Gibberellins synthesized by the entomopathogenic bacterium, <i>Photorhabdus temperata</i> M1021 as one of the factors of rice plant growth promotion

<div><p>In the present study, different types of gibberellins (GAs) in the culture filtrate (CF) of <i>Photorhabdus temperata</i> M1021 were quantified. The analysis of CF helped in profiling various bioactive GAs: GA₁, GA₃, GA₄, and GA₇. Several physiologically inactive GAs: GA₉, GA₁₂, and GA₂₀ were detected as well. Siderophore production was also investigated by growing <i>P. temperata</i> M1021 on chrome azurol-S blue agar plates. Furthermore, the strain was inoculated into ‘<i>Waito</i>-C’ (<i>Oryza sativa</i> L.) rice plants, which significantly (<i>P</i> < 0.05) increased plant growth attributes such as plant length, chlorophyll content, and fresh and dry biomass compared with those in controls. In a separate experiment, canola (<i>Brassica napus</i> L.) seeds treated with CF of M1021 were significantly (<i>P</i> < 0.05) accelerated germination rate as well as biomass production. Findings of the present study suggest that the strain M1021 contributes an important role in the plant growth by synthesizing a wide array of bioactive metabolites.</p></div

Complete genome analysis of <i>Serratia marcescens</i> RSC-14: A plant growth-promoting bacterium that alleviates cadmium stress in host plants

<div><p><i>Serratia marcescens</i> RSC-14 is a Gram-negative bacterium that was previously isolated from the surface-sterilized roots of the Cd-hyperaccumulator <i>Solanum nigrum</i>. The strain stimulates plant growth and alleviates Cd stress in host plants. To investigate the genetic basis for these traits, the complete genome of RSC-14 was obtained by single-molecule real-time sequencing. The genome of <i>S</i>. <i>marcescens</i> RSC-14 comprised a 5.12-Mbp-long circular chromosome containing 4,593 predicted protein-coding genes, 22 rRNA genes, 88 tRNA genes, and 41 pseudogenes. It contained genes with potential functions in plant growth promotion, including genes involved in indole-3-acetic acid (IAA) biosynthesis, acetoin synthesis, and phosphate solubilization. Moreover, annotation using NCBI and Rapid Annotation using Subsystem Technology identified several genes that encode antioxidant enzymes as well as genes involved in antioxidant production, supporting the observed resistance towards heavy metals, such as Cd. The presence of IAA pathway-related genes and oxidative stress-responsive enzyme genes may explain the plant growth-promoting potential and Cd tolerance, respectively. This is the first report of a complete genome sequence of Cd-tolerant <i>S</i>. <i>marcescens</i> and its plant growth promotion pathway. The whole-genome analysis of this strain clarified the genetic basis underlying its phenotypic and biochemical characteristics, underpinning the beneficial interactions between RSC-14 and plants.</p></div

Scanning electron micrograph of <i>S</i>. <i>marcescens</i> RSC-14.

<p>Fatty acid analysis indicated that the sum of C:14 3OH (3.8%), C16:0 (29.8%), C16:1 (8.2%) and C18:1 (5%) in RSC-14 is about 50%, which is consistent with the ratio of 50 to 80% observed in other <i>S</i>. <i>marcescens</i> strains [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0171534#pone.0171534.ref033" target="_blank">33</a>]</p

Bacterial metabolic pathways involved in indole-3-acetic acid, tryptophan, and acetoin biosynthesis in <i>S</i>. <i>marcescens</i> RSC-14.

<p><b>(a)</b> Structural gene cluster of the tryptophan biosynthesis pathway. <b>(b)</b> The biosynthetic pathways were constructed based on the KEGG database, NCBI genome annotation, and the RAST server. Black shaded arrows indicate known pathway steps for which related genes were not detected in the RSC-14 genome. Red arrows indicate putative enzymes that are encoded by the genome. The enzymes that were identified in the RSC-14 genome are shown with their NCBI locus tag.</p

Phylogenetic tree highlighting the position of <i>S</i>. <i>marcescens</i> RSC-14 with other closely related species within the genus of <i>Serratia</i>.

<p>The phylogenetic tree was constructed based on concatenated sequences of 16S rRNA, <i>gyr</i>B, and <i>rpo</i>B genes aligned in ClustalW2 using the neighbor-joining algorithm in CLC Main Workbench and rooted with <i>Photorhabdus luminescens subsp</i>. <i>laumondii</i> TTO1. All <i>Serratia</i> species clustered together and were distinct from other Enterobacteriaceae. The tree also highlights the close relationship of <i>S</i>. <i>marcescens</i> RSC-14 strain with the <i>S</i>. <i>marcescens</i> type strain WW4.</p

Venn diagram of the CDSs shared by the genomes of five closely related <i>Serratia</i> spp.; <i>S</i>. <i>marcescens</i> FGI94 (CP003942), <i>S</i>. <i>marcescens</i> WW4 (CP003959), <i>S</i>. <i>liquefaciens</i> ATCC27592 (CP006252) and <i>S</i>. <i>plymuthica</i> S13 (CP006566).

<p>The number outside the overlapping regions represents the number of CDSs present in each genome without homologs in other <i>Serratia</i> strains. While the overlapping regions indicates the CDSs shared by the respective strains.</p

Comparative genome statistics of <i>S</i>. <i>marcescens</i> RSC-14 and other <i>Serratia</i> spp.

<p>Comparative genome statistics of <i>S</i>. <i>marcescens</i> RSC-14 and other <i>Serratia</i> spp.</p

Genes (and their locus tags) involved in phosphate solubilization.

<p>Genes (and their locus tags) involved in phosphate solubilization.</p