Identification of a biomarker for Bacillus thuringiensis strains with high toxicity against Spodoptera frugiperda based on insecticidal gene linkage analysis.

BACKGROUND: Bacillus thuringiensis (Bt) is a Gram-positive bacterium that produces various insecticidal proteins used to control insect pests. Spodoptera frugiperda is a global insect pest which causes serious damage to crops, but bio-insecticides currently available to control this pest have limited activity and so new ones are always being sought. In this study we have tested the hypothesis that a biomarker for strain toxicity could be found that would greatly facilitate the identification of new potential products. RESULTS: Using genomic sequencing data we constructed a linkage network of insecticidal genes from 1957 Bt genomes and found that four gene families, namely cry1A, cry1I, cry2A and vip3A, showed strong linkage. For 95 strains isolated from soil samples we assayed them for toxicity towards S. frugiperda and for the presence of the above gene families. All of the strains that showed high toxicity also contained a member of the vip3A gene family. Two of them were more toxic than a commercially available strain and genomic sequencing identified a number of potentially novel toxin-encoding genes. CONCLUSIONS: The presence of a vip3A gene in the genome of a Bt strain proved to be a strong indicator of toxicity towards S. frugiperda validating this biomarker approach as a strategy for future discovery programs. © 2024 Society of Chemical Industry.

Correction: Bopape et al. The Genome of a Pigeonpea Compatible Rhizobial Strain '10ap3' Appears to Lack Common Nodulation Genes. Genes 2023, 14, 1084.

Prof. Dr. Ahmed Idris Hassen was not included as an author in the original publication [...].

Characterization of rhizobia for beneficial traits that promote nodulation in legumes under abiotically stressed conditions.

The growing interest in using rhizobia as inoculants in sustainable agricultural systems has prompted the screening of rhizobia species for beneficial traits that enhance nodulation and nitrogen fixation under abiotic stressed conditions. This study reports phenotypic and phylogenetic characterization of rhizobia strains previously isolated from the root nodules of several indigenous and exotic legumes growing in South Africa and other countries. The Rhizobia strains were screened for their ability to tolerate various abiotic stresses (temperature 16, 28, and 36 °C; acidity/alkalinity pH 5, 7, and 9; heavy metals 50, 100, and 150 mM AlCl3.6H2O; and salinity 50, 100, and 150 mM NaCl). Phylogenetic characterization of the isolates was determined using multilocus sequence analysis of the 16S rRNA, recA, acdS, exoR, nodA, and nodC genes. The analysis indicated that the isolates are phylogenetically related to Sinorhizobium, Bradyrhizobium, Rhizobium, Mesorhizobium, and Aminobacter genera and exhibited significant variations in their tolerance to abiotic stresses. Amid the increasing threats of the global stresses, these current results provide baseline information in the selection of rhizobia for use as inoculants under extreme temperatures, acidity/alkalinity, and salinity stress conditions in South Africa.

Genome sequence of an indole-3-acetic acid and siderophores producing Pseudomonas monsensis SARCC-3054 with the potential as a microbial inoculant for enhanced crop production.

The genome of Pseudomonas monsensis strain SARCC-3054 was sequenced after being confirmed as a potential plant growth-promoting rhizobacteria in both in vitro and in vivo assays. The 6.3 MB genome has a GC content of 60.2% and is divided into 59 contigs that contain several plant beneficial genes and proteins.

Draft Genome Sequences of Pantoea agglomerans Strains BD1274 and BD1212, Isolated from Onion Seeds, Reveal Major Differences in Pathogenicity and Functional Genes.

Pantoea agglomerans strains BD1274 and BD1212 were isolated from Allium cepa seeds. Strain BD1274 induced a disease symptom on a healthy onion, whereas strain BD1212 did not and remains nonpathogenic. A comparative genomic study revealed that the strains differ in their genomic compositions, particularly in the genes that confer pathogenicity.

Microbial and functional diversity of Cyclopia intermedia rhizosphere microbiome revealed by analysis of shotgun metagenomics sequence data.

Cyclopia spp., commonly referred to as honeybush due to the honey scented flowers, are indigenous legumes mainly growing in the Cape Floristic Region of the Western Cape, South Africa. Dozens of species, including Cyclopia intermedia, C. subternata, C. plicata, C. genistoides are used to make the well-known, popular and widely enjoyed beverage called 'honeybush tea'. In the past, most rhizosphere microbial studies associated with Cyclopia spp. focused mainly on the taxonomy and diversity of the root nodule associated symbiotic nitrogen fixing rhizobia. The work presented here is the first report on the microbial and functional diversity of rhizosphere microbiome associated with Cyclopia intermedia. Metagenomic shotgun sequencing was performed on the rhizosphere soil sample collected from this Cyclopia sp. using illumina Hiseq 2500 platform which resulted in an α- diversity of 312 species. Analysis of the metagenome sequence using the Metagenomic analysis server (MG-RAST) indicated that bacteria constitute the dominant domain followed by Eukaryota, Archaea and other sequences derived from fungi and viruses. Functional diversity of the metagenome based on analysis using the Cluster Orthologous Group (COG) method showed metabolism as the most important function in the community. The raw sequence data is uploaded in FASTQ format on MG-RAST server with ID mgm4855911.3 which can be accessed at http://www.mg-rast.org/linkin.cgi?project=mgp90368. The data on the microbial and functional diversity of the rhizosphere community of Cyclopia intermedia generates a baseline information about the microbial ecology of this indigenous legume. The microbial profile data can also be used as indicators of soil health characteristic of the rhizosphere of this important legume.

Emergence of ß-rhizobia as new root nodulating bacteria in legumes and current status of the legume-rhizobium host specificity dogma.

Recent developments in the legume rhizobium symbiotic interaction particularly those related to the emergence of novel strains of bacteria that nodulate and fix nitrogen in legumes is gaining momentum. These novel strains of bacteria were mostly isolated from the root nodules of indigenous and invasive legumes belonging to the sub families Papilionoideae and Mimosoideae in South Africa, South America and South East China. These rhizobia are phylogenetically and taxonomically different from the traditional 'alpha rhizobia' and are termed 'ß-rhizobia' as they belong to the ß-sub class of Proteobacteria. There are also new reports of novel species of root nodulating bacteria from the α-Proteobacteria, not known for several decades since the discovery of rhizobia. However, in this review focus is given to the emerging ß-rhizobia isolated from the indigenous Papilionoid legumes in the Cape Floristic regions in South Africa and the indigenous and invasive Mimosoid legumes in South America and South East Asia respectively. The nodulation of the indigenous South African Papilionoid legumes including that of Aspalathus linearis (rooibos) is discussed in a bit detail. Previous reports indicated that A. linearis is very specific in its rhizobium requirement and was reported to be nodulated by the slow growing Bradyrhizobium spp. This review however summarizes that the bacteria associated with the root nodules of A. linearis belong to members of both the alpha (α) Proteobacteria that include Mesorhizobium, Rhizobium and Bradyrhizobium spp. and the beta (ß) Proteobacteria represented by the genus Burkholderia (now reclassified as Paraburkholderia). In addition, the occurrence of Paraburkholderia as the newly emerging root nodule symbionts of various other legumes has been discussed. In doing so, the review highlights that nodulation is no longer restricted to the traditional 'rhizobia' group following the emergence of the new beta rhizobia as potential nodulators of various indigenous legumes. It thus provides some insights on the status of the legume-rhizobium host specificity concept and the loss of this specificity in several symbiotic associations that puts the long held dogma of host specificity of the legume rhizobium symbiosis in a dilemma.

Draft Genome Sequence of Mesorhizobium sp. Strain SARCC-RB16n, an Effective Nodulating and Nitrogen-Fixing Symbiont of Rooibos [Aspalathus linearis (Burm. f.)] in South Africa.

The draft genome sequence of Mesorhizobium sp. strain SARCC-RB16n reveals the presence of major symbiotic (nod and nif) and additional plant growth-promoting (PGPR) genes associated with enhanced growth of Aspalathus linearis (Burm. f.) in South Africa. The genome sequence provides vital information for the development of a commercial inoculant for rooibos cultivation.

Draft Genome Sequence of Rhizobium tropici SARCC-755, a Free-Living Rhizobium That Nodulated and Promoted Growth in Pigeonpea [Cajanus cajan (L.) Millsp.].

Rhizobium tropici SARCC-755 is a free-living soil bacterium that formed nodules on pigeonpea roots in the present study. However, the draft genome sequence reveals that this Rhizobium species contains the nolR gene but lacks the common nodulation (nodABC) genes and probably uses other pathways to induce nodules on the legume plant.

Rhizobacteria-induced systemic tolerance against drought stress in Sorghum bicolor (L.) Moench.

Induction of systemic tolerance in sorghum [Sorghum bicolor (L.) Moench] against drought stress was studied by screening a large collection of rhizobacterial isolates for their potential to exhibit this essential plant growth-promoting trait. This was done by means of a greenhouse assay that measured the relative change in both plant height and -biomass (roots and shoots) between rhizobacteria-primed versus non-primed (naïve) plants under drought stress conditions. In order to elucidate the metabolomic changes in S. bicolor that conferred the drought stress tolerance after treatment (priming) with selected isolates, untargeted ultra-high performance liquid chromatography-high definition mass spectrometry (UHPLC-HDMS)-based metabolomics was carried out. Intracellular metabolites were methanol-extracted from rhizobacteria-primed and naïve S. bicolor roots and shoots. Extracts were analysed on a UHPLC-HDMS system and the generated data were chemometrically mined to determine signatory metabolic profiles and bio-markers related to induced systemic tolerance. The metabolomic results showed significant treatment-related differential metabolic reprogramming between rhizobacteria-primed and naïve plants, correlating to the ability of the selected isolates to protect S. bicolor against drought stress. The selected isolates, identified by means of 16S rRNA gene sequencing as members of the genera Bacillus and Pseudomonas, were screened for 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity by means of an in vitro assay and the presence of the acdS gene was subsequently confirmed by PCR for strain N66 (Pseudomonas sp.). The underlying key metabolic changes in the enhanced drought stress tolerance observed in rhizobacteria-primed S. bicolor plants included (1) augmented antioxidant capacity; (2) growth promotion and root architecture modification as a result of the upregulation of the hormones gibberellic acid, indole acetic acid and cytokinin; (3) the early activation of induce systemic tolerance through the signalling hormones brassinolides, salicylic acid and jasmonic acid and signalling molecules sphingosine and psychosine; (4) the production of the osmolytes proline, glutamic acid and choline; (5) the production of the epicuticular wax docosanoic acid and (6) ACC deaminase activity resulting in lowered ethylene levels. These results unravelled key molecular details underlying the PGPR-induced systemic tolerance in sorghum plants, providing insights for the plant priming for abiotic stress.

Paraburkholderia strydomiana sp. nov. and Paraburkholderia steynii sp. nov.: rhizobial symbionts of the fynbos legume Hypocalyptus sophoroides.

Twelve nodulating Paraburkholderia strains isolated from indigenous South African fynbos legume Hypocalyptus sophoroides were investigated to determine their taxonomic status. Genealogical concordance analysis, based on six loci (16S rRNA, atpD, recA, rpoB, lepA and gltB), revealed that they separate into two consistent and exclusive groups. Average nucleotide identity and DNA-DNA hybridisation comparisons indicated that they were sufficiently divergent from their closest known phylogenetic relatives (Paraburkholderia caledonica and Paraburkholderia terrae, respectively) to be regarded as novel species. This was also supported by the results of fatty acid analysis and metabolic characterisation. For these two isolate groups, we accordingly propose the new species Paraburkholderia strydomiana sp. nov. with WK1.1fT (= LMG 28731T = SARCC1213T) as its type strain and Paraburkholderia steynii sp. nov. with HC1.1baT (= LMG 28730T = SARCC696T) as its type strain. Our data thus showed that H. sophoroides may be considered a promiscuous symbiotic partner due to its ability to associate with multiple species of Paraburkholderia.

The Draft Genome Sequence of Burkholderia sp. Strain Nafp2/4-1b Confirms Its Ability To Produce the Plant Growth-Promoting Traits Pyoverdine Siderophores, 1-Aminocyclopropane-1-Carboxylate Deaminase, and the Phytohormone Auxin.

Burkholderia sp. strain Nafp2/4-1b is a rhizobacterium isolated from the rhizosphere of grassland in South Africa. This draft genome report confirms the presence of genes related to iron acquisition, alleviation of abiotic stress in plants, and other essential traits of plant growth-promoting rhizobacteria (PGPR) that signify the potential of this strain as a plant growth-promoting agent.