relative abundance of endophyte taxa was not determined in this study. Illumina‐based next‐generation sequencing approaches (NGS; metabarcoding) are being used to describe relative abundance of microbial operational taxonomic units (OTUs) in plants and soil (Sun et al ; Zarraonaindia et al ; Blaustein et al ; Wang et al ). Extension of the work to incorporate deep sequencing approaches (e.g.…”

Distinct microbial communities among different tissues of citrus tree Citrus reticulata cv. Chachiensis

“…Our results suggested that the microbial communities from different tissues varied significantly and the microenvironments of tree tissues could affect the composition of its microbial community.www.nature.com/scientificreports www.nature.com/scientificreports/ trees 23 . Most previous investigation on citrus-associated microbiomes are analyses on huanglongbing-infected, or specially-treated samples [24][25][26][27][28][29] .Citrus reticulata cv. Chachiensis is an important citrus variety widely cultivated around the world and the orange peel of the fruit was regarded as the valuable material which could be processed as food, tea drinks, and seasoning 30 .…”

“…www.nature.com/scientificreports www.nature.com/scientificreports/ trees 23 . Most previous investigation on citrus-associated microbiomes are analyses on huanglongbing-infected, or specially-treated samples [24][25][26][27][28][29] .…”

Core endophyte communities of different citrus varieties from citrus growing regions in China

“…Healthy trees had more endophytes compared to symptomatic and asymptomatic trees, which may have been because the www.nature.com/scientificreports www.nature.com/scientificreports/ healthy trees were free of CLas. Previous studies reported that microbial communities in citrus trees are negatively affected by CLas 37,41,42 . In addition, microbial colonization of the branches, stems, roots, and leaves are affected by various factors.…”