Enhancing Pisum sativum growth and symbiosis under heat stress: the synergistic impact of co-inoculated bacterial consortia and ACC deaminase-lacking Rhizobium.

The 1-aminocyclopropane-1-carboxylate (ACC) deaminase is a crucial bacterial trait, yet it is not widely distributed among rhizobia. Hence, employing a co-inoculation approach that combines selected plant growth-promoting bacteria with compatible rhizobial strains, especially those lacking ACC deaminase, presents a practical solution to alleviate the negative effects of diverse abiotic stresses on legume nodulation. Our objective was to explore the efficacy of three non-rhizobial endophytes, Phyllobacterium salinisoli (PH), Starkeya sp. (ST) and Pseudomonas turukhanskensis (PS), isolated from native legumes grown in Tunisian arid regions, in improving the growth of cool-season legume and fostering symbiosis with an ACC deaminase-lacking rhizobial strain under heat stress. Various combinations of these endophytes (ST + PS, ST + PH, PS + PH, and ST + PS + PH) were co-inoculated with Rhizobium leguminosarum 128C53 or its ΔacdS mutant derivative on Pisum sativum plants exposed to a two-week heat stress period.Our findings revealed that the absence of ACC deaminase activity negatively impacted both pea growth and symbiosis under heat stress. Nevertheless, these detrimental effects were successfully mitigated in plants co-inoculated with ΔacdS mutant strain and specific non-rhizobial endophytes consortia. Our results indicated that heat stress significantly altered the phenolic content of pea root exudates. Despite this, there was no impact on IAA production. Interestingly, these changes positively influenced biofilm formation in consortia containing the mutant strain, indicating synergistic bacteria-bacteria interactions. Additionally, no positive effects were observed when these endophytic consortia were combined with the wild-type strain. This study highlights the potential of non-rhizobial endophytes to improve symbiotic performance of rhizobial strains lacking genetic mechanisms to mitigate stress effects on their legume host, holding promising potential to enhance the growth and yield of targeted legumes by boosting symbiosis.

Structure-Based Engineering of a Sesquiterpene Cyclase to Generate an Alcohol Product: Conversion of epi-Isozizaene Synthase into α-Bisabolol Synthase.

The sesquiterpene cyclase epi-isozizaene synthase (EIZS) from Streptomyces coelicolor catalyzes the metal-dependent conversion of farnesyl diphosphate (FPP) into the complex tricyclic product epi-isozizaene. This remarkable transformation is governed by an active site contour that serves as a template for catalysis, directing the conformations of multiple carbocation intermediates leading to the final product. Mutagenesis of residues defining the active site contour remolds its three-dimensional shape and reprograms the cyclization cascade to generate alternative cyclization products. In some cases, mutagenesis enables alternative chemistry to quench carbocation intermediates, e.g., through hydroxylation. Here, we combine structural and biochemical data from previously characterized EIZS mutants to design and prepare F95S-F198S EIZS, which converts EIZS into an α-bisabolol synthase with moderate fidelity (65% at 18 °C, 74% at 4 °C). We report the complete biochemical characterization of this double mutant as well as the 1.47 Å resolution X-ray crystal structure of its complex with three Mg2+ ions, inorganic pyrophosphate, and the benzyltriethylammonium cation, which partially mimics a carbocation intermediate. Most notably, the two mutations together create an active site contour that stabilizes the bisabolyl carbocation intermediate and positions a water molecule for the hydroxylation reaction. Structural comparison with a naturally occurring α-bisabolol synthase reveals common active site features that direct α-bisabolol generation. In showing that EIZS can be redesigned to generate a sesquiterpene alcohol product instead of a sesquiterpene hydrocarbon product, we have expanded the potential of EIZS as a platform for the development of designer cyclases that could be utilized in synthetic biology applications.

Multi-trait efficiency and interactivity of bacterial consortia used to enhance plant performance under water stress conditions.

Water stress is a major limiting factor for agricultural production under current and projected climate change scenarios. As a sustainable strategy, plant growth-promoting bacterial consortia have been used to reduce plant water stress. However, few studies have examined the effects of stress on multi-trait efficiency and interactivity of bacterial species. In this study, we used several in-vitro experiments, plant assays and greenhouse trials to investigate the effects of stress and bacterial consortia on 1-aminocyclopropane-1-carboxylic acid deaminase (ACCD) activities, indole-3-acetic acid (IAA) production and plant growth-promoting traits (Phosphate-solubilization, starch hydrolysis, siderophores and ammonium production). We further assessed biofilm formation and the chemotactic behaviour in response to ACC. A total of fifteen ACCD rhizobacteria with multiple growth-promoting traits from the dominant plant species from the hyperseasonal Aripo Savannas were screened in this study. Five of the isolates were further analyzed based on their ACCD activities and were tested in single and dual consortium to assess their abilities in promoting growth under simulated drought stress (-0.35 MPa) and chemically induced ACC conditions (0.03 mM). Our findings showed that bacteria which produce high concentrations of IAA affected the isolates' ability to promote growth under stress, irrespective of microbial combination with ACCD activity above the minimal threshold of 20 nmol α-ketobutyrate mg-1 h-1. Biofilm production with co-culture interaction varied greatly across treatments, however, the general trend showed an increase in biofilm under stress induce conditions. The best performing co-culture, UWIGT-83 and UWIGT-120 (Burkholderia sp.) showed enhanced growth in germination assays and in greenhouse trials with Capsicum chinense (Moruga red hot peppers) under drought stress, when compared to non-inoculated treatments. The findings highlight the importance of testing interactivity of bacterial species with multiple growth promoting traits under stress conditions; and proposed the use of ACC growth media as a novel biofilm screening method for selecting potential stress plant growth-promoting bacteria. Better screening strategies for appropriate plant growth-promoting bacteria may narrow the inconsistency observed between laboratory and field trials.

Broad Chain-Length Specificity of the Alkane-Forming Enzymes NoCER1A and NoCER3A/B in Nymphaea odorata.

Many terrestrial plants produce large quantities of alkanes for use in epicuticular wax and the pollen coat. However, their carbon chains must be long to be useful as fuel or as a petrochemical feedstock. Here, we focus on Nymphaea odorata, which produces relatively short alkanes in its anthers. We identified orthologs of the Arabidopsis alkane biosynthesis genes AtCER1 and AtCER3 in N. odorata and designated them NoCER1A, NoCER3A and NoCER3B. Expression analysis of NoCER1A and NoCER3A/B in Arabidopsis cer mutants revealed that the N. odorata enzymes cooperated with the Arabidopsis enzymes and that the NoCER1A produced shorter alkanes than AtCER1, regardless of which CER3 protein it interacted with. These results indicate that AtCER1 frequently uses a C30 substrate, whereas NoCER1A, NoCER3A/B and AtCER3 react with a broad range of substrate chain lengths. The incorporation of shorter alkanes disturbed the formation of wax crystals required for water-repellent activity in stems, suggesting that chain-length specificity is important for surface cleaning. Moreover, cultured tobacco cells expressing NoCER1A and NoCER3A/B effectively produced C19-C23 alkanes, indicating that the introduction of the two enzymes is sufficient to produce alkanes. Taken together, our findings suggest that these N. odorata enzymes may be useful for the biological production of alkanes of specific lengths. 3D modeling revealed that CER1s and CER3s share a similar structure that consists of N- and C-terminal domains, in which their predicted active sites are respectively located. We predicted the complex structure of both enzymes and found a cavity that connects their active sites.

Functional analysis of novel variants identified in cis in the PCCB gene in a patient with propionic acidemia.

Next-generation sequencing has improved the diagnosis of inborn errors of metabolism, allowing rapid confirmation of cases detected by clinical/biochemical studies or newborn screening. The challenge, however, remains for establishing the pathogenicity of the identified variants, especially for novel missense changes or small in-frame deletions. In this work we report a propionic acidemia patient exhibiting a severe neonatal form with coma and hyperammonaemia. Genetic analysis identified the previously described pathogenic PCCB variant p.R512C in the maternal allele and two novel PCCB variants in cis in the paternal allele, p.G246del and p.S322F. Expression analysis in a eukaryotic system confirmed the deleterious effect of the novel missense variant and of the one amino acid deletion, as they both exhibited reduced protein levels and reduced or null PCC activity compared to the wild-type construct. Accordingly, the double mutant resulted in no residual activity. This study increases the knowledge of the genotype-phenotype correlations in the rare disease propionic acidemia and highlights the necessity of functional analysis of novel variants to understand their contribution to disease severity and to accurately classify their pathogenic status. In conclusion, two novel PCCB pathogenic variants have been identified, expanding the current mutational spectrum of propionic acidemia.

Phyllosphere symbiont promotes plant growth through ACC deaminase production.

Plant growth promoting bacteria can confer resistance to various types of stress and increase agricultural yields. The mechanisms they employ are diverse. One of the most important genes associated with the increase in plant biomass and stress resistance is acdS, which encodes a 1-aminocyclopropane-1-carboxylate- or ACC-deaminase. The non-proteinogenic amino acid ACC is the precursor and means of long-distance transport of ethylene, a plant hormone associated with growth arrest. Expression of acdS reduces stress induced ethylene levels and the enzyme is abundant in rhizosphere colonizers. Whether ACC hydrolysis plays a role in the phyllosphere, both as assembly cue and in growth promotion, remains unclear. Here we show that Paraburkholderia dioscoreae Msb3, a yam phyllosphere symbiont, colonizes the tomato phyllosphere and promotes plant growth by action of its ACC deaminase. We found that acdS is required for improved plant growth but not for efficient leaf colonization. Strain Msb3 readily proliferates on the leaf surface of tomato, only occasionally spreading to the leaf endosphere through stomata. The strain can also colonize the soil or medium around the roots but only spreads into the root if the plant is wounded. Our results indicate that the degradation of ACC is not just an important trait of plant growth promoting rhizobacteria but also one of leaf dwelling phyllosphere bacteria. Manipulation of the leaf microbiota by means of spray inoculation may be more easily achieved than that of the soil. Therefore, the application of ACC deaminase containing bacteria to the phyllosphere may be a promising strategy to increasing plant stress resistance, pathogen control, and harvest yields.

Community structure and abundance of ACC deaminase containing bacteria in soils with 16S-PICRUSt2 inference or direct acdS gene sequencing.

Bacteria containing the enzyme 1-aminocyclopropane-1-carboxylate deaminase (ACCD+) can reduce plant ethylene levels and increase root development and elongation resulting in increased resiliency to drought and other plant stressors. Although these bacteria are ubiquitous in the soil, non-culture-based methods for their enumeration and identification are not well developed. In this study we compare two culture-independent approaches for identifying ACCD+ bacteria. First, quantitative PCR (qPCR) and direct acdS sequencing with newly designed gene-specific primers; and second, phylogenetic construction of 16S rRNA amplicon libraries with the PICRUSt2 tool. Using soils from eastern Colorado, we showed complementary yet differing results in ACCD+ abundance and community structure responding to water availability. Across all sites, gene abundances estimated from qPCR with the acdS gene-specific primers and phylogenetic reconstruction using PICRUSt2 were significantly correlated. However, PICRUSt2 identified members of the Acidobacteria, Proteobacteria, and Bacteroidetes phyla (now known as Acidobacteriota, Pseudomonadota, and Bacteroidota according to the International Code of Nomenclature of Prokaryotes) as ACCD+ bacteria, whereas the acdS primers amplified only members of the Proteobacteria phyla. Despite these differences, both measures showed that bacterial abundance of ACCD+ decreased as soil water content decreased along a potential evapotranspiration (PET) gradient at three sites in eastern Colorado. One major advantage of using 16S sequencing and PICRUSt2 in metagenomic studies is the ability to get a potential functional profile of all known KEGG (Kyoto Encyclopedia of Genes and Genomes) enzymes within the bacterial community of a single soil sample. The 16S-PICRUSt2 method paints a broader picture of the biological and biochemical function of the soil microbiome compared to direct acdS sequencing; however, phylogenetic analysis based on 16S gene relatedness may not reflect that of the functional gene of interest.

Assessing the role of ACC deaminase-producing bacteria in alleviating salinity stress and enhancing zinc uptake in plants by altering the root architecture of French bean (Phaseolus vulgaris) plants.

MAIN CONCLUSION: The consortium inoculation with strains R1 and R4 modified the root system to boost seedling growth, increase the zinc content of French bean pods, and reduce salinity stress. The present study demonstrated the effect of two 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase-producing plant growth-promoting rhizobacteria (Pantoea agglomerans R1 and Pseudomonas fragi R4) alone and consortia on the root system development, French bean growth, and zinc content as well as salinity stress tolerance. Both the strains were characterized for ACC utilization activity (426.23 and 380.54 nmol α-ketobutyrate mg protein-1 h-1), indole acetic acid (IAA) production, phosphate solubilization, ammonia, hydrogen cyanide (HCN), and siderophore production. The strains exhibited zinc solubilization in both plate and broth assays with zinc oxide and zinc carbonate as zinc sources as validated by atomic absorption spectroscopy (AAS). Single or combined inoculations with the selected strains significantly modulated the architectural and morphological traits of the root system of French bean plants. Furthermore, the application of R1and R4 consortia has enhanced zinc content in roots (60.83 mg kg-1), shoots (15.41 mg kg-1), and pods (30.04 mg kg-1) of French bean plants grown in ZnCO3 amended soil. In another set of pot experiments, the consortium bacterization has significantly enhanced length as well as fresh and dry biomass of roots and shoots of the French bean plant under saline stress conditions. Additionally, inoculation with ACC-degrading rhizobacterial strains has increased chlorophyll and carotenoid contents, osmoprotectant content, and antioxidative enzyme (catalase and peroxidase) activity in comparison to their counterparts exposed to salt treatments only. Current findings suggested ACC deaminase-producing rhizobacterial strains hold the potential to improve root architecture which in turn promotes plant growth under salt-stressed conditions as well as enhances micronutrient concentration in host plants.

Assessing the Immune Cell Subset and Genetic Mutations in Patients With Palindromic Rheumatism Seronegative for Rheumatoid Factor and Anti-Cyclic Citrullinated Peptide.

OBJECTIVE: The etiology underlying cases of palindromic rheumatism (PR) not associated with other rheumatic diseases in patients who are seronegative for rheumatoid factor and anti-cyclic citrullinated peptide (seronegative PR) is unclear. We aimed to investigate the immune cells and genes involved. METHODS: This was a single-center comparative study of 48 patients with seronegative PR and 48 healthy controls. Mass cytometry and RNA sequencing were used to identify distinct immune cell subsets in blood. Among the 48 seronegative PR patients, plasma samples from 40 patients were evaluated by enzyme-linked immunosorbent assay for cytokine levels, and peripheral blood samples from 25 patients were evaluated by flow cytometry for mononuclear cell subsets. Plasma samples from 21 patients were evaluated by real-time polymerase chain reaction for differential gene and protein expression, and samples from 3 patients were analyzed with whole-exome sequencing for gene mutations. RESULTS: Immunophenotyping revealed a markedly increased frequency of CD14+CD11b+CD36+ and CD4+CD25-CD69+ cells in seronegative PR patients with active flares compared with healthy controls (P < 0.0001 for both cell subset comparisons). Gene enrichment analyses of RNA-sequencing data from sorted CD14+CD11b+CD36+ and CD4+CD25-CD69+ cells showed involvement of the inflammatory/stress response, phagocytosis, and regulation of apoptosis functional pathways. Up-regulated expression of CXCL16 and IL10RA was observed in monocytes from PR patients. Up-regulation of PFKFB3, DDIT4, and TGFB1, and down-regulation of PDIA6 were found in monocytes and lymphocytes from PR patients with active flares and PR patients in intercritical periods. Plasma levels of S100A8/A9 and interleukin-1ß were elevated in PR patients. Whole-exome sequencing revealed novel polygenic mutations in HACL1, KDM5A, RASAL1, HAVCR2, PRDM9, MBOAT4, and JRKL. CONCLUSION: In seronegative PR patients, we identified a distinct CD14+CD11b+CD36+ cell subset that can induce an inflammatory response under stress and exert antiinflammatory effects after phagocytosis of apoptotic cells, and a CD4+CD25-CD69+ T cell subset with pro- and antiinflammatory properties. Individuals with genetic mutations involving epigenetic modification, potentiation and resolution of stress-induced inflammation/apoptosis, and a dysregulated endoplasmic reticulum stress response could be predisposed to seronegative PR.

Identification of endophytic fungi with ACC deaminase-producing isolated from halophyte Kosteletzkya Virginica.

Seashore mallow (Kosteletzkya virginica), as a noninvasive perennial halophytic oilseed-producing dicot, is native from the Gulf to the Atlantic coasts of the U.S. The purpose of our research was to investigate 1-aminocyclopropane-1carboxylic acid deaminase (ACCD) producing endophytic fungi from K.virginica. A total of 59 endophytic fungal strains, isolated from roots in K.virginica of seedlings, were grouped into 12 genera including in Penicillium, Aspergillus, Fusarium, Trichoderma, Rhizopycnis sp., Ceriporia Donk, Trametes sp., Schizophyllum commune sp., Alternaria, Cladosporium, Cylindrocarpon, and Scytalidium according to sequences of ITS. The ACD activity of 10 endophytic fungi isolated was detected. T.asperellum had the highest ACC deaminase activity among all 10 isolated genera of fungal strains, followed by T. viride. Dry weight and fresh weight of plant, plant height, root length, SOD activity, and chlorophyll content of wheat and soybean inoculated with T.asperellum or T. viride was increased compared with non-inoculated control plants under non salt or salt stress. Further analysis showed that T.asperellum or T.viride strains induced downregulation of the expression of ethylene synthesis-related genes such as ACC oxidase (ACO) and ACC synthase (ACS), thereby reducing ethylene synthesis and damage to plants under salt stress. These endophytic fungi can be used as alternative bioinoculants to increase crop yield in saline soil.

Phenome-wide analysis of Taiwan Biobank reveals novel glycemia-related loci and genetic risks for diabetes.

To explore the complex genetic architecture of common diseases and traits, we conducted comprehensive PheWAS of ten diseases and 34 quantitative traits in the community-based Taiwan Biobank (TWB). We identified 995 significantly associated loci with 135 novel loci specific to Taiwanese population. Further analyses highlighted the genetic pleiotropy of loci related to complex disease and associated quantitative traits. Extensive analysis on glycaemic phenotypes (T2D, fasting glucose and HbA1c) was performed and identified 115 significant loci with four novel genetic variants (HACL1, RAD21, ASH1L and GAK). Transcriptomics data also strengthen the relevancy of the findings to metabolic disorders, thus contributing to better understanding of pathogenesis. In addition, genetic risk scores are constructed and validated for absolute risks prediction of T2D in Taiwanese population. In conclusion, our data-driven approach without a priori hypothesis is useful for novel gene discovery and validation on top of disease risk prediction for unique non-European population.

AcdR protein is an activator of transcription of 1-aminocyclopropane-1-carboxylate deaminase in Methylobacterium radiotolerans JCM 2831.

It has been previously shown that a number of plant associated methylotrophic bacteria contain an enzyme aminocyclopropane carboxylate (ACC) deaminase (AcdS) hydrolyzing ACC, the immediate precursor of ethylene in plants. The genome of the epiphytic methylotroph Methylobacterium radiotolerans JCM2831 contains an open reading frame encoding a protein homologous to transcriptional regulatory protein AcdR of the Lrp (leucine-responsive regulatory protein) family. The acdR gene of M. radiotolerans was heterologously expressed in Escherichia coli and purified. The results of gel retardation experiments have shown that AcdR specifically binds the DNA fragment containing the promoter-operator region of the acdS gene. ACC decreased electrophoretic mobility of the AcdR-DNA complex whereas leucine had no effect on the complex mobility. The mutant strains of M. radiotolerans obtained by insertion of a tetracycline cassette in the acdS or acdR gene lost the ACC-deaminase activity but the strains with complementation of the mutation recovered this function. The acdS- mutant but not acdR- strain expressed the xylE reporter gene under the control of acdS promoter region thus resulting in a catechol 2,3-dioxygenase activity. This suggested that AcdR in vivo functions as activator of transcription of the acdS gene. The results obtained in this study showed that in phytosymbiotic methylotroph Methylobacterium radiotolerans AcdR mediates activation of the acdS gene transcription in the presence of an inducer ACC or 2-aminoisobutyrate and the excess of the regulatory protein assists in transcription initiation even in the absence of the inducer. The model of regulation of acdS transcription in M. radiotolerans was proposed.

Combinatorial Biosynthesis of Terpenoids through Mixing-and-Matching Sesquiterpene Cyclase and Cytochrome P450 Pairs.

Terpenoids are an important class of natural products with diverse structures and bioactivities. Their hydrocarbon scaffolds are mainly derived from the terpenes produced by terpene cyclases (TCs). Otherwise, new hydrocarbon scaffolds can be achieved through oxidative rearrangement catalyzed by oxygenases such as P450s. Herein, we report the functional characterization of α/ß-trans-bergamotene-producing TCs and their multifunctional P450 partners mined from different fungal species. In addition, novel sesquiterpenoids with hydrocarbon scaffolds different from bergamotenes were generated by combinatorial biosynthesis through mixing-and-matching these TC and P450 pairs. Our results provide a successful example of expanding the chemical diversity of terpenoids by combining genome mining and synthetic biology.

ACC deaminase producing rhizobacterium Enterobacter cloacae ZNP-4 enhance abiotic stress tolerance in wheat plant.

Plant growth promoting rhizobacterium (PGPR) designated as ZNP-4, isolated from the rhizosphere of Ziziphus nummularia, was identified as Enterobacter cloacae following 16S rRNA sequence analysis. The isolated strain exhibited various plant growth promoting (PGP) traits. The 1-aminocyclopropane-1-carboxylic acid deaminase (ACCD) activity was evaluated under diverse physiological conditions that could be useful for minimizing the abiotic stress-induced inhibitory effects on wheat plants. The strain showed resistance to salt (NaCl) and metal (ZnSO4) stress. The effect of E. cloacae ZNP-4 on the augmentation of plant growth was studied under salinity stress of 150 mM (T1 treatment) & 200 mM (T2 treatment) NaCl. The inoculation of strain ZNP-4 significantly improved the various growth parameters of wheat plant such as shoot length (41%), root length (31%), fresh weight (28%), dry weight (29%), photosynthetic pigments chlorophyll a (62%) and chlorophyll b (34%). Additionally, the strain was found to be efficient for minimizing the imposed Zn stress in terms of improving plant growth, biomass and photosynthetic pigments in pots containing different levels of metal stress of 150 mg kg-1 (treatment T1) and 250 mg kg-1 (treatment T2). Isolate ZNP-4 also improved the proline content and decreased malondialdehyde (MDA) level under both salinity and metal stress, therefore maintaining the membrane integrity. Furthermore, bacterial inoculation increased the activities of antioxidative enzymes such as superoxide dismutase (SOD), catalase (CAT), and peroxidase (POX). The positive effects of PGPR occurred concurrently with the decrease in abiotic stress-induced reactive oxygen species (ROS) molecules such as hydrogen peroxide (H2O2) and superoxide (O2-) contents. Overall, the observed results indicate that use of bacteria with such beneficial traits could be used as bio-fertilizers for many crops growing under stress conditions.

Perspective of ACC-deaminase producing bacteria in stress agriculture.

The 1-aminocyclopropane-1-carboxylate deaminase (ACCD) enzyme plays an important role in stress alleviation of both biotic and abiotic stressors in plants and thereby enhances their growth under harsh environmental conditions. In-depth analysis of AcdS gene encoding for ACC deaminase reveals its presence in diverse microorganisms including bacteria and fungi. Particularly, plant growth-promoting bacteria (PGPB) containing ACCD supports plant growth by modulating the level of 'stress ethylene' and cleaving its precursor 1-aminocyclopropane-1-carboxylic acid (ACC) into α-ketobutyrate and ammonia, enabling PGPB to utilize ACC as a carbon and nitrogen source. The reduced synthesis of ethylene in plants further relieves the ethylene inhibition of plant growth and development, and improves plant resistance to various stressors. Therefore, the dual role of microbial ACCD makes it a cost-effective and eco-friendly biocatalyst for sustainable agricultural productions. The inducible ACCD encoding gene AcdS is differentially regulated by varying environmental conditions. Successful generation of transgenic plants with microbial AcdS gene enhanced biotic and abiotic stress tolerance in plants. In the present review, we discuss the importance of ACCD-producing PGPB for their ability to reduce ethylene production and the promotion of plant growth under stress conditions. We also highlighted the development of transgenic plants by overexpressing bacterial AcdS gene to improve their performance under stress conditions.

Comparative metabolomics with Metaboseek reveals functions of a conserved fat metabolism pathway in C. elegans.

Untargeted metabolomics via high-resolution mass spectrometry can reveal more than 100,000 molecular features in a single sample, many of which may represent unidentified metabolites, posing significant challenges to data analysis. We here introduce Metaboseek, an open-source analysis platform designed for untargeted comparative metabolomics and demonstrate its utility by uncovering biosynthetic functions of a conserved fat metabolism pathway, α-oxidation, using C. elegans as a model. Metaboseek integrates modules for molecular feature detection, statistics, molecular formula prediction, and fragmentation analysis, which uncovers more than 200 previously uncharacterized α-oxidation-dependent metabolites in an untargeted comparison of wildtype and α-oxidation-defective hacl-1 mutants. The identified metabolites support the predicted enzymatic function of HACL-1 and reveal that α-oxidation participates in metabolism of endogenous ß-methyl-branched fatty acids and food-derived cyclopropane lipids. Our results showcase compound discovery and feature annotation at scale via untargeted comparative metabolomics applied to a conserved primary metabolic pathway and suggest a model for the metabolism of cyclopropane lipids.

Label-free proteomics approach reveals candidate proteins in rice (Oryza sativa L.) important for ACC deaminase producing bacteria-mediated tolerance against salt stress.

The omics-based studies are important for identifying characteristic proteins in plants to elucidate the mechanism of ACC deaminase producing bacteria-mediated salt tolerance. This study evaluates the changes in the proteome of rice inoculated with ACC deaminase producing bacteria under salt-stress conditions. Salt stress resulted in a significant decrease in photosynthetic pigments, whereas inoculation of Methylobacterium oryzae CBMB20 had significantly increased pigment contents under normal and salt-stress conditions. A total of 76, 51 and 33 differentially abundant proteins (DAPs) were identified in non-inoculated salt-stressed plants, bacteria-inoculated plants under normal and salt stress conditions respectively. The abundances of proteins responsible for ethylene emission and programmed cell death were increased, and that of photosynthesis-related proteins were decreased in non-inoculated plants under salt stress. However, bacteria-inoculated plants had shown higher abundance of antioxidant proteins, RuBisCo and ribosomal proteins that are important for enhancing stress tolerance and improving plant physiological traits. Collectively, salt stress might affect plant physiological traits by impairing photosynthetic machinery and accelerating apoptosis leading to a decline in biomass. However, inoculation of plants with bacteria can assist in enhancing photosynthetic activity, antioxidant activities and ethylene regulation related proteins for attenuating salt-induced apoptosis and sustaining growth and development.

Sphingobacterium faecale sp. nov., a 1-aminocyclopropane-1-carboxylate deaminase producing bacterium isolated from camel faeces.

An investigation of the diversity of 1-aminocyclopropane-1-carboxylate deaminase producing bacteria associated with camel faeces revealed the presence of a novel bacterial strain designated C459-1T. It was Gram-stain-negative, short-rod-shaped and non-motile. Strain C459-1T was observed to grow optimally at 35 °C, at pH 7.0 and in the presence of 0 % NaCl on Luria-Bertani agar medium. The cells were found to be positive for catalase and oxidase activities. The major fatty acids (>10 %) were identified as iso-C15 : 0, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and iso-C17 : 0 3-OH. The predominant menaquinone was MK-7. The major polar lipids consisted of phosphatidylethanolamine, one sphingophospholipid, two unknown aminophospholipids, three unknown glycolipids and five unknown lipids. The genomic DNA G+C content was 40.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain C459-1T was affiliated with the genus Sphingobacterium and had the highest sequence similarity to Sphingobacterium tabacisoli h337T (97.0 %) and Sphingobacterium paucimobilis HER1398T (95.6 %). The average nucleotide identity and digital DNA-DNA hybridization values between strain C459-1T and S. tabacisoli h337T were 83.8 and 33.8 %, respectively. Phenotypic characteristics including enzyme activities and carbon source utilization differentiated strain C459-1T from other Sphingobacterium species. Based on its phenotypic, chemotaxonomic and phylogenetic properties, strain C459-1T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium faecale sp. nov. is proposed, with strain is C459-1T (CGMCC 1.18716T=KCTC 82381T) as the type strain.

Role of ACC deaminase producing bacteria for abiotic stress management and sustainable agriculture production.

Plants are immobile and are exposed to various biotic and abiotic stresses, including heat, cold, drought, flooding, nutrient deficiency, heavy metal exposure, phytopathogens, and pest attacks. The stressors significantly affect agricultural productivity when exceed a certain threshold. It has been reported that most of the stressed plants are reported to have increased ethylene synthesis from its precursor 1-aminocyclopropane-1-carboxylic acid (ACC). Ethylene is a plant hormone that plays a vital role in the regulation of various physiological processes, such as respiration, nitrogen fixation, and photosynthesis. The increment in the plant hormone ethylene would reduce plant growth and development, and if the ethylene level increased beyond the limit, it could also result in plant death. Therefore, plant growth-promoting bacteria (PGPB) possessing ACC deaminase activity play an essential role in the management of biotic and abiotic stresses by hydrolysing 1-aminocyclopropane-1-carboxylic acid using ACC deaminase. In this review, the importance of ACC deaminase-producing bacteria in promoting plant growth under various abiotic stressors is discussed.