Analogous wheat root rhizosphere microbial successions in field and greenhouse trials in the presence of biocontrol agents Paenibacillus peoriae SP9 and Streptomyces fulvissimus FU14

Abstract

Two Pythium-infested soils were used to compare the wheat root and rhizosphere soil microbial communities from plants grown in the field or in greenhouse trials and their stability in the presence of biocontrol agents. Bacteria showed the highest diversity at early stages of wheat growth in both field and greenhouse trials, while fungal diversity increased later on, at 12 weeks of the crop cycle. The microbial communities were stable in roots and rhizosphere samples across both soil types used in this study. Such stability was also observed irrespective of the cultivation system (field or greenhouse) or addition of biocontrol coatings to wheat seeds to control Pythium disease (in this study soil infected with Pythium sp. clade F was tested). In greenhouse plant roots, Archaeorhizomyces, Debaryomyces, Delftia, and unclassified Pseudeurotiaceae were significantly reduced when compared to plant roots obtained from the field trials. Some operational taxonomic units (OTUs) represented genetic determinants clearly transmitted vertically by seed endophytes (specific OTUs were found in plant roots) and the plant microbiota was enriched over time by OTUs from the rhizosphere soil. This study provided key information regarding the microbial communities associated with wheat roots and rhizosphere soils at different stages of plant growth and the role that Paenibacillus and Streptomyces strains play as biocontrol agents in supporting plant growth in infested soils.

Keywords: Pythium; biocontrol agent; cereals microbiota; endophyte; field trial; greenhouse; next-generation sequencing; plant microbiota.

Figure 1

Study plan and samples used for microbial molecular analyses

Figure 2

Wheat plants obtained after 4, 8, and 12 weeks of crop growth in field and greenhouse trials run at Turretfield (soil type A) and Spalding (soil type B). Plants were grown using control, Paenibacillus peoriae SP9, and Streptomyces fulvissimus FU14 biocontrol‐treated seeds. *p < .05

Figure 3

Taxonomic groups found in the wheat roots (a) and rhizosphere soils (b) at each stage of the crop. (c) Lists of genera found in: (L1) all seeds (control and coated‐seeds) and roots at 4 weeks and not detected in the initial soils and 4‐week rhizosphere soils, (L2) all roots and rhizosphere soils at 4 weeks, (L3) all roots and rhizosphere soils at 8 and 12 weeks, and (L4) core genera found in all roots and 4, 8, and 12 weeks. These lists were based on the operational taxonomic units (OTUs) found in each set of samples compared to the other sets

Figure 4

Nonmetric multidimensional scaling (NMDS) and canonical analysis of principal components (CAP) of samples: (a) NMDS of bacteria and fungi in all sample types (seed, sand, root, rhizosphere soil), (b) CAP analysis of taxonomic groups found in all root samples, and (c) NMDS analysis of root samples obtained from different systems and soils. Tur, Turretfield field trial; TurGl, Turretfield soil greenhouse trial; Spal, Spalding soil greenhouse trial; sand, in vitro trial using coat sterilized seeds. Analyses done in PRIMER 6 using squared root transformed data, resemblance matrices using Bray–Curtis similarities and dummy variable

Figure 5

Post hoc analyses of (a) root samples obtained from field and greenhouse trials conducted in soil type A and (b) root samples obtained from greenhouse trials conducted in soil type A versus soil type B. These analyses were done in STAMP 2.1.3 using two groups analysis and Welch's t test (two‐sided, Welch's inverted for confidence interval method)

Figure 6

Top 50 central genera of bacteria (a) and fungi (b) obtained by network analyses of the community structure (from yellow to red the number of connections is increased and the genera were found in the centre of the complete network shown in Supporting Information 13). Network analysis was conducted using molecular ecological network analysis pipeline (MENA; http://ieg4.rccc.ou.edu/MENA/) to generate the networks with a cut‐off of 0.84, Cytoscape environment to visualize networks, and cytoHubba application with maximal clique centrality (MCC) scores to select the top 50 genera for relevance in roots and rhizosphere soil samples. Bacteria and fungi were analysed in separate files

Figure 7

Relative abundance of (a) Paenibacillus and (b) Streptomyces in root and rhizosphere soils collected from control, Paenibacillus peoriae SP9‐, and Stre ptomyces fulvissimus FU14‐treated plants. Post hoc analyses of (c) root samples obtained from control, SP9‐, and FU14‐treated plants, and (d) rhizosphere soil samples obtained from control, SP9‐, and FU14‐treated plants. These analyses were done in STAMP 2.1.3 using two groups analysis and Welch's t test (two‐sided, Welch's inverted for confidence interval method)