Deciphering the Rhizosphere and Geocaulosphere Microbiomes of Potato Following Inoculation with the Biocontrol Agent Pseudomonas fluorescens Strain LBUM223

Abstract

The phenazine-1-carboxylic acid (PCA)-producing Pseudomonas fluorescens strain LBUM223 shows biocontrol potential against Streptomyces scabies, which causes common scab of potato. To better characterize the impact of inoculating this specific biocontrol agent under field conditions, the microbiomes of the rhizosphere and the geocaulosphere of potato plants were characterized using next-generation sequencing. A single initial application or biweekly applications of LBUM223 were performed up to 11 weeks after planting. Rhizosphere and geocaulosphere soils (when potato tubers were produced) were sampled every 2 weeks. Following soil DNA extractions, 16S rRNA gene amplification and sequencing were performed using the Illumina MiSeq technology. The QIIME pipeline was used for data analyses. Results were generated from 45 rhizosphere and 27 geocaulosphere samples, for which 63,502 and 44,469 different operational taxonomical units were observed. Diversity comparisons between both datasets were performed. To our knowledge, this is the first time that the geocaulosphere microbiome is characterized and compared with the rhizosphere microbiome following inoculation with a specific microorganism. Eleven phyla accounted for 95% of the diversity, with Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria being the most abundant ones. Overall, the results obtained suggest that P. fluorescens strain LBUM223 does not significantly alter the autochthonous rhizosphere nor geocaulosphere microbiomes.

Inoculation With the Plant-Growth-Promoting Rhizobacterium Pseudomonas fluorescens LBUM677 Impacts the Rhizosphere Microbiome of Three Oilseed Crops

“…DSMZ 13134 only showed a transient effect on the rhizosphere microbial community structure associated with barley ( Hordeum vulgare ) in the first 3 weeks post-inoculation ( Buddrus-Schiemann et al, 2010 ). Pseudomonas stutzeri A1501 inoculation showed no significant microbial enrichments in the rhizosphere of maize ( Zea mays L.) ( Ke et al, 2019 ) and inoculation of Pseudomonas synxantha LBUM223 (previously Pseudomonas fluorescens ) did not alter the indigenous bacterial populations in the rhizosphere or the geocaulosphere of potato ( Solanum tuberosum L.) ( Roquigny et al, 2018 ). No significant differences in richness and diversity between inoculated and non-inoculated rhizosphere microbial populations were also observed in lettuce ( Lactuca sativa ) ( Cipriano et al, 2016 ).…”

“…Many studies found that a significant effect is generally rare, transient, and spatially limited. Some examples include inoculation of nitrogen-fixing Azospirillum strains in tomato ( Solanum lycopersicum L.), wheat ( Triticum sativum L.), and maize ( Zea mays L.) rhizospheres ( Bashan et al, 1995 ; Castro-Sowinski et al, 2007 ; Felici et al, 2008 ) and various Pseudomonas strains in maize, barley ( Hordeum vulgare L.), and potato ( Solanum tuberosum L.) rhizospheres ( Castro-Sowinski et al, 2007 ; Buddrus-Schiemann et al, 2010 ; Roquigny et al, 2018 ). However, there have also been studies that have shown a direct effect on the plant microbiome due to bacterial inoculations.…”

Micronutrients and Soil Microorganisms in the Suppression of Potato Common Scab

“…Inoculation does not significantly alter the autochthonous rhizosphere nor geocaulosphere microbiomes in the field [139] Rice bran amendment Bacillus, Streptomyces, Chitinophaga and Actinomadura significantly increased; unclassified Koribacteraceae and unclassified Gaiellaceae were significantly reduced [106] Iron amendment Bacillales and Gaiellales [33]…”

“…In a few studies, the suppression of pathogenic strains or the decrease in genes from the pathogenic island were also determined [149,156]. Surprisingly, in some studies, no effect on the autochthonous microbial community was observed after inoculation [111,139], while in others, proportions of several taxa were altered [146].…”

Phenazines in plant‐beneficial Pseudomonas spp.: biosynthesis, regulation, function and genomics

“…This suggests that phenazine production is important for competitive colonization of the rhizosphere. Despite phenazines broad-spectrum antibiotic activity, rhizosphere colonization by phenazine-producing Pseudomonas seems to have a limited impact on rhizosphere microbial populations (Bankhead et al, 2004;Roquigny et al, 2018). However, even if phenazine antibiotics have little effect against microbial competitors, they provide direct beneficial effects to their producers.…”