Whole-genome sequencing and comparative analysis of two plant-associated strains of Rhodopseudomonas palustris (PS3 and YSC3)

Abstract

Rhodopseudomonas palustris strains PS3 and YSC3 are purple non-sulfur phototrophic bacteria isolated from Taiwanese paddy soils. PS3 has beneficial effects on plant growth and enhances the uptake efficiency of applied fertilizer nutrients. In contrast, YSC3 has no significant effect on plant growth. The genomic structures of PS3 and YSC3 are similar; each contains one circular chromosome that is 5,269,926 or 5,371,816 bp in size, with 4,799 or 4,907 protein-coding genes, respectively. In this study, a large class of genes involved in chemotaxis and motility was identified in both strains, and genes associated with plant growth promotion, such as nitrogen fixation-, IAA synthesis- and ACC deamination-associated genes, were also identified. We noticed that the growth rate, the amount of biofilm formation, and the relative expression levels of several chemotaxis-associated genes were significantly higher for PS3 than for YSC3 upon treatment with root exudates. These results indicate that PS3 responds better to the presence of plant hosts, which may contribute to the successful interactions of PS3 with plant hosts. Moreover, these findings indicate that the existence of gene clusters associated with plant growth promotion is required but not sufficient for a bacterium to exhibit phenotypes associated with plant growth promotion.

Plant growth promoting rhizobacteria isolated from halophytes and drought-tolerant plants: genomic characterisation and exploration of phyto-beneficial traits

“…As P-availability in soil is generally limited, the presence of P-solubilizing bacteria could be essential 16 . Many P-solubilizing microorganisms require external pqq for strong P-solubilization in vitro 61 .…”

“…Other strains had orthologs of the relevant genes but lacked the activity. Considering the fact that bacteria may lose some of their abilities when the corresponding cation is present in adequate amounts, or in case that it is provided by a consortium of microbiota 16 , it is evident that the environment where bacteria are grown is of outmost importance. This explanation may be relevant for SAESo12 (isolated from the P-rich environment of Santorini, Emporio) that possessed the relevant orthologous genes but lacked the activity.…”

“…In order to infer the taxonomic affiliation of the eight strains, a phylogenetic tree was constructed based on Multilocus Sequence Analysis (MLSA) of five housekeeping genes (rpaA -rpoA -infB -gyrB -atpD) (Fig. S1) 16,18 . The sequences of these individual genes of the strains identified by Prokka searches, along with those from reference strains of closest relatives retrieved from the NCBI database, were aligned using ClustalW 86 , and were combined to form a concatenated sequence by BioEdit 87 .…”

Selection of Acid Tolerant Purple Nonsulfur Bacteria for Application in Agriculture

“…Strain KKSSR91 was identified as R. palustris with 99% similarity to R. palustris YSC3 ( Figure 5). R. palustris strains YSC3 and PS3 isolated from Taiwanese paddy soils produced different significant effects on plant growth and PS3was found to be more effective (Lo et al, 2018). Based on the results of seed germination, plant growth promotion by strain KKSSR91 was more similar to the behavior of strain PS3 than strain YSC3.…”

Effectiveness of Plant Beneficial Microbes: Overview of the Methodological Approaches for the Assessment of Root Colonization and Persistence

“…However, the presence of PGPrelated genes is essential but not sufficient for a bacterium to exert beneficial effects on plant growth in a real environment. In fact, although the presence of key attributes essential for possible colonization and interaction with the host plant were recovered in two Rhodopseudomonas palustris strains (PS3 and YSC3), these strains exhibited different expression patterns of genes related to PGP activities, probably due to the different physiological responses of these strains to specific compounds in the root exudates that act as signal molecules (Lo et al, 2018). Therefore, the effectiveness of PGP activities of a specific strain could also be affected by the different exudates released into the soil by different plants.…”