Complete Genome Sequence of Cellulomonas sp. JZ18, a Root Endophytic Bacterium Isolated from the Perennial Desert Tussock-Grass Panicum turgidum.

Cellulomonas sp. JZ18 is a gram-positive, rod shaped bacterium that was previously isolated from the root endosphere of the perennial desert tussock-grass Panicum turgidum. Genome coverage of PacBio sequencing was approximately 199X. Genome assembly generated a single chromosome of 7,421,843 base pairs with a guanine-cytosine (GC) content of 75.60% with 3240 protein coding sequences, 361 pseudo genes, three ribosomal RNA operons, three non-coding RNAs and 45 transfer RNAs. Comparison of JZ18's genome with type strains from the same genus, using digital DNA-DNA hybridization and average nucleotide identity calculations, revealed that JZ18 might potentially belong to a new species. Functional analysis revealed the presence of genes that may complement previously observed biochemical and plant phenotypes. Furthermore, the presence of a number of enzymes could be of potential use in industrial processes as biocatalysts. Genome sequencing and analysis, coupled with comparative genomics, of endophytic bacteria for their potential plant growth promoting activities under different soil conditions will accelerate the knowledge and applications of biostimulants in sustainable agriculture.

Root endophyte induced plant thermotolerance by constitutive chromatin modification at heat stress memory gene loci.

Global warming has become a critical challenge to food security, causing severe yield losses of major crops worldwide. Conventional and transgenic breeding strategies to enhance plant thermotolerance are laborious and expensive. Therefore, the use of beneficial microbes could be an alternative approach. Here, we report that the root endophyte Enterobacter sp. SA187 induces thermotolerance in wheat in the laboratory as well as in open-field agriculture. To unravel the molecular mechanisms, we used Arabidopsis thaliana as model plant. SA187 reprogramed the Arabidopsis transcriptome via HSFA2-dependent enhancement of H3K4me3 levels at heat stress memory gene loci. Unlike thermopriming, SA187-induced thermotolerance is mediated by ethylene signaling via the transcription factor EIN3. In contrast to the transient chromatin modification by thermopriming, SA187 induces constitutive H3K4me3 modification of heat stress memory genes, generating robust thermotolerance in plants. Importantly, microbial community composition of wheat plants in open-field agriculture is not influenced by SA187, indicating that beneficial microbes can be a powerful tool to enhance thermotolerance of crops in a sustainable manner.

Genome Insights of the Plant-Growth Promoting Bacterium Cronobacter muytjensii JZ38 With Volatile-Mediated Antagonistic Activity Against Phytophthora infestans.

Salinity stress is a major challenge to agricultural productivity and global food security in light of a dramatic increase of human population and climate change. Plant growth promoting bacteria can be used as an additional solution to traditional crop breeding and genetic engineering. In the present work, the induction of plant salt tolerance by the desert plant endophyte Cronobacter sp. JZ38 was examined on the model plant Arabidopsis thaliana using different inoculation methods. JZ38 promoted plant growth under salinity stress via contact and emission of volatile compounds. Based on the 16S rRNA and whole genome phylogenetic analysis, fatty acid analysis and phenotypic identification, JZ38 was identified as Cronobacter muytjensii and clearly separated and differentiated from the pathogenic C. sakazakii. Full genome sequencing showed that JZ38 is composed of one chromosome and two plasmids. Bioinformatic analysis and bioassays revealed that JZ38 can grow under a range of abiotic stresses. JZ38 interaction with plants is correlated with an extensive set of genes involved in chemotaxis and motility. The presence of genes for plant nutrient acquisition and phytohormone production could explain the ability of JZ38 to colonize plants and sustain plant growth under stress conditions. Gas chromatography-mass spectrometry analysis of volatiles produced by JZ38 revealed the emission of indole and different sulfur volatile compounds that may play a role in contactless plant growth promotion and antagonistic activity against pathogenic microbes. Indeed, JZ38 was able to inhibit the growth of two strains of the phytopathogenic oomycete Phytophthora infestans via volatile emission. Genetic, transcriptomic and metabolomics analyses, combined with more in vitro assays will provide a better understanding the highlighted genes' involvement in JZ38's functional potential and its interaction with plants. Nevertheless, these results provide insight into the bioactivity of C. muytjensii JZ38 as a multi-stress tolerance promoting bacterium with a potential use in agriculture.

Complete genome sequence of the endophytic bacterium Cellulosimicrobium sp. JZ28 isolated from the root endosphere of the perennial desert tussock grass Panicum turgidum.

Cellulosimicrobium sp. JZ28, a root endophytic bacterium from the desert plant Panicum turgidum, was previously identified as a plant growth-promoting bacterium. The genome of JZ28 consists of a 4378,193 bp circular chromosome and contains 3930 CDSs with an average GC content of 74.5%. Whole-genome sequencing analysis revealed that JZ28 was closely related to C. aquatile 3 bp. The genome harbors genes responsible for protection against oxidative, osmotic and salinity stresses, such as the production of osmoprotectants. It also contains genes with a role in the production of volatiles, such as hydrogen sulfide, which promote biotic and abiotic stress tolerance in plants. The presence of three copies of chitinase genes indicates a possible role of JZ28 as biocontrol agent against fungal pathogens, while a number of genes for the degradation of plant biopolymers indicates potential application in industrial processes. Genome sequencing and mining of culture-dependent collections of bacterial endophytes from desert plants provide new opportunities for biotechnological applications.

Tailoring plant-associated microbial inoculants in agriculture: a roadmap for successful application.

Plants are now recognized as metaorganisms which are composed of a host plant associated with a multitude of microbes that provide the host plant with a variety of essential functions to adapt to the local environment. Recent research showed the remarkable importance and range of microbial partners for enhancing the growth and health of plants. However, plant-microbe holobionts are influenced by many different factors, generating complex interactive systems. In this review, we summarize insights from this emerging field, highlighting the factors that contribute to the recruitment, selection, enrichment, and dynamic interactions of plant-associated microbiota. We then propose a roadmap for synthetic community application with the aim of establishing sustainable agricultural systems that use microbial communities to enhance the productivity and health of plants independently of chemical fertilizers and pesticides. Considering global warming and climate change, we suggest that desert plants can serve as a suitable pool of potentially beneficial microbes to maintain plant growth under abiotic stress conditions. Finally, we propose a framework for advancing the application of microbial inoculants in agriculture.

Complete Genome Sequence of Paenibacillus sp. JZ16, a Plant Growth Promoting Root Endophytic Bacterium of the Desert Halophyte Zygophyllum Simplex.

Paenibacillus sp. JZ16 is a gram-positive, rod-shaped, motile root endophytic bacterium of the pioneer desert halophytic plant Zygophyllum simplex. JZ16 was previously shown to promote salinity stress tolerance in Arabidopsis thaliana and possesses a highly motile phenotype on nutrient agar. JZ16 genome sequencing using PacBio generated 82,236 reads with a mean insert read length of 11,432 bp and an estimated genome coverage of 127X, resulting in a chromosome of 7,421,843 bp with a GC content of 49.25% encoding 6710 proteins, 8 rRNA operons, 117 ncRNAs and 73 tRNAs. Whole-genome sequencing analysis revealed a potentially new species for JZ16. Functional analysis revealed the presence of a number of enzymes involved in the breakdown of plant-based polymers. JZ16 could be of potential use in agricultural applications for promoting biotic and abiotic stress tolerance and for biotechnological processes (e.g., as biocatalysts for biofuel production). The culture-dependent collection of bacterial endophytes from desert plants combined with genome sequence mining provides new opportunities for industrial applications.

Phylogenetically diverse endophytic bacteria from desert plants induce transcriptional changes of tissue-specific ion transporters and salinity stress in Arabidopsis thaliana.

Salinity severely hampers crop productivity worldwide and plant growth promoting bacteria could serve as a sustainable solution to improve plant growth under salt stress. However, the molecular mechanisms underlying salt stress tolerance promotion by beneficial bacteria remain unclear. In this work, six bacterial isolates from four different desert plant species were screened for their biochemical plant growth promoting traits and salinity stress tolerance promotion of the unknown host plant Arabidopsis thaliana. Five of the isolates induced variable root phenotypes but could all increase plant shoot and root weight under salinity stress. Inoculation of Arabidopsis with five isolates under salinity stress resulted in tissue-specific transcriptional changes of ion transporters and reduced Na+/K+ shoot ratios. The work provides first insights into the possible mechanisms and the commonality by which phylogenetically diverse bacteria from different desert plants induce salinity stress tolerance in Arabidopsis. The bacterial isolates provide new tools for studying abiotic stress tolerance mechanisms in plants and a promising agricultural solution for increasing crop yields in semi-arid regions.

Desert plant bacteria reveal host influence and beneficial plant growth properties.

Deserts, such as those found in Saudi Arabia, are one of the most hostile places for plant growth. However, desert plants are able to impact their surrounding microbial community and select beneficial microbes that promote their growth under these extreme conditions. In this study, we examined the soil, rhizosphere and endosphere bacterial communities of four native desert plants Tribulus terrestris, Zygophyllum simplex, Panicum turgidum and Euphorbia granulata from the Southwest (Jizan region), two of which were also found in the Midwest (Al Wahbah area) of Saudi Arabia. While the rhizosphere bacterial community mostly resembled that of the highly different surrounding soils, the endosphere composition was strongly correlated with its host plant phylogeny. In order to assess whether any of the native bacterial endophytes might have a role in plant growth under extreme conditions, we analyzed the properties of 116 cultured bacterial isolates that represent members of the phyla Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes. Our analysis shows that different strains have highly different biochemical properties with respect to nutrient acquisition, hormone production and growth under stress conditions. More importantly, eleven of the isolated strains could confer salinity stress tolerance to the experimental model plant Arabidopsis thaliana suggesting some of these plant-associated bacteria might be useful for improving crop desert agriculture.

Boosting Alfalfa (Medicago sativa L.) Production With Rhizobacteria From Various Plants in Saudi Arabia.

This study focused on rhizobacteria to promote sustainable crop production in arid regions of Saudi Arabia. The study isolated 17 tightly root-adhering rhizobacteria from various plants at Hada Al Sham in Saudi Arabia. All 17 rhizobacterial isolates were confirmed as plant growth promoting rhizobacteria by classical biochemical tests. Using 16S rDNA gene sequence analyses, the strains were identified as Bacillus, Acinetobacter and Enterobacter. Subsequently, the strains were assessed for their ability to improve the physiology, nutrient uptake, growth, and yield of alfalfa plants grown under desert agriculture conditions. The field trials were conducted in a randomized complete block design. Inoculation of alfalfa with any of these 17 strains improved the relative water content; chlorophyll a; chlorophyll b; carotenoid contents; nitrogen (N), phosphorus, and potassium contents; plant height; leaf-to-stem ratio; and fresh and dry weight. Acinetobacter pittii JD-14 was most effective to increase fresh and dry weight of alfalfa by 41 and 34%, respectively, when compared to non-inoculated control plants. Nevertheless, all strains enhanced crop traits when compared to controls plants, indicating that these desert rhizobacterial strains could be used to develop an eco-friendly biofertilizer for alfalfa and possibly other crop plants to enhance sustainable production in arid regions.