https://cedarcreek.umn.edu/biblio/fulltext/Trivedi-etal_TrendsMicrobol_2013.pdf

Microbial modulators of soil carbon storage: integrating genomic and metabolic knowledge for global prediction

Background
Traditional agro-systems in arid areas are a bulwark for preserving soil stability and fertility, in the sight of “reverse desertification”. Nevertheless, the impact of desert farming practices on the diversity and abundance of the plant associated microbiome is poorly characterized, including its functional role in supporting plant development under drought stress.

/pdf/a-drought-resistance-promoting-microbiome-is-selected-by-1rnm5hbqad.pdf

A drought resistance-promoting microbiome is selected by root system under desert farming.

Elephant grass (Pennisetum purpureum Schumach) and Hybrid Pennisetum (Pennisetum americanum × P. purpureum Schumach) are tall, fast-growing perennial C4 bunchgrasses that have been in recent developed as the most appropriate biomass feedstock in many countries for exploring various biofuel products. However, the challenges of increasing plant biomass yield and enhancing their stress tolerance, especially on marginal lands, have been existed for a long while. In the past several years, bacterial endophytes used as bio-fertilizers for improving crop production have offered an opportunity to facilitate high biomass yield of energy crops in a more sustainable manner. A total of 16 endophytic bacteria strains were isolated and purified from the roots of elephant grass, which were classified into four bacterial genera: Sphingomonas, Pantoea, Bacillus, and Enterobacter. Four strains, pp01, pp02, pp04, and pp06, represented four different genera, were then selected and tested in vitro for their plant growth promoting properties, effects on plant growth and salt stress tolerance of Hybrid Pennisetum. The inoculation with these four bacterial mixture demonstrated a significant plant growth promotion for Hybrid Pennisetum from the normal to salt stress conditions at 0, 50, 100, and 200 mM NaCl, respectively. The highest promotion rate for biomass yield was 116.01 and 81.72 % for shoot fresh weight and dry weight, respectively. The bacterial strains tested were shown to solubilize insoluble phosphate, fix nitrogen, produce indole acetic acid and ammonia, but only strains from Sphingomonas, Bacillus, and Enterobacter can produce siderophore. In addition, the endophyte strains tested were all able to successfully colonize the roots of Hybrid Pennisetum, reaching upto 12.12 ± 0.98 CFU/g fresh roots at the 3rd day of inoculation. The four endophytic bacteria from elephant grass significantly promoted plant growth and biomass yield, alleviated the harmful effects of salt stress on Hybrid Pennisetum. These bacteria have indicated some unique properties that are very valuable for exploiting bio-inoculants aiding in the efforts to establish a sustainable and large-scale feedstock production system for Hybrid Pennisetum, particularly, on the saline marginal lands.

/pdf/the-endophytic-bacteria-isolated-from-elephant-grass-16jmg3auje.pdf

The endophytic bacteria isolated from elephant grass (Pennisetum purpureum Schumach) promote plant growth and enhance salt tolerance of Hybrid Pennisetum.

Endophytes, which mostly include bacteria, fungi and actinomycetes, are the endosymbionts that reside asymptomatically in plants for at least a part of their life cycle. They have emerged as a valuable source of novel metabolites, industrially important enzymes and as stress relievers of host plant, but still many aspects of endophytic biology are unknown. Functions of individual endophytes are the result of their continuous and complex interactions with the host plant as well as other members of the host microbiome. Understanding plant microbiomes as a system allows analysis and integration of these complex interactions. Modern genomic studies involving metaomics and comparative studies can prove to be helpful in unravelling the grey areas of endophytism. A deeper knowledge of the mechanism of host infestation and role of endophytes could be exploited to improve the agricultural management in terms of plant growth promotion, biocontrol and bioremediation. Genome sequencing, comparative genomics, microarray, next gen sequencing, metagenomics, metatranscriptomics are some of the techniques that are being used or can be used to unravel plant endophyte relationship.The modern techniques and approaches need to be explored to study endophytes and their putative role in host plant ecology. This review highlights “omics” tools that can be explored for understanding the role of endophytes in the plant microbiome. Keywords: Endophytism, microbiome, endophytes, genomics, metagenomics

/pdf/omics-tools-for-better-understanding-the-plant-endophyte-i4vtu3xhob.pdf

"Omics" Tools for Better Understanding the Plant-Endophyte Interactions.

Author(s): Firrincieli, Andrea; Otillar, Robert; Salamov, Asaf; Schmutz, Jeremy; Khan, Zareen; Redman, Regina S; Fleck, Neil D; Lindquist, Erika; Grigoriev, Igor V; Doty, Sharon L

https://depts.washington.edu/envaplab/papers/GenomicAnalysisEndophyticYeast.pdf

Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1.

Enterobacter cloacae GS1 was isolated by in-planta enrichment of a rice rhizoplane bacterial community. It displayed strong seed adherence ability (2.5 × 105 cfu/seed) and colonized rice roots reaching up to 1.65 × 109 cfu/g of fresh root weight in a gnotobiotic root colonization system. E. cloacae GS1 was motile, able to solubilize tricalcium phosphate, and produced indole acetic acid like substances (15 μg/ml). As an introduced bioinoculant in non-sterile soil, E. cloacae GS1 colonized rice roots and significantly improved the fresh weight, root length, shoot length, and nitrogen content in inoculated rice seedlings as compared to uninoculated controls. This isolate was tagged with green fluorescent protein and various stages of root colonization in gnotobiotic hydroponic environment and non-sterile soil environment were followed by fluorescence microscopy. Owing to its effective root colonizing ability and growth promoting potential, Enterobacter cloacae GS1 is a promising symbiotic bioinoculant for rice. (© 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

Root colonization of a rice growth promoting strain of Enterobacter cloacae

Fluorescent pseudomonads catabolize glucose simultaneously by two different pathways, namely, the oxidative pathway in periplasm and the phosphorylative pathway in cytoplasm. This study provides evidence for the role of glucose metabolism in the regulation of pyoverdine synthesis in Pseudomonas putida S11. We have characterized the influence of direct oxidation of glucose in periplasm on pyoverdine synthesis in P. putida S11. We identified a Tn5 transposon mutant of P. putida S11 showing increased pyoverdine production in minimal glucose medium (MGM). This mutant designated as IST1 had Tn5 insertion in glucose dehydrogenase (gcd) gene. To verify the role of periplasmic oxidation of glucose on pyoverdine synthesis, we constructed mutants S11 Gcd(-) and S11 PqqF(-) by antibiotic cassette mutagenesis. These mutants of P. putida S11 with loss of glucose dehydrogenase gene (gcd) or cofactor pyrroloquinoline quinone biosynthesis gene (pqqF) showed increased pyoverdine synthesis and impaired acid production in MGM. In minimal gluconate medium, the pyoverdine production of wild-type strain S11 and mutants S11 Gcd(-) and S11 PqqF(-) was higher than in MGM indicating that gluconate did not affect pyoverdine synthesis. In MGM containing PIPES-NaOH (pH 7.5) buffer which prevent pH changes due to gluconic acid production, strain S11 produced higher amount of pyoverdine similar to mutants S11 Gcd(-) and S11 PqqF(-). Therefore, it is proposed that periplasmic oxidation of glucose to gluconic acid decreases the pH of MGM and thereby influences pyoverdine synthesis of strain S11. The increased pyoverdine synthesis enhanced biotic and abiotic surface colonization of the strain S11.

Influence of periplasmic oxidation of glucose on pyoverdine synthesis in Pseudomonas putida S11

Here we report the genome sequence of a plant growth-promoting rhizobacterium, Pseudomonas putida S11. The length of the draft genome sequence is approximately 5,970,799 bp, with a G+C content of 62.4%. The genome contains 6,076 protein-coding sequences.

Genome Sequence of the Plant Growth-Promoting Rhizobacterium Pseudomonas putida S11

Fluorescent pseudomonads produce a characteristic fluorescent pigment, pyoverdines as their primary siderophore for iron acquisition under iron-limiting conditions. Here, we report the identification of a random transposon mutant IST3 of Pseudomonasputida S11 showing tolerance to iron starvation stress condition and increased pyoverdine production. The insertion of the Tn5 transposon was found to be in pstS gene of pstSR operon encoding sensor histidine kinase protein of the two-component signal transduction system. A pyoverdine negative derivative of IST3 mutant constructed was sensitive to iron stress condition. It indicated that increased survival of IST3 under iron-limiting condition was due to higher pyoverdine production. The iron starvation tolerant mutant (IST3) exhibited enhanced pyoverdine-mediated iron uptake in minimal medium which significantly improved its biofilm formation, seed adhesion and competitive root colonization.

Influence of siderophore pyoverdine synthesis and iron-uptake on abiotic and biotic surface colonization of Pseudomonas putida S11

S11 was isolated from the sugarcane rhizosphere. Itefﬁciently colonizes corn roots and promotes plant growth. Thisstrain was submitted to the Microbial Type Culture Collectionand Gene Bank (MTCC), Chandigarh, India, with the accessionnumberMTCC5670.Earlier,weidentiﬁedthatamutationofthetwo-component signal transduction system (

Pseudomonas putida S11 Growth-Promoting Rhizobacterium Genome Sequence of the Plant

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