Isolation of plant-growth-promoting Bacillus strains from soybean root nodules

Back to the future: Using herbarium specimens to isolate nodule-associated bacteria

Herbarium specimens are increasingly being used as sources of information to understand the ecology and evolution of plants and their associated microbes. Most studies have used specimens as a source of genetic material using culture-independent approaches. We demonstrate that herbarium specimens can also be used to culture nodule-associated bacteria, opening the possibility of using specimens to understand plant-microbe interactions at new spatiotemporal scales. We used historic and contemporary nodules of a common legume, Medicago lupulina, to create a culture collection. We were able to recover historic bacteria in 15 genera from three specimens (collected in 1950, 2004, and 2015). This work is the first of its kind to isolate historic bacteria from herbarium specimens. Future work should include inoculating plants with historic strains to see if they produce nodules and if they affect plant phenotype and fitness. Although we were unable to recover any Ensifer, the main symbiont of Medicago lupulina, we recovered some other potential nodulating species, as well as many putative growth-promoting bacteria.

Comparative microbiome diversity in root-nodules of three Desmodium species used in push-pull cropping system

Background

Desmodium species used as intercrops in push-pull cropping systems are known to repel insect-pests, suppress Striga species weeds, and shift soil microbiome. However, the mechanisms through which Desmodium species impact the soil microbiome, either through its root exudates, changes in soil nutrition, or shading microbes from its nodules into the rhizosphere, are less understood. Here, we investigated the diversity of root-nodule microbial communities of three Desmodium species- Desmodium uncinatum (SLD), Desmodium intortum (GLD), and Desmodium incanum (AID) which are currently used in smallholder maize push-pull technology (PPT).

Methods

Desmodium species root-nodule samples were collected from selected smallholder farms in western Kenya, and genomic DNA was extracted from the root-nodules. The amplicons underwent paired-end Illumina sequencing to assess bacterial and fungal populations.

Results

We found no significant differences in composition and relative abundance of bacterial and fungal species within the root-nodules of the three Desmodium species. While a more pronounced shift was observed for fungal community compositions compared to bacteria, no significant differences were observed in the general diversity (evenness and richness) of fungal and bacterial populations among the three Desmodium species. Similarly, beta diversity was not significantly different among the three Desmodium species. The root-nodule microbiome of the three Desmodium species was dominated by Bradyrhizobium and Fusarium species. Nevertheless, there were significant differences in the proportion of marker gene sequences responsible for energy and amino acid biosynthesis among the three Desmodium species, with higher sequence proportions observed in SLD.

Conclusion

There is no significant difference in the microbial community of the three Desmodium species used in PPT. However, root-nodule microbiome of SLD had significantly higher marker gene sequences responsible for energy and amino acid biosynthesis. Therefore, it is likely that the root-nodules of the three Desmodium species host similar microbiomes and influence soil health, consequently impacting plant growth and agroecosystem functioning.

Plants and endophytes interaction: a "secret wedlock" for sustainable biosynthesis of pharmaceutically important secondary metabolites

Many plants possess immense pharmacological properties because of the presence of various therapeutic bioactive secondary metabolites that are of great importance in many pharmaceutical industries. Therefore, to strike a balance between meeting industry demands and conserving natural habitats, medicinal plants are being cultivated on a large scale. However, to enhance the yield and simultaneously manage the various pest infestations, agrochemicals are being routinely used that have a detrimental impact on the whole ecosystem, ranging from biodiversity loss to water pollution, soil degradation, nutrient imbalance and enormous health hazards to both consumers and agricultural workers. To address the challenges, biological eco-friendly alternatives are being looked upon with high hopes where endophytes pitch in as key players due to their tight association with the host plants. The intricate interplay between plants and endophytic microorganisms has emerged as a captivating subject of scientific investigation, with profound implications for the sustainable biosynthesis of pharmaceutically important secondary metabolites. This review delves into the hidden world of the "secret wedlock" between plants and endophytes, elucidating their multifaceted interactions that underpin the synthesis of bioactive compounds with medicinal significance in their plant hosts. Here, we briefly review endophytic diversity association with medicinal plants and highlight the potential role of core endomicrobiome. We also propose that successful implementation of in situ microbiome manipulation through high-end techniques can pave the way towards a more sustainable and pharmaceutically enriched future.

Evaluation of the Co-inoculation Effect of Rhizobium and Plant Growth Promoting Non-rhizobial Endophytes on Vigna radiata

A unique feature of leguminous plants is the establishment of symbiotic bacterial genera inside root or stem nodules that is being recently re-evaluated for investigating the micro-flora discrete to nitrogen fixation. The present research was carried out to evaluate non-rhizobial endophytes and Rhizobium from root nodules of Vigna radiata and ascertain their co-inoculation effect in pot and field conditions. Each strain displayed one or more plant growth-promoting behaviors in varying degrees. The ability to fix nitrogen was observed in all strains; however, a noticeable enhancement in nitrogen fixation was observed when all three strains were co-inoculated. All three strains were found to possess the nifH gene, which plays a key role in the nitrogen fixation process. However, only Rhizobium sp. AAU B3 also had the nodD gene present. Furthermore, combinations of all three strains produced the highest levels of phosphate solubilization, potash mobilisation, Indole Acetic Acid (IAA), and the stress-relieving enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase. Interestingly, the succession of the root nodule formation within root hairs seedlings was observed under a fluorescence microscope and two NRE were found to be located inside the root nodules, indicating that they are endophytic. Additionally, a pot and field investigation revealed that the combination of chosen Rhizobium and NRE strains had a favorable impact on the growth and yield characteristics of a green gram. Selected bio-inoculants can reduce the utilization of synthetic fertilizers by 75%, which might lead to the restoration of the soil's health. Therefore, these bio-inoculants might be explored commercially for sustainable agriculture production.

Genomic insight into the environmental adaptations and toxigenic features of endophytic Bacillus cereus CaB1 isolated from Capsicum annuum L

In the study, a previously isolated plant beneficial endophytic B. cereus CaB1 was selected for the detailed analysis by whole-genome sequencing. The WGS has generated a total of 1.9 GB high-quality data which was assembled into a 5,257,162 bp genome with G + C content of 35.2%. Interestingly, CaB1 genome was identified to have 40 genes with plant beneficial functions by bioinformatic analysis. At the same time, it also showed the presence of various virulence factors except the diarrhoeal toxin, cereulide. Upon comparative analysis of CaB1 with other B. cereus strains, it was found to have random distributions of virulence and plant growth promoting traits. The core genome phylogenetic analysis of the Bacillus cereus strains further showed the close relation of plant associated strains with isolates from spoiled food products. The observed genome flexibility of B. cereus thus indicates its ability to make use of diverse hosts, which can result either in beneficial or harmful effects.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03463-9.

Genetic and Physiological Characterization of Soybean-Nodule-Derived Isolates from Bangladeshi Soils Revealed Diverse Array of Bacteria with Potential Bradyrhizobia for Biofertilizers

Genetic and physiological characterization of bacteria derived from nodules of leguminous plants in the exploration of biofertilizer is of paramount importance from agricultural and environmental perspectives. Phylogenetic analysis of the 16S rRNA gene of 84 isolates derived from Bangladeshi soils revealed an unpredictably diverse array of nodule-forming and endosymbiotic bacteria-mostly belonging to the genus Bradyrhizobium. A sequence analysis of the symbiotic genes (nifH and nodD1) revealed similarities with the 16S rRNA gene tree, with few discrepancies. A phylogenetic analysis of the partial rrn operon (16S-ITS-23S) and multi-locus sequence analysis of atpD, glnII, and gyrB identified that the Bradyrhizobium isolates belonged to Bradyrhizobium diazoefficiens, Bradyrhizobium elkanii, Bradyrhizobium liaoningense and Bradyrhizobium yuanmingense species. In the pot experiment, several isolates showed better activity than B. diazoefficiens USDA110, and the Bho-P2-B2-S1-51 isolate of B. liaoningense showed significantly higher acetylene reduction activity in both Glycine max cv. Enrei and Binasoybean-3 varieties and biomass production increased by 9% in the Binasoybean-3 variety. Tha-P2-B1-S1-68 isolate of B. diazoefficiens significantly enhanced shoot length and induced 10% biomass production in Binasoybean-3. These isolates grew at 1-4% NaCl concentration and pH 4.5-10 and survived at 45 °C, making the isolates potential candidates for eco-friendly soybean biofertilizers in salty and tropical regions.

Molecular Characterization of Native Bacillus thuringiensis Strains from Root Nodules with Toxicity Against the Fall Armyworm (FAW, Spodoptera frugiperda) and Brinjal Ash Weevil (Myllocerus subfasciatus)

The fall armyworm is an exotic pest which destroys a wide variety of crops Querywhereas the brinjal ash weevil is a serious pest of eggplant and other solanaceous vegetables. The goal of this research is to find a sustainable and ecologically friendly bio-control agent for managing FAW and brinjal ash weevils. Twelve natural Bacillus thuringiensis strains were isolated from cowpea root nodules, and the Gram-positive cells with characteristic Bt crystal structures were discovered using phase contrast and scanning electron microscopy. There were bipyramidal, cuboidal, rhombus, and spherical crystals. The Bt cry gene content was characterized by PCR analysis, which revealed the presence of cry1, cry1I, cry3, cry7, cry7,8, cry14, cry26, and cry55 genes. The identity of Bt was confirmed by cloning and sequencing the cry genes. In the nucleotide sequences, no pseudo genes or indels were found in cry sequences. SDS-PAGE examination indicated the presence of bands ranging in size from 13 to 130 kDa, with 50-60 kDa being the most common. When compared to the control, the new native Bt strains were lethal, with pathogenicity ranging from 93 to 100% against S. frugiperda larvae and M. subfasciatus adults. The studies revealed that the native strains with conserved regions of 16S rRNA genes were compared to NCBI database sequences and classified as native Bt strains with 99-100% similarity to known Bt strains. In conclusion, native Bt strains from cowpea root nodules were shown to have bio-insecticidal activity against fall armyworm larvae and brinjal ash weevil adults.

Toxic Effects of Industrial Flocculants Addition on Bioconversion of Black Soldier Fly Larvae (Hermetia illucens L.)

Simple Summary

The black soldier fly (BSF) is a saprophagous insect that has been applied to organic waste management while providing high-quality insect protein. Flocculants are widely present in organic wastes that could be treated by black soldier fly larvae (BSFL), such as food wastes, municipal sludge, and cyanobacteria sludge. This study investigated the effect of flocculants on bioconversion of BSFL. The results showed that the addition of flocculant affected the bioconversion efficiency and nutritional composition of BSFL. The relative abundance of bacterial genera related to lipid metabolism decreased with increasing flocculant concentrations while disease-related taxa increased in relative abundance. This study could serve as a reference for related research and applications in the future.

Abstract

Black soldier fly is a saprophagous insect that has been widely reported in recent years due to its excellent performance in bioremediation. Due to the widespread presence of flocculants in the organic waste treated by black soldier fly larvae, this study aimed to evaluate the potential impacts and risks of flocculant addition (a combination of poly aluminum chloride and polyacrylamide with the ratio of 50:1). Results showed that the growth and weight of BSFL in the high-exposure groups (≥200 mg/L) were inhibited. The bioaccumulation of aluminum (Al) in larvae was estimated, and the proportions of different Al forms in the frass from high to low were the residual state (41.38% to 67.92%), water-soluble state (16.88% to 37.03%), acid-soluble state (8.45% to 18.72%), and alkali-soluble state (3.38% to 5.14%). The relative abundance of bacterial genera related to lipid metabolism decreased with increasing flocculant concentrations while disease-related taxa increased in relative abundance. The results serve as a reference for subsequent research and application of the treatment of flocculant-contaminated waste by BSFL.

Metagenomic study of the communities of bacterial endophytes in the desert plant Senna Italica and their role in abiotic stress resistance in the plant

Abstract Plant leaves and roots are home to diverse communities of bacteria, which play a significant role in plant health and growth. Although one of the most unfriendly environments for plant growth is deserts, desert plants can influence their surrounding microbial population and choose favorable bacteria that encourage their growth under these severe circumstances. Senna italica is known for its excellent medicinal values as a traditional medical plant, but little is known about its associated endophytic bacterial community under extreme conditions. In the present study, metagenomic sequencing of 16S rRNA was used to report the diversity of endophytic bacterial communities associated with the leaves and roots of the desert medicinal plant Senna italica that was collected from the Asfan region in northeast Jeddah, Saudi Arabia. Analyses of the 16S rRNA sequences at the taxonomic phylum level revealed that bacterial communities in the roots and leaves samples belonged to five phyla, including Cyanobacteria, Proteobacteria, Actinobacteria, Firmicutes, and unclassified phyla. Results indicated that the most common phyla were Cyanobacteria/Chloroplast and Actinobacteria. Analysis of the 16S rRNA sequences at the taxonomic phylum level revealed that bacterial communities in the roots and leaves samples belonged to twelve genera at the taxonomic genus level. The most abundant ones were highlighted for further analysis, including Okibacterium and Streptomyces found in Actinobacteria, which were the dominant genus in roots samples. However, Streptophyta found in Cyanobacteria/Chloroplast was the dominant genus in leaf samples. Metagenomic analysis of medicinal plants leads to identifying novel organisms or genes that may have a role in abiotic stress resistance in the plant. The study of endophytic microbiome taxonomic, phylogenetic, and functional diversity will better know innovative candidates that may be selected as biological agents to enhance agricultural and industrial processes, especially for crop desert agricultural improvement.

Designing efficient genetic code expansion in Bacillus subtilis to gain biological insights

Bacillus subtilis is a model gram-positive bacterium, commonly used to explore questions across bacterial cell biology and for industrial uses. To enable greater understanding and control of proteins in B. subtilis, here we report broad and efficient genetic code expansion in B. subtilis by incorporating 20 distinct non-standard amino acids within proteins using 3 different families of genetic code expansion systems and two choices of codons. We use these systems to achieve click-labelling, photo-crosslinking, and translational titration. These tools allow us to demonstrate differences between E. coli and B. subtilis stop codon suppression, validate a predicted protein-protein binding interface, and begin to interrogate properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo. We expect that the establishment of this simple and easily accessible chemical biology system in B. subtilis will help uncover an abundance of biological insights and aid genetic code expansion in other organisms.

Isolation and characterization of two highly insecticidal, endophytic strains of Bacillus thuringiensis

Recent discovery of endophytic strains of Bacillus thuringiensis significantly improves the knowledge on its ecology. It also may be a new source for the isolation of insecticidal strains. This report shows the characterization of two endophytic, highly insecticidal strains of B. thuringiensis. Strains LBIT-1250L and LBIT-1251P were isolated from lavender and Poinsettia sap, respectively. Their parasporal crystals were very similar in morphology to those shown by serotypes israelensis and kurstaki, respectively. Bioassays on Aedes aegypti fourth instar larvae and on Manduca sexta first instar larvae, respectively, showed significantly higher levels of toxicity than those of their standard counterparts, IPS-82 (israelensis) and HD-1 (kurstaki) strains, respectively. Characterization of both strains included the sequencing of flagellin (hag) gene, plasmid and Bc Rep-PCR patterns and crystal protein content. All four characterization features indicated that LBIT1250L is highly related to the IPS-82 standard (serotype H-14: israelensis); while the LBIT-1251P was highly related to the HD-1 standard (serotype H-3a3b3c kurstaki). These results indicate that endophytic strains of B. thuringiensis may be a new source of potential insecticidal strains and opens more in-depth studies about the role of this bacterium in such a specialized habitat.

Soybean Root Nodule and Rhizosphere Microbiome: Distribution of Rhizobial and Nonrhizobial Endophytes

Soybean root nodules are known to contain a high diversity of both rhizobial endophytes and nonrhizobial endophytes (NREs). Nevertheless, the variation of these bacteria among different root nodules within single plants has not been reported. So far, it is unclear whether the selection of NREs among different root nodules within single plants is a random process or is strictly controlled by the host plant to favor a few specific NREs based on their beneficial influence on plant growth. As well, it is also unknown if the relative frequency of NREs within different root nodules is consistent or if it varies based on the location or size of a root nodule. We assessed the microbiomes of 193 individual soybean root nodules from nine plants using high-throughput DNA sequencing. Bradyrhizobium japonicum strains occurred in high abundance in all root nodules despite the presence of other soybean-compatible rhizobia, such as Ensifer, Mesorhizobium, and other species of Bradyrhizobium in soil. Nitrobacter and Tardiphaga were the two nonrhizobial genera that were uniformly detected within almost all root nodules, though they were in low abundance. DNA sequences related to other NREs that have frequently been reported, such as Bacillus, Pseudomonas, Flavobacterium, and Variovorax species, were detected in a few nodules. Unlike for Bradyrhizobium, the low abundance and inconsistent occurrence of previously reported NREs among different root nodules within single plants suggest that these microbes are not preferentially selected as endophytes by host plants and most likely play a limited part in plant growth as endophytes.IMPORTANCE Soybean (Glycine max L.) is a valuable food crop that also contributes significantly to soil nitrogen by developing a symbiotic association with nitrogen-fixing rhizobia. Bacterial endophytes (both rhizobial and nonrhizobial) are considered critical for the growth and resilience of the legume host. In the past, several studies have suggested that the selection of bacterial endophytes within root nodules can be influenced by factors such as soil pH, nutrient availability, host plant genotype, and bacterial diversity in soil. However, the influence of size or location of root nodules on the selection of bacterial endophytes within soybean roots is unknown. It is also unclear whether the selection of nonrhizobial endophytes within different root nodules of a single plant is a random process or is strictly regulated by the host. This information can be useful in identifying potential bacterial species for developing bioinoculants that can enhance plant growth and soil nitrogen.

Thuricin17 Production and Proteome Differences in Bacillus thuringiensis NEB17 Cell-Free Supernatant Under NaCl Stress

Bacillus thuringiensis strain NEB17, produces a bacteriocin, thuricin17 (Th17) and is known to promote the growth more effectively under salt stress conditions. In this study, bacterial salt stress tolerance screening and the possible changes in its secretome under two levels of NaCl stress was evaluated. The salt tolerance screening suggested that the bacterium is able to grow and survive in up to 900 mM NaCl. Thuricin17 production at salt levels from 100 to 500 mM NaCl was quantified using High Performance Liquid Chromatography (HPLC). Salt stress adversely affected the production of Th17 at levels as low as 100 mM NaCl; and the production stopped at 500 mM NaCl, despite the bacterium thriving at these salt levels. Hence, a comparative proteomic study was conducted on the supernatant of the bacterium after 42 h of growth, when Th17 production peaked in the control culture, as determined by Liquid Chromatography - Tandem Mass Spectrometry (LC-MS/MS). Optimal (salt free) bacterial culture served as a control and 200 and 500 mM NaCl as stress conditions. As salt levels increased, the major enzyme classes, transferases, hydrolases, lyases, and ligases showed increased abundance as compared to the control, mostly related to molecular function mechanisms. Some of the notable up-regulated proteins in 500 mM NaCl stress conditions included an S-layer protein, chitin binding domain 3 protein, enterotoxins, phosphopentomutase, glucose 6-phosphate isomerase and bacterial translation initiation factor; while notable down-regulated proteins included hemolytic enterotoxin, phospholipase, sphingomyelinase C, cold shock DNA-binding protein family and alcohol dehydrogenase. These results indicate that, as the salt stress levels increase, the bacterium probably shuts down the production of Th17 and regulates its molecular functional mechanisms to overcome stress. This study indicates that end users have the option of using Th17 as a biostimulant or the live bacterial inoculum depending on the soil salt characteristics, for crop production. The mass spectrometry proteomics data have been deposited to Mass Spectrometry Interactive Virtual Environment (MassIVE) with the dataset identifier PXD024069, and doi: 10.25345/C5RB8T.

Rhizobacteria From Root Nodules of an Indigenous Legume Enhance Salinity Stress Tolerance in Soybean

Soybean is the most widely grown legume worldwide, but it is a glycophyte and salinity stress can decrease its yield potential up to 50%. Plant growth promoting rhizobacteria (PGPR) are known to enhance growth and induce tolerance to abiotic stresses including salinity. The aim of this study was to isolate such PGPR from the root nodules of Amphicarpaea bracteata, a North American relative of soybean. Isolated strains were identified, and 15 strains were screened for potential utilization as PGPR of soybean through a series of greenhouse trials. Four isolates that greatly improved shoot and root growth were further selected and screened under a range of salt concentrations. Two of the most promising strains, Rhizobium sp. SL42 and Hydrogenophaga sp. SL48 were ascertained to exert the greatest beneficial effects on soybean growth and salinity tolerance. They were co-inoculated with Bradyrhizobium japonicum 532C (Bj) and the plants were grown up to the harvest stage. The treatment of Bj+SL42 resulted in higher shoot biomass than the control, 18% at the vegetative stage, 16% at flowering, 7.5% at pod-filling, and 4.6% at harvest and seed weight was increased by 4.3% under salt stress (ECe = 7.4 ds/m). Grain yield was raised under optimal conditions by 7.4 and 8.1% with treatments Bj+SL48 and Bj+SL42+SL48, respectively. Nitrogen assimilation and shoot K+/Na+ ratio were also higher in the co-inoculation treatments. This study suggested that inoculation with bacteria from an indigenous legume can induce stress tolerance, improve growth and yield to support sustainability, and encourage ecological adaptability of soybean.

Unlocking the potential of plant growth-promoting rhizobacteria on soil health and the sustainability of agricultural systems

The concept of soil health refers to specific soil properties and the ability to support and sustain crop growth and productivity, while maintaining long-term environmental quality. The key components of healthy soil are high populations of organisms that promote plant growth, such as the plant growth promoting rhizobacteria (PGPR). PGPR plays multiple beneficial and ecological roles in the rhizosphere soil. Among the roles of PGPR in agroecosystems are the nutrient cycling and uptake, inhibition of potential phytopathogens growth, stimulation of plant innate immunity, and direct enhancement of plant growth by producing phytohormones or other metabolites. Other important roles of PGPR are their environmental cleanup capacities (soil bioremediation). In this work, we review recent literature concerning the diverse mechanisms of PGPR in maintaining healthy conditions of agricultural soils, thus reducing (or eliminating) the toxic agrochemicals dependence. In conclusion, this review provides comprehensive knowledge on the current PGPR basic mechanisms and applications as biocontrol agents, plant growth stimulators and soil rhizoremediators, with the final goal of having more agroecological practices for sustainable agriculture.

Illumina sequencing of 16S rRNA tag shows disparity in rhizobial and non-rhizobial diversity associated with root nodules of mung bean (Vigna radiata L.) growing in different habitats in Pakistan

In Rhizobium-legume symbiosis, the nodule is the most frequently studied compartment, where the endophytic/symbiotic microbiota demands critical investigation for development of specific inocula. We identified the bacterial diversity within root nodules of mung bean from different growing areas of Pakistan using Illumina sequencing of 16S rRNA gene. We observed specific OTUs related to specific site where Bradyrhizobium was found to be the dominant genus comprising of 82-94% of total rhizobia in nodules with very minor fraction of sequences from other rhizobia at three sites. In contrast, Ensifer (Sinorhizobium) was single dominant genus comprising 99.9% of total rhizobial sequences at site four. Among non-rhizobial sequences, the genus Acinetobacter was abundant (7-18% of total sequences), particularly in Bradyrhizobium-dominated nodule samples. Rhizobia and non-rhizobial PGPR isolated from nodule samples include Ensifer, Bradyrhizobium, Acinetobacter, Microbacterium and Pseudomonas strains. Co-inoculation of multi-trait PGPR Acinetobacter sp. VrB1 with either of the two rhizobia in field exhibited more positive effect on nodulation and plant growth than single-strain inoculation which favors the use of Acinetobacter as an essential component for development of mung bean inoculum. Furthermore, site-specific dominance of rhizobia and non-rhizobia revealed in this study may contribute towards decision making for development and application of specific inocula in different habitats.

Endophytic fungal diversity isolated from different agro-ecosystem of Enset (Ensete ventericosum) in Gedeo zone, SNNPRS, Ethiopia

BACKGROUND

Endophytic Fungi (EF) are an underexplored group of microorganisms as only a few plants have been studied with regards to their community. Diversity of EF found in young and old leaves of Enset plant has not been well studied. We analyzed and compared the colonization frequency (CF), richness diversity and fungal communities of the EF inhabiting the young and old leaves of Enset plant from Southern region of Ethiopia. Standard methods were used for isolation and identification of endophytic species from Enset leaves.

RESULTS

The study investigates the difference in quantity, in variety, in consistent pattern of community of EF along with different Enset varieties. A total number of 18 samples were analyzed and 108 morphospecies of EF were isolated and distributed among 17 genera. Aspergillus sp. and Penicillium sp. were the most common fungi reported in Enset plant. The largest numbers of EF isolates were observed in Maziya and Arkiya variety and the diversity index and species richness were found to be significant in Enset plant among these varieties. A high number of EF was isolated from old leaves in comparison to young leaves among all the varieties studied. Composition of EF at different altitudinal location also varied within each sites.

CONCLUSION

Isolation, characterization and distribution of the EF from Enset plant is the first approach that has been conducted in the developing country like Ethiopia. The findings of the present study show that the Enset agro-forestry system produces potential variability in the colonization, richness diversity and composition of EF in Enset plants. The assemblage of EF in healthy tissues of Enset plants may indicate that some of the fungi are possible latent pathogens and some may become saprophytic.

Phylogenetic diversity of aerobic spore-forming Bacillalles isolated from Brazilian soils

The phylum Firmicutes comprises seven classes where most species are either aerobic or anaerobic endospore former. Inside Firmicutes, species allocated in the genus Bacillus and related genera are collectively named aerobic endospore-forming bacteria (AEFB), and the soil is their major reservoir. AEFB have great importance in health, agriculture, and biotechnology although the more studied species are Bacillus subtilis and the human pathogens Bacillus cereus and Bacillus anthracis. AEFB have great importance in health, agriculture, and biotechnology; although the knowledge about these organisms is based on few species, notably, Bacillus subtilis, Bacillus cereus, and Bacillus anthracis. In this work, we generated partial 16S rRNA gene sequences of both strands of 192 AEFB strains isolated from soils of Distrito Federal, Brazil (SDF strains). The resulting consensus sequences were used to obtain taxonomic assignment and establish the phylogenetic relationships among these strains. Through this approach, we could observe that classified SDF strains were distributed among genera Bacillus (169 strains; 88.02%), Paenibacillus (11; 5.73%), Lysinibacillus (6; 3.13%), Brevibacillus (4; 2.08%), Terribacillus (1; 0.52%), and Rummeliibacillus (1; 0.52%). Phylogenetic trees revealed these 192 SDF strains can be segregated into eight groups spanning families Bacillaceae and Paenibacillaceae belonging to the order Bacillales. To expand the knowledge about the diversity of these SDF strains, further studies regarding characterization with different methodologies are underway.

Unprecedented bacterial community richness in soybean nodules vary with cultivar and water status

BACKGROUND

Soybean (Glycine max) and other legumes are key crops grown around the world, providing protein and nutrients to a growing population, in a way that is more sustainable than most other cropping systems. Diazotrophs inhabiting root nodules provide soybean with nitrogen required for growth. Despite the knowledge of culturable Bradyrhizobium spp. and how they can differ across cultivars, less is known about the overall bacterial community (bacteriome) diversity within nodules, in situ. This variability could have large functional ramifications for the long-standing scientific dogma related to the plant-bacteriome interaction. Water availability also impacts soybean, in part, as a result of water-deficit sensitive nodule diazotrophs. There is a dearth of information on the effects of cultivar and water status on in situ rhizobia and non-rhizobia populations of nodule microbiomes. Therefore, soybean nodule microbiomes, using 16S rRNA and nifH genes, were sampled from nine cultivars treated with different field water regimes. It was hypothesized that the nodule bacteriome, composition, and function among rhizobia and non-rhizobia would differ in response to cultivar and soil water status.

RESULTS

16S rRNA and nifH showed dominance by Bradyrhizobiaceae, but a large diversity was observed across phylogenetic groups with < 1% and up to 45% relative abundance in cultivars. Other groups primarily included Pseudomonadaceae and Enterobacteriaceae. Thus, nodule bacteriomes were not only dominated by rhizobia, but also described by high variability and partly dependent on cultivar and water status. Consequently, the function of the nodule bacteriomes differed, especially due to cultivar. Amino acid profiling within nodules, for example, described functional changes due to both cultivar and water status.

CONCLUSIONS

Overall, these results reveal previously undescribed richness and functional changes in Bradyrhizobiaceae and non-rhizobia within the soybean nodule microbiome. Though the exact role of these atypical bacteria and relative variations in Bradyrhizobium spp. is not clear, there is potential for exploitation of these novel findings of microbiome diversity and function. This diversity needs consideration as part of bacterial-inclusive breeding of soybean to improve traits, such as yield and seed quality, and environmental resilience.

Lipopeptide mediated biocontrol activity of endophytic Bacillus subtilis against fungal phytopathogens

Background

The use of chemical fungicides against fungal pathogens adversely affects soil and plant health thereby resulting in overall environmental hazards. Therefore, biological source for obtaining antifungal agents is considered as an environment-friendly alternative for controlling fungal pathogens.

Results

In this study, seven endophytic bacteria were isolated from sugarcane leaves and screened for its antifungal activity against 10 fungal isolates belonging to the genera Alternaria, Cochliobolus, Curvularia, Fusarium, Neodeightonia, Phomopsis and Saccharicola isolated from diseased leaves of sugarcane. Among the seven bacterial isolates, SCB-1 showed potent antagonistic activity against the tested fungi. Based on the phenotypic data, Fatty Acid Methyl Esters (FAME) and 16S rRNA gene sequence analysis, the isolate SCB-1 was identified as Bacillus subtilis. The bacterial isolate was screened negative for chitinase production; however, chloroform and methanol extracts of the bacterial culture caused significant inhibition in the growth of the fungal isolates on semisolid media. Volatile component assay showed highest inhibitory activity against Saccharicola bicolor (SC1.4). A PCR based study detected the presence of the genes involved in biosynthesis of surfactin, bacillaene, difficidin, macrolactins and fengycin. Mass spectrometric analysis of the bacterial extract detected the presence of antifungal lipopeptide surfactin, but other metabolites were not detected. The biocontrol activity of the bacterial isolate was established when bacterial pretreated mung bean seeds were able to resist Fusarium infection, however, the untreated seeds failed to germinate.

Conclusion

The antifungal potential of isolate Bacillus subtilis SCB-1 was established against taxonomically diverse fungal pathogens including the genera Saccharicola, Cochliobolus, Alternaria and Fusarium. The potent antifungal compound surfactin as well as volatiles produced by the bacterial isolate could be responsible for its bio-control activity against fungal infections.

Electronic supplementary material

The online version of this article (10.1186/s12866-019-1440-8) contains supplementary material, which is available to authorized users.

Isolation and characterization of a novel bacterium Pseudomonas aeruginosa for biofertilizer production from kitchen waste oil

Kitchen waste oil is composed of long chain triglycerides (LCTs) that has high energy density. However, it is hard to be degraded by microbes, thereby leading to increasing levels of environmental pollution due to landfill disposition. In this study, we isolated and characterized a novel bacterium Pseudomonas aeruginosa PA-3 that could convert kitchen waste oil into biofertilizer. PA-3 could survive on trilaurin or kitchen waste oil as the sole carbon source, and 10 g L-1 trilaurin or kitchen waste oil was completely consumed within 7 days. Interestingly, the degradation products of kitchen waste oil can be used as biofertilizer in promoting cabbage growth. The plant height, leaf area and stem diameter of cabbage plants were all increased with the addition of kitchen waste oil cultivation products into the soil. Kitchen waste oil degradation products were analyzed by gas chromatography mass spectrometry (GC-MS), and short chain alcohols or fatty acids were observed to be the main products. To unravel the mechanism underlying the accelerated cabbage growth, bacterial diversity of the soil was investigated after using this biofertilizer. Results showed that agricultural probiotics accumulated with the addition of kitchen waste oil cultivation products. Finally, the whole genome of PA-3 was sequenced and analyzed, which showed the existence of a complete β-oxidation pathway in the genome of PA-3. To our knowledge, this is the first study on kitchen waste oil degradation and re-utilization by bacteria, which provides a new method for waste source re-utilization.

The response of soybean to nod factors and a bacteriocin

Microbe-to-plant signals can enhance the growth of a wide range of crops. The responses by soybean (Glycine max var. 91M01) to 2 signal molecules were investigated: Bradyrhizobium japonicum 532C lipo-chitooligosaccharide (Nod Bj V [C:18, MeFuc]) (LCO); and Bacillus thuringiensis strain NEB17 bacteriocin thuricin 17 (Th17). The objective was to assess and quantify the response by soybean, in terms of factors that contribute to yield, to the experimental signal molecules in germination experiments and field experiments. Soybean germination was stimulated by the experimental concentrations of Th17 under controlled 15°C and 22°C conditions, and 10-6 M LCO under 15°C. There were negative relationships between Th17 concentration and both the number of trifoliate leaves and the dry weight of nodules: lower concentrations resulted in plants with more leaves and nodules while higher concentrations resulted in plants with fewer leaves and nodules. The 10-8 M LCO treatment had a significant effect on the dry weight of nodules at the flowering stage of plant development (F4,21 = 6.06, p = 0.0019). Considering the harvest stage data from both field trials of 2011, the lower experimental concentrations of Th17 resulted in taller plants. The study of Th17 has the potential to expand our understanding of this relatively recent and unexpected finding; and to understand how best to apply this finding, to allow increased production of soybean. Collectively, these results indicate that Th17 has potential in this regard.

No adverse effects of transgenic maize on population dynamics of endophytic Bacillus subtilis strain B916-gfp

Endophytic bacterial communities play a key role in promoting plant growth and combating plant diseases. However, little is known about their population dynamics in plant tissues and bulk soil, especially in transgenic crops. This study investigated the colonization of transgenic maize harboring the Bacillus thuringiensis (Bt) cry1Ah gene by Bacillus subtilis strain B916‐gfp present in plant tissues and soil. Bt and nontransgenic maize were inoculated with B916‐gfp by seed soaking, or root irrigation under both laboratory greenhouse and field conditions. During the growing season, B916‐gfp colonized transgenic as well as nontransgenic plants by both inoculation methods. No differences were observed in B916‐gfp population size between transgenic and nontransgenic plants, except at one or two time points in the roots and stems that did not persist over the examination period. Furthermore, planting transgenic maize did not affect the number of B916‐gfp in bulk soil in either laboratory or field trials. These results indicate that transgenic modification of maize with the cry1Ah gene has no influence on colonization by the endophytic bacteria B916‐gfp present in the plant and in bulk soil.

A Proteomic Approach to Lipo-Chitooligosaccharide and Thuricin 17 Effects on Soybean GerminationUnstressed and Salt Stress

Salt stress is an important abiotic stressor affecting crop growth and productivity. Of the 20 percent of the terrestrial earth's surface available as agricultural land, 50 percent is estimated by the United Nations Environment Program to be salinized to the level that crops growing on it will be salt-stressed. Increased soil salinity has profound effects on seed germination and germinating seedlings as they are frequently confronted with much higher salinities than vigorously growing plants, because germination usually occurs in surface soils, the site of greatest soluble salt accumulation. The growth of soybean exposed to 40 mM NaCl is negatively affected, while an exposure to 80 mM NaCl is often lethal. When treated with the bacterial signal compounds lipo-chitooligosaccharide (LCO) and thuricin 17 (Th17), soybean seeds (variety Absolute RR) responded positively at salt stress of up to 150 mM NaCl. Shotgun proteomics of unstressed and 100 mM NaCl stressed seeds (48 h) in combination with the LCO and Th17 revealed many known, predicted, hypothetical and unknown proteins. In all, carbon, nitrogen and energy metabolic pathways were affected under both unstressed and salt stressed conditions when treated with signals. PEP carboxylase, Rubisco oxygenase large subunit, pyruvate kinase, and isocitrate lyase were some of the noteworthy proteins enhanced by the signals, along with antioxidant glutathione-S-transferase and other stress related proteins. These findings suggest that the germinating seeds alter their proteome based on bacterial signals and on stress, the specificity of this response plays a crucial role in organ maturation and transition from one stage to another in the plants' life cycle; understanding this response is of fundamental importance in agriculture and, as a result, global food security. The mass spectrometry proteomics data have been deposited to the ProteomeXchange with identifier PXD004106.

Endophytic Bacterium Pseudomonas fluorescens RG11 May Transform Tryptophan to Melatonin and Promote Endogenous Melatonin Levels in the Roots of Four Grape Cultivars

Endophytes have been verified to synthesize melatonin in vitro and promote abiotic stress-induced production of endogenous melatonin in grape (Vitis vinifera L.) roots. This study aimed to further characterize the biotransformation of tryptophan to melatonin in the endophytic bacterium Pseudomonas fluorescens RG11 and to investigate its capacity for enhancing endogenous melatonin levels in the roots of different grape cultivars. Using ultra performance liquid chromatography-tandem mass spectrometry combined with 15N double-labeled L-tryptophan as the precursor for melatonin, we detected isotope-labeled 5-hydroxytryptophan, serotonin, N-acetylserotonin, and melatonin, but tryptamine was not detected during the in vitro incubation of P. fluorescens RG11. Furthermore, the production capacity of these four compounds peaked during the exponential growth phase. RG11 colonization increased the endogenous levels of 5-hydroxytryptophan, N-acetylserotonin, and melatonin, but reduced those of tryptamine and serotonin, in the roots of the Red Globe grape cultivar under salt stress conditions. Quantitative real-time PCR revealed that RG11 reduced the transcription of grapevine tryptophan decarboxylase and serotonin N-acetyltransferase genes when compared to the un-inoculated control. These results correlated with decreased reactive oxygen species bursts and cell damage, which were alleviated by RG11 colonization under salt stress conditions. Additionally, RG11 promoted plant growth and enhanced the levels of endogenous melatonin in different grape cultivars. Intraspecific variation in the levels of melatonin precursors was found among four grape cultivars, and the associated root crude extracts appeared to significantly induce RG11 melatonin biosynthesis in vitro. Overall, this study provides useful information that enhances the existing knowledge of a potential melatonin synthesis pathway in rhizobacteria, and it reveals plant-rhizobacterium interactions that affect melatonin biosynthesis in plants subjected to abiotic stress conditions.

In vitro antagonistic activity, plant growth promoting traits and phylogenetic affiliation of rhizobacteria associated with wild plants grown in arid soil

The role of plant growth-promoting rhizobacteria (PGPR) in adaptation of plants in extreme environments is not yet completely understood. For this study native bacteria were isolated from rhizospeheric arid soils and evaluated for both growth-promoting abilities and antagonistic potential against phytopathogenic fungi and nematodes. The phylogentic affiliation of these representative isolates was also characterized. Rhizobacteria associated with 11 wild plant species from the arid soil of Almadinah Almunawarah, Kingdom of Saudi Arabia (KSA) were investigated. From a total of 531 isolates, only 66 bacterial isolates were selected based on their ability to inhibit Fusarium oxysporum, and Sclerotinia sclerotiorum. The selected isolates were screened in vitro for activities related to plant nutrition and plant growth regulation as well as for antifungal and nematicidal traits. Isolated bacteria were found to exhibit capabilities in fix atmospheric nitrogen, produce ammonia, indoleacetic acid (IAA), siderophores, solubilize phosphate and zinc, and showed an antagonistic potential against some phytopathogenic fungi and one nematode species (Meloidogyne incognita) to various extent. Isolates were ranked by their potential ability to function as PGPR. The 66 isolates were genotyped using amplified rDNA restriction analysis (ARDRA) and 16S rRNA gene sequence analysis. The taxonomic composition of the representative genotypes from both rhizosphere and rhizoplane comprised Bacillus, Enterobacter and Pseudomonas. Out of the 10 genotypes, three strains designated as PHP03, CCP05, and TAP02 might be regarded as novel strains based on their low similarity percentages and high bootstrap values. The present study clearly identified specific traits in the isolated rhizobacteria, which make them good candidates as PGPR and might contribute to plant adaption to arid environments. Application of such results in agricultural fields may improve and enhance plant growth in arid soils.

Control efficacy of an endophytic Bacillus amyloliquefaciens strain BZ6-1 against peanut bacterial Wilt, Ralstonia solanacearum

We aimed to isolate and identify endophytic bacteria that might have efficacy against peanut bacterial wilt (BW) caused by Ralstonia solanacearum. Thirty-seven endophytic strains were isolated from healthy peanut plants in R. solanacearum-infested fields and eight showed antagonistic effects against R. solanacearum. Strain BZ6-1 with the highest antimicrobial activity was identified as Bacillus amyloliquefaciens based on morphology, biochemistry, and 16S rRNA analysis. Culture conditions of BZ6-1 were optimized using orthogonal test method and inhibitory zone diameter in dual culture plate assay reached 34.2 mm. Furthermore, main antimicrobial substances of surfactin and fengycin A homologues produced by BZ6-1 were analyzed by high performance liquid chromatography electrospray ionization tandem mass spectrometry. Finally, pot experiments were adopted to test the control efficiency of BZ6-1 against peanut BW. Disease incidence decreased significantly from 84.5% in the control to 12.1% with addition of 15 mL (10(8) cfu mL(-1)) culture broth for each seedling, suggesting the feasibility of strain BZ6-1 in the biological control of peanut plants BW.

Diversity of sporadic symbionts and nonsymbiotic endophytic bacteria isolated from nodules of woody, shrub, and food legumes in Ethiopia

Fifty-five bacterial isolates were obtained from surface-sterilized nodules of woody and shrub legumes growing in Ethiopia: Crotalaria spp., Indigofera spp., and Erythrina brucei, and the food legumes soybean and common bean. Based on partial 16S rRNA gene sequence analysis, the majority of the isolates were identified as Gram-negative bacteria belonging to the genera Achromobacter, Agrobacterium, Burkholderia, Cronobacter, Enterobacter, Mesorhizobium, Novosphingobium, Pantoea, Pseudomonas, Rahnella, Rhizobium, Serratia, and Variovorax. Seven isolates were Gram-positive bacteria belonging to the genera Bacillus, Paenibacillus, Planomicrobium, and Rhodococcus. Amplified fragment length polymorphism (AFLP) fingerprinting showed that each strain was genetically distinct. According to phylogenetic analysis of recA, glnII, rpoB, and 16S rRNA gene sequences, Rhizobium, Mesorhizobium, and Agrobacterium were further classified into six different genospecies: Agrobacterium spp., Agrobacterium radiobacter, Rhizobium sp., Rhizobium phaseoli, Mesorhizobium sp., and putative new Rhizobium species. The strains from R. phaseoli, Rhizobium sp. IAR30, and Mesorhizobium sp. ERR6 induced nodules on their host plants. The other strains did not form nodules on their original host. Nine endophytic bacterial strains representing seven genera, Agrobacterium, Burkholderia, Paenibacillus, Pantoea, Pseudomonas, Rhizobium, and Serratia, were found to colonize nodules of Crotalaria incana and common bean on co-inoculation with symbiotic rhizobia. Four endophytic Rhizobium and two Agrobacterium strains had identical nifH gene sequences with symbiotic Rhizobium strains, suggesting horizontal gene transfer. Most symbiotic and nonsymbiotic endophytic bacteria showed plant growth-promoting properties in vitro, which indicate their potential role in the promotion of plant growth when colonizing plant roots and the rhizosphere.

Plant growth promotion in cereal and leguminous agricultural important plants: from microorganism capacities to crop production

Plant growth-promoting rhizobacteria (PGPR) are free-living bacteria which actively colonize plant roots, exerting beneficial effects on plant development. The PGPR may (i) promote the plant growth either by using their own metabolism (solubilizing phosphates, producing hormones or fixing nitrogen) or directly affecting the plant metabolism (increasing the uptake of water and minerals), enhancing root development, increasing the enzymatic activity of the plant or "helping" other beneficial microorganisms to enhance their action on the plants; (ii) or may promote the plant growth by suppressing plant pathogens. These abilities are of great agriculture importance in terms of improving soil fertility and crop yield, thus reducing the negative impact of chemical fertilizers on the environment. The progress in the last decade in using PGPR in a variety of plants (maize, rice, wheat, soybean and bean) along with their mechanism of action are summarized and discussed here.

Taxonomic and symbiotic diversity of bacteria isolated from nodules of Acacia tortilis subsp. raddiana in arid soils of Tunisia

A collection of rhizobia isolated from Acacia tortilis subsp. raddiana nodules from various arid soils in Tunisia was analyzed for their diversity at both taxonomic and symbiotic levels. The isolates were found to be phenotypically diverse. The majority of the isolates tolerated 3% NaCl and grew at 40 °C. Genetic characterization emphasized that most of the strains (42/50) belong to the genus Ensifer, particularly the species Ensifer meliloti, Ensifer garamanticus, and Ensifer numidicus. Symbiotic properties of isolates showed diversity in their capacity to nodulate their host plant and to fix atmospheric nitrogen. The most effective isolates were closely related to E. garamanticus. Nodulation tests showed that 3 strains belonging to Mesorhizobium genus failed to renodulate their host plant, which is surprising for symbiotic rhizobia. Furthermore, our results support the presence of non-nodulating endophytic bacteria belonging to the Acinetobacter genus in legume nodules.

Biogeography of symbiotic and other endophytic bacteria isolated from medicinal Glycyrrhiza species in China

A total of 159 endophytic bacteria were isolated from surface-sterilized root nodules of wild perennial Glycyrrhiza legumes growing on 40 sites in central and northwestern China. Amplified fragment length polymorphism (AFLP) genomic fingerprinting and sequencing of partial 16S rRNA genes revealed that the collection mainly consisted of Mesorhizobium, Rhizobium, Sinorhizobium, Agrobacterium and Paenibacillus species. Based on symbiotic properties with the legume hosts Glycyrrhiza uralensis and Glycyrrhiza glabra, we divided the nodulating species into true and sporadic symbionts. Five distinct Mesorhizobium groups represented true symbionts of the host plants, the majority of strains inducing N2-fixing nodules. Sporadic symbionts consisted of either species with infrequent occurrence (Rhizobium galegae, Rhizobium leguminosarum) or species with weak (Sinorhizobium meliloti, Rhizobium gallicum) or no N2 fixation ability (Rhizobium giardinii, Rhizobium cellulosilyticum, Phyllobacterium sp.). Multivariate analyses revealed that the host plant species and geographic location explained only a small part (14.4%) of the total variation in bacterial AFLP patterns, with the host plant explaining slightly more (9.9%) than geography (6.9%). However, strains isolated from G. glabra were clearly separated from those from G. uralensis, and strains obtained from central China were well separated from those originating from Xinjiang in the northwest, indicating both host preference and regional endemism.

Isolation and Characterization of Nodule-Associated Exiguobacterium sp. from the Root Nodules of Fenugreek (Trigonella foenum-graecum) and Their Possible Role in Plant Growth Promotion

One of the ways to increase the competitive survivability of rhizobial biofertilizers and thus achieve better plant growth under such conditions is by modifying the rhizospheric environment or community by addition of nonrhizobial nodule-associated bacteria (NAB) that cause better nodulation and plant growth when coinoculated with rhizobia. A study was performed to investigate the most commonly associated nodule-associated bacteria and the rhizospheric microorganisms associated with the Fenugreek (Trigonella foenum-graecum) plant. Isolation of nonrhizobial isolates from root nodules of Fenugreek was carried out along with the rhizospheric isolates. About 64.7% isolates obtained from Fenugreek nodules were gram-negative coccobacilli, 29.41% were gram-positive bacilli, and all rhizospheric isolates except one were gram-positive bacilli. All the isolates were characterized for their plant growth promoting (PGP) activities. Two of the NAB isolates M2N2c and B1N2b (Exiguobacterium sp.) showed maximum positive PGP features. Those NAB isolates when coinoculated with rhizobial strain—S. meliloti, showed plant growth promotion with respect to increase in plant's root and shoot length, chlorophyll content, nodulation efficiency, and nodule dry weight.

Bacillus endoradicis sp. nov., an endophytic bacterium isolated from soybean root

A gram-positive, aerobic, motile rod, designated strain CCBAU 05776(T), was isolated from the inner tissues of a healthy soybean (Glycine max L.) root collected from an agricultural field in the countryside of Shijiazhuang city, Hebei Province, China. Phylogenetic analysis of the 16S rRNA gene indicated that this strain was most closely related to Bacillus muralis LMG 20238(T) and Bacillus simplex NBRC 15720(T) with similarity of 96.5 % and 96.3 %, respectively, lower than the suggested threshold (97.0 %) for separating bacterial species. In phenotypic characterization, the novel strain differed from the two most related species in that it did not hydrolyse casein or starch but could grow on MacConkey agar. It grew between 15 and 45 °C and tolerated up to 7 % NaCl (w/v). Strain CCBAU 05776(T) grew in media with pH 5.5 to 10 (optimal growth at pH 7.0-8.0). The predominant cellular fatty acids were iso-C(15 : 0) (40.81 %) and C(16 : 1)ω7c alcohol (10.61 %). The predominant isoprenoid quinone was menaquinone 7 (MK-7). The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C was 40.8 mol% (T(m)). DNA-DNA relatedness of the novel isolate with B. muralis and B. simplex was 42.4 % and 32.7 %, respectively. Based upon the consensus of phylogenetic and phenotypic analyses, strain CCBAU 05776(T) represents a novel species within the genus Bacillus, for which the name Bacillus endoradicis sp. nov. is proposed. The type strain is CCBAU 05776(T) ( = LMG 25492(T)  = HAMBI 3097(T)).

Molecular diversity and phylogeny of rhizobia associated with Lablab purpureus (Linn.) grown in Southern China

As an introduced plant, Lablab purpureus serves as a vegetable, herbal medicine, forage and green manure in China. In order to investigate the diversity of rhizobia associated with this plant, a total of 49 rhizobial strains isolated from ten provinces of Southern China were analyzed in the present study with restriction fragment length polymorphism and/or sequence analyses of housekeeping genes (16S rRNA, IGS, atpD, glnII and recA) and symbiotic genes (nifH and nodC). The results defined the L. purpureus rhizobia as 24 IGS-types within 15 rrs-IGS clusters or genomic species belonging to Bradyrhizobium, Rhizobium, Ensifer (synonym of Sinorhizobium) and Mesorhizobium. Bradyrhizobium spp. (81.6%) were the most abundant isolates, half of which were B. elkanii. Most of these rhizobia induced nodules on L. purpureus, but symbiotic genes were only amplified from the Bradyrhizobium and Rhizobium leguminosarum strains. The nodC and nifH phylogenetic trees defined five lineages corresponding to B. yuanmingense, B. japonicum, B. elkanii, B. jicamae and R. leguminosarum. The coherence of housekeeping and symbiotic gene phylogenies demonstrated that the symbiotic genes of the Lablab rhizobia were maintained mainly through vertical transfer. However, a putative lateral transfer of symbiotic genes was found in the B. liaoningense strain. The results in the present study clearly revealed that L. purpureus was a promiscuous host that formed nodules with diverse rhizobia, mainly Bradyrhizobium species, harboring different symbiotic genes.

Diversity and applications of Bacillus bacteriocins

Members of the genus Bacillus are known to produce a wide arsenal of antimicrobial substances, including peptide and lipopeptide antibiotics, and bacteriocins. Many of the Bacillus bacteriocins belong to the lantibiotics, a category of post-translationally modified peptides widely disseminated among different bacterial clades. Lantibiotics are among the best-characterized antimicrobial peptides at the levels of peptide structure, genetic determinants and biosynthesis mechanisms. Members of the genus Bacillus also produce many other nonmodified bacteriocins, some of which resemble the pediocin-like bacteriocins of the lactic acid bacteria (LAB), while others show completely novel peptide sequences. Bacillus bacteriocins are increasingly becoming more important due to their sometimes broader spectra of inhibition (as compared with most LAB bacteriocins), which may include Gram-negative bacteria, yeasts or fungi, in addition to Gram-positive species, some of which are known to be pathogenic to humans and/or animals. The present review provides a general overview of Bacillus bacteriocins, including primary structure, biochemical and genetic characterization, classification and potential applications in food preservation as natural preservatives and in human and animal health as alternatives to conventional antibiotics. Furthermore, it addresses their environmental applications, such as bioprotection against the pre- and post-harvest decay of vegetables, or as plant growth promoters.

Diversity of endophytic bacteria within nodules of the Sphaerophysa salsula in different regions of Loess Plateau in China

A total of 115 endophytic bacteria were isolated from root nodules of the wild legume Sphaerophysa salsula grown in two ecological regions of Loess Plateau in China. The genetic diversity and phylogeny of the strains were revealed by restriction fragment length polymorphism and sequencing of 16S rRNA gene and enterobacterial repetitive intergenic consensus-PCR. Their symbiotic capacity was checked by nodulation tests and analysis of nifH gene sequence. This is the first systematic study on endophytic bacteria associated with S. salsula root nodules. Fifty of the strains found were symbiotic bacteria belonging to eight putative species in the genera Mesorhizobium, Rhizobium and Sinorhizobium, harboring similar nifH genes; Mesorhizobium gobiense was the main group and 65 strains were nonsymbiotic bacteria related to 17 species in the genera Paracoccus, Sphingomonas, Inquilinus, Pseudomonas, Serratia, Mycobacterium, Nocardia, Streptomyces, Paenibacillus, Brevibacillus, Staphylococcus, Lysinibacillus and Bacillus, which were universally coexistent with symbiotic bacteria in the nodules. Differing from other similar studies, the present study is the first time that symbiotic and nonsymbiotic bacteria have been simultaneously isolated from the same root nodules, offering the possibility to accurately reveal the correlation between these two kinds of bacteria. These results provide valuable information about the interactions among the symbiotic bacteria, nonsymbiotic bacteria and their habitats.