Isolation, selection, and characterization of beneficial rhizobacteria from pea, lentil, and chickpea grown in western Canada

Suitable Methods of Inoculation and Quantification of Fusarium Root Rot in Lentil

Lentil (Lens culinaris L. subsp. culinaris) is an important grain legume grown worldwide. As its popularity grows among consumers and more acres are produced, new root rot complexes have become more prevalent. This work sought to develop methods for studying root rot caused by Fusarium avenaceum in lentil using controlled environments. The objectives were to (i) find an effective and seed-safe sterilization technique, (ii) optimize the inoculation technique and lentil growing environment, and (iii) develop visual and automated disease scoring systems. Results showed the use of detergent and a low concentration (0.1%) of NaClO (the active ingredient in bleach) maintained germinability and effectively eliminated bacterial and fungal contamination on seeds. Other treatments, such as ethanol, reduced seed germination or failed to kill pathogenic fungi such as Fusarium spp. Placing inoculum at a moderate rate of 1 × 10⁶ spores both directly on the seed and on top of the media covering the seed improved severity scores and reduced escapes compared with placement on top of the media only. Visual severity scoring systems and diagrammatic scales were developed for scoring the cotyledon region and roots. A computer vision algorithm was designed to improve the efficiency of scoring the cotyledon region and roots for disease severity using a simple RGB camera and lightbox. Visual and computer scores were best correlated when images were visually scored on a monitor, and multiple images were averaged. The scores generated from the computer vision algorithm had better correlations with visual scores for cotyledon rot (r = 0.92 and β₁ = 0.96) than root rot (r = 0.62 and β₁ = 0.67).

Genome mining, antimicrobial and plant growth-promoting potentials of halotolerant Bacillus paralicheniformis ES-1 isolated from salt mine

Salinity severely affects crop yield by hindering nitrogen uptake and reducing plant growth. Plant growth-promoting bacteria (PGPB) are capable of providing cross-protection against biotic/abiotic stresses and facilitating plant growth. Genome-level knowledge of PGPB is necessary to translate the knowledge into a product as efficient biofertilizers and biocontrol agents. The current study aimed to isolate and characterize indigenous plant growth-promoting strains with the potential to promote plant growth under various stress conditions. In this regard, 72 bacterial strains were isolated from various saline-sodic soil/lakes; 19 exhibited multiple in vitro plant growth-promoting traits, including indole 3 acetic acid production, phosphate solubilization, siderophore synthesis, lytic enzymes production, biofilm formation, and antibacterial activities. To get an in-depth insight into genome composition and diversity, whole-genome sequence and genome mining of one promising Bacillus paralicheniformis strain ES-1 were performed. The strain ES-1 genome carries 12 biosynthetic gene clusters, at least six genomic islands, and four prophage regions. Genome mining identified plant growth-promoting conferring genes such as phosphate solubilization, nitrogen fixation, tryptophan production, siderophore, acetoin, butanediol, chitinase, hydrogen sulfate synthesis, chemotaxis, and motility. Comparative genome analysis indicates the region of genome plasticity which shapes the structure and function of B. paralicheniformis and plays a crucial role in habitat adaptation. The strain ES-1 has a relatively large accessory genome of 649 genes (~ 19%) and 180 unique genes. Overall, these results provide valuable insight into the bioactivity and genomic insight into B. paralicheniformis strain ES-1 with its potential use in sustainable agriculture.

Carbon Footprint Management by Agricultural Practices

Global attention to climate change issues, especially air temperature changes, has drastically increased over the last half-century. Along with population growth, greater surface temperature, and higher greenhouse gas (GHG) emissions, there are growing concerns for ecosystem sustainability and other human existence on earth. The contribution of agriculture to GHG emissions indicates a level of 18% of total GHGs, mainly from carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O). Thus, minimizing the effects of climate change by reducing GHG emissions is crucial and can be accomplished by truly understanding the carbon footprint (CF) phenomenon. Therefore, the purposes of this study were to improve understanding of CF alteration due to agricultural management and fertility practices. CF is a popular concept in agro-environmental sciences due to its role in the environmental impact assessments related to alternative solutions and global climate change. Soil moisture content, soil temperature, porosity, and water-filled pore space are some of the soil properties directly related to GHG emissions. These properties raise the role of soil structure and soil health in the CF approach. These properties and GHG emissions are also affected by different land-use changes, soil types, and agricultural management practices. Soil management practices globally have the potential to alter atmospheric GHG emissions. Therefore, the relations between photosynthesis and GHG emissions as impacted by agricultural management practices, especially focusing on soil and related systems, must be considered. We conclude that environmental factors, land use, and agricultural practices should be considered in the management of CF when maximizing crop productivity.

In-Depth Characterization of Plant Growth Promotion Potentials of Selected Alkanes-Degrading Plant Growth-Promoting Bacterial Isolates

The use of plant growth-promoting rhizobacteria (PGPR) as a bioremediation enhancer in plant-assisted phytoremediation requires several steps, consisting of the screening, selection, and characterization of isolates. A subset of 50 bacterial isolates representing a wide phylogenetic range were selected from 438 morphologically different bacteria that were originally isolated from a petroleum hydrocarbon (PHC)-polluted site of a former petrochemical plant. Selected candidate bacteria were screened using six conventional plant growth-promoting (PGP) traits, complemented with the genetic characterization of genes involved in alkane degradation, as well as other pertinent functions. Finally, the bacterial isolates were subjected to plant growth promotion tests using a gnotobiotic approach under normal and stressed conditions. Our results indicated that 35 bacterial isolates (70%) possessed at least four PGP traits. Twenty-nine isolates (58%) were able to utilize n-hexadecane as a sole carbon source, whereas 43 isolates (86%) were able to utilize diesel as the sole carbon source. The presence of catabolic genes related to hydrocarbon degradation was assessed using endpoint PCR, with the alkane monooxygenase (alkB) gene found in 34 isolates, the cytochrome P450 hydroxylase (CYP153) gene found in 24 isolates, and the naphthalene dioxygenase (nah1) gene found to be present in 33 isolates. Thirty-six strains (72%) promoted canola root elongation in the growth pouch assay. After several rounds of screening, seven bacterial candidates (individually or combined in a consortium) were tested for canola root and shoot growth promotion in substrates amended by different concentrations of n-hexadecane (0%, 1%, 2%, and 3%) under gnotobiotic conditions. Our results showed that Nocardia sp. (WB46), Pseudomonas plecoglossicida (ET27), Stenotrophomonas pavanii (EB31), and Gordonia amicalis (WT12) significantly increased the root length of canola grown in 3% n-hexadecane compared with the control treatment, whereas Nocardia sp. (WB46) and Bacillus megaterium (WT10) significantly increased shoot length compared to control treatment at the same concentration of n-hexadecane. The consortium had a significant enhancement effect on root length compared to all isolates inoculated individually or to the control. This study demonstrates that the combination of PGPR traits and the PHC degradation potential of bacteria can result in an enhanced beneficial effect in phytoremediation management, which could lead to the development of innovative bacterial inoculants for plants to remediate PHC-contaminated soils.

Salix purpurea and Eleocharis obtusa Rhizospheres Harbor a Diverse Rhizospheric Bacterial Community Characterized by Hydrocarbons Degradation Potentials and Plant Growth-Promoting Properties

Phytoremediation, a method of phytomanagement using the plant holobiont to clean up polluted soils, is particularly effective for degrading organic pollutants. However, the respective contributions of host plants and their associated microbiota within the holobiont to the efficiency of phytoremediation is poorly understood. The identification of plant-associated bacteria capable of efficiently utilizing these compounds as a carbon source while stimulating plant-growth is a keystone for phytomanagement engineering. In this study, we sampled the rhizosphere and the surrounding bulk soil of Salixpurpurea and Eleocharis obusta from the site of a former petrochemical plant in Varennes, QC, Canada. Our objectives were to: (i) isolate and identify indigenous bacteria inhabiting these biotopes; (ii) assess the ability of isolated bacteria to utilize alkanes and polycyclic aromatic hydrocarbons (PAHS) as the sole carbon source, and (iii) determine the plant growth-promoting (PGP) potential of the isolates using five key traits. A total of 438 morphologically different bacterial isolates were obtained, purified, preserved and identified through PCR and 16S rRNA gene sequencing. Identified isolates represent 62 genera. Approximately, 32% of bacterial isolates were able to utilize all five different hydrocarbons compounds. Additionally, 5% of tested isolates belonging to genera Pseudomonas, Acinetobacter, Serratia, Klebsiella, Microbacterium, Bacillus and Stenotrophomonas possessed all five of the tested PGP functional traits. This culture collection of diverse, petroleum-hydrocarbon degrading bacteria, with multiple PGP traits, represents a valuable resource for future use in environmental bio- and phyto-technology applications.

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.

Fighting plant pathogens with cold-active microorganisms: biopesticide development and agriculture intensification in cold climates

Cold-adapted (CA) microorganisms (= psychrophiles or psychrotolerants) are key players of many ecological interactions in natural ecosystems. Some of them can colonize the rhizosphere of plants and cause damage to their hosts; others, on the contrary, protect plants from their pathogens through direct and indirect mechanisms, thus promoting plant growth and development. These "protective" microbes are known as biocontrol agents (BCA). BCA either limit or inhibit the growth of plant pathogens, owing to the excretion of a panoply of secondary metabolites (including soluble and volatile antibiotics, siderophores, quorum sensing interfering agents). BCA can also control plant pathogens through indirect mechanisms, including competence for nutrients and space, or else by interfering with their chemical communication. That explains why some of these BCA have been included in the formulation of commercial biopesticides, which are environmentally friendly products containing live cells used to control plant diseases and pests. At present, the development of biopesticides from mesophilic microorganisms is an established technology. Unfortunately, these biopesticides are not active at low temperatures. On the other hand, the information concerning the potential use of CA-BCA for the same goal is at its infancy. Here, we review the current knowledge concerning the isolation, identification, and characterization of CA microbes which act as antagonists of plant pathogens, including the mechanisms they deploy to antagonize plant pathogens. We also illustrate their biotechnological potential to develop CA biopesticides and discuss their utility in the context of mountainous agriculture. KEY POINTS: • Many naturally occurring cold-active microbes antagonize plant pathogens. • The mechanisms of biocontrol exerted by these microbes are either direct or indirect. • Cold-active biocontrol agents can be used to develop biopesticides. • Cold-active biopesticides are crucial for sustainably intensifying agriculture in cold climates.

A high Mn(II)-tolerance strain, Bacillus thuringiensis HM7, isolated from manganese ore and its biosorption characteristics

Microorganisms play a significant part in detoxifying and immobilizing excessive metals. The present research isolated a strain (HM7) with high Mn(II) tolerance from Mn(II)-contaminated soil samples. The 16S rDNA sequence analysis showed that HM7 had a 99% similarity to Bacillus thuringiensis, which can survive under a high concentration 4,000 mg/L of Mn(II), and the highest removal rate was up to 95.04% at the concentration of 400 mg/L. The highest Mn(II) removal rate was detected at the contact time 72 h, temperature 30 °C, and pH 5.0, while the differences in strain growth and Mn(II) removal rate among different inoculation doses were insignificant. Scanning electron microscopy indicated B. thuringiensis HM7 cells appeared irregular and cracked under Mn(II) stress. Fourier transform infrared exhibited that functional groups like carboxyl, hydroxyl, amino, sulfhydryl groups, and amide bands might take part in the complexation of Mn(II). In addition, HM7 suggested the ability of indoleacetic acid production, siderophore production, and P’ solubilization potential. Therefore, HM7 might have a potential to promote metal absorption by changing the form of heavy metals, and the experiments supported the application of B. thuringiensis HM7 as a biological adsorbent in Mn(II) contaminated environment remediation.

Communication of plants with microbial world: Exploring the regulatory networks for PGPR mediated defense signaling

Agricultural manipulation of potentially beneficial rhizosphere microbes is increasing rapidly due to their multi-functional plant-protective and growth related benefits. Plant growth promoting rhizobacteria (PGPR) are mostly non-pathogenic microbes which exert direct benefits on plants while there are rhizosphere bacteria which indirectly help plant by ameliorating the biotic and/or abiotic stress or induction of defense response in plant. Regulation of these direct or indirect effect takes place via highly specialized communication system induced at multiple levels of interaction i.e., inter-species, intra-species, and inter-kingdom. Studies have provided insights into the functioning of signaling molecules involved in communication and induction of defense responses. Activation of host immune responses upon bacterial infection or rhizobacteria perception requires comprehensive and precise gene expression reprogramming and communication between hosts and microbes. Majority of studies have focused on signaling of host pattern recognition receptors (PRR) and nod-like receptor (NLR) and microbial effector proteins under mining the role of other components such as mitogen activated protein kinase (MAPK), microRNA, histone deacytylases. The later ones are important regulators of gene expression reprogramming in plant immune responses, pathogen virulence and communications in plant-microbe interactions. During the past decade, inoculation of PGPR has emerged as potential strategy to induce biotic and abiotic stress tolerance in plants; hence, it is imperative to expose the basis of these interactions. This review discusses microbes and plants derived signaling molecules for their communication, regulatory and signaling networks of PGPR and their different products that are involved in inducing resistance and tolerance in plants against environmental stresses and the effect of defense signaling on root microbiome. We expect that it will lead to the development and exploitation of beneficial microbes as source of crop biofertilizers in climate changing scenario enabling more sustainable agriculture.

Exploring Bacterial Communities in Aquaponic Systems

Aquaponics is a production system based on the dynamic equilibrium between fish, plants, and microorganisms. In order to better understand the role of microorganisms in this tripartite relationship, we studied the bacterial communities hosted in eight aquaponic and aquaculture systems. The bacterial communities were analyzed by 16S rRNA gene deep sequencing. At the phylum level, the bacterial communities from all systems were relatively similar with a predominance of Proteobacteria and Bacteroidetes. At the genus level, however, the communities present in the sampled systems were more heterogeneous. The biofilter samples harbored more diverse communities than the corresponding sump samples. The core microbiomes from the coupled and decoupled systems shared more common operational taxonomic units than with the aquaculture systems. Eventually, some of the taxa identified in the systems could have beneficial functions for plant growth and health, but a deeper analysis would be required to identify the precise functions involved in aquaponics.

Pseudomonads contribute to regulation ofPratylenchus penetrans(Nematoda) populations on apple

Inoculation with antagonistic soil microorganisms has shown potential to suppress replant disease of apple in orchard soils. Pseudomonas spp. may have the potential to reduce Pratylenchus penetrans populations on apple. Pseudomonas spp. were isolated from the rhizosphere of sweet cherry and screened for antagonistic characteristics. Two highly antagonistic Pseudomonas isolates, P10-32 and P10-42, were evaluated for growth promotion of apple seedlings, suppression of P. penetrans populations, and root colonization in soil from three orchards. During the isolate screening, Pseudomonas fluorescens P10-32 reduced in vitro growth of fungal pathogens, had protease activity, had capacity to produce pyrrolnitrin, suppressed P. penetrans populations, and increased plant biomass. Pseudomonas fluorescens P10-42 reduced in vitro growth of fungal pathogens, had protease activity, suppressed P. penetrans populations, and increased plant biomass. In potted orchard soil, inoculating apple with P. fluorescens P10-32 suppressed P. penetrans populations in one of the three soils examined. Inoculation with P. fluorescens P10-42 improved plant growth in two of the soils and suppressed P. penetrans abundance in one soil. In one of the soils, P. fluorescens P10-42 was detected on the roots 56 days postinoculation. Overall, we conclude that Pseudomonas spp. play a role in suppressing P. penetrans on apple in orchard soil.

Biosorption characteristics of a highly Mn(II)-resistant Ralstonia pickettii strain isolated from Mn ore

Microorganisms play an important role in immobilizing and detoxifying excessive Mn; however, there is so far a lack of sufficient information concerning highly Mn(II)-tolerant bacteria. The present study was conducted to analyze the bio-sorption characteristics of a strain (HM8) isolated from manganese ore wastes. Analytical data from the 16S rDNA sequence determination showed that the species, HM8, had a 99% similarity to Ralstonia pickettii. Results from the designed physiological, biochemical and isothermal adsorption tests indicated that HM8 did not only grow well at a Mn(II) concentration level of 10,000 mg/L but also removed 1,002.83 mg/L of Mn(II) from the bulk solution of the culture, showing that the isolated strain possessed strong capabilities to tolerate and remove Mn(II). In the isothermal bio-sorption experiments performed to investigate the effects of relevant factors on Mn(II) sorption, the highest Mn(II) removal rate was obtained at the contact time 72 h, temperature 40°C, and pH 6.0, while the differences in both strain growth and Mn(II) removal rate between different inoculated HM8 doses were found to be insignificant within the tested range. Scanning electron microscopy showed that, under Mn(II) stress, HM8 cells appeared irregular and cracked, with apparent wrinkles on the surface. The peaks in the Fourier transform infrared spectra showed that hydroxyl and carboxyl groups were the main functional groups for Mn(II) adsorption. The experimental data supported the practical application of HM8 as a biological adsorbent for remediation of heavily Mn contaminated sites.

Efficacy of Pseudomonas fluorescens for control of Mucor rot of apple during commercial storage and potential modes of action

The ability of Pseudomonas fluorescens isolates 1-112, 2-28, and 4-6, to control Mucor piriformis (Mucor rot) on Gala, McIntosh, Ambrosia, and Spartan apple cultivars in commercial cold storage and their possible mechanisms of action were investigated. Isolates 1-112 and 2-28 provided significant levels of disease control on McIntosh and Spartan apples, while isolate 4-6 provided control of Mucor rot on Gala and Spartan apples, compared with control fruits after 15 weeks of storage at 0 °C. Mycelial growth of M. piriformis was markedly inhibited by cell-free supernatant and volatile organic compounds produced by P. fluorescens isolates, in vitro. In filter-sterilized apple juice, living cells of all 3 P. fluorescens isolates or their metabolites significantly inhibited spore germination by 99.8% and 61.6%, on average, respectively. Electron microscopy indicated that all 3 isolates of P. fluorescens colonized the hyphae of M. piriformis, but only isolate 1-112 was observed to colonize M. piriformis spores in vitro. In the wounds of apple, all 3 isolates formed a biofilm on the fungal hyphae and on the fruit tissue. Potential mechanisms of antagonism utilized by P. fluorescens against M. piriformis may include competition for nutrients and space, production of inhibitory metabolites and volatiles, and biofilm formation, leading to inhibition of spore germination and mycelial growth.

Barcoded Pyrosequencing Reveals a Shift in the Bacterial Community in the Rhizosphere and Rhizoplane of Rehmannia glutinosa under Consecutive Monoculture

The production and quality of Rehmannia glutinosa can be dramatically reduced by replant disease under consecutive monoculture. The root-associated microbiome, also known as the second genome of the plant, was investigated to understand its impact on plant health. Culture-dependent and culture-independent pyrosequencing analysis was applied to assess the shifts in soil bacterial communities in the rhizosphere and rhizoplane under consecutive monoculture. The results show that the root-associated microbiome (including rhizosphere and rhizoplane microbiomes) was significantly impacted by rhizocompartments and consecutive monoculture. Consecutive monoculture of R. glutinosa led to a significant decline in the relative abundance of the phyla Firmicutes and Actinobacteria in the rhizosphere and rhizoplane. Furthermore, the families Flavobacteriaceae, Sphingomonadaceae, and Xanthomonadaceae enriched while Pseudomonadaceae, Bacillaceae, and Micrococcaceae decreased under consecutive monoculture. At the genus level, Pseudomonas, Bacillus, and Arthrobacter were prevalent in the newly planted soil, which decreased in consecutive monocultured soils. Besides, culture-dependent analysis confirmed the widespread presence of Pseudomonas spp. and Bacillus spp. in newly planted soil and their strong antagonistic activities against fungal pathogens. In conclusion, R. glutinosa monoculture resulted in distinct root-associated microbiome variation with a reduction in the abundance of beneficial microbes, which might contribute to the declined soil suppressiveness to fungal pathogens in the monoculture regime.

The Effects of the Endophytic Bacterium Pseudomonas fluorescens Sasm05 and IAA on the Plant Growth and Cadmium Uptake of Sedum alfredii Hance

Endophytic bacteria have received attention for their ability to promote plant growth and enhance phytoremediation, which may be attributed to their ability to produce indole-3-acetic acid (IAA). As a signal molecular, IAA plays a key role on the interaction of plant and its endomicrobes. However, the different effects that endophytic bacteria and IAA may have on plant growth and heavy metal uptake is not clear. In this study, the endophytic bacterium Pseudomonas fluorescens Sasm05 was isolated from the stem of the zinc (Zn)/cadmium (Cd) hyperaccumulator Sedum alfredii Hance. The effects of Sasm05 and exogenous IAA on plant growth, leaf chlorophyll concentration, leaf Mg²⁺-ATPase and Ca²⁺-ATPase activity, cadmium (Cd) uptake and accumulation as well as the expression of metal transporter genes were compared in a hydroponic experiment with 10 μM Cd. The results showed that after treatment with 1 μM IAA, the shoot biomass and chlorophyll concentration increased significantly, but the Cd uptake and accumulation by the plant was not obviously affected. Sasm05 inoculation dramatically increased plant biomass, Cd concentration, shoot chlorophyll concentration and enzyme activities, largely improved the relative expression of the three metal transporter families ZRT/IRT-like protein (ZIP), natural resistance associated macrophage protein (NRAMP) and heavy metal ATPase (HMA). Sasm05 stimulated the expression of the SaHMAs (SaHMA2, SaHMA3, and SaHMA4), which enhanced Cd root to shoot translocation, and upregulated SaZIP, especially SaIRT1, expression to increase Cd uptake. These results showed that although both exogenous IAA and Sasm05 inoculation can improve plant growth and photosynthesis, Sasm05 inoculation has a greater effect on Cd uptake and translocation, indicating that this endophytic bacterium might not only produce IAA to promote plant growth under Cd stress but also directly regulate the expression of putative key Cd uptake and transport genes to enhance Cd accumulation of plant.

Identifying and Managing Root Rot of Pulses on the Northern Great Plains

Pulse crops (annual grain legumes such as field pea, lentil, dry bean, and chickpea) have become an important component of the cropping system in the northern Great Plains of North America over the last three decades. In many areas, the intensity of damping-off, seedling blight, root rot, and premature ripening of pulse crops is increasing, resulting in reduction in stand establishment and yield. This review provides a brief description of the important pathogens that make up the root rot complex and summarizes root rot management on pulses in the region. Initially, several specific Fusarium spp., a range of Pythium spp., and Rhizoctonia solani were identified as important components of the root rot disease complex. Molecular approaches have recently been used to identify the importance of Aphanomyces euteiches on pulses, and to demonstrate that year-to-year changes in precipitation and temperature have an important effect on pathogen prevalence. Progress has been made on management of root rot, but more IPM tools are required to provide effective disease management. Seed-treatment fungicides can reduce damping-off and seedling blight for many of the pathogens in this disease complex, but complex cocktails of active ingredients are required to protect seedlings from the pathogen complex present in most commercial fields. Partial resistance against many of the pathogens in the complex has been identified, but is not yet available in commercial cultivars. Cultural practices, especially diversified cropping rotations and early, shallow seeding, have been shown to have an important role in root rot management. Biocontrol agents may also have potential over the long term. Improved methods being developed to identify and quantify the pathogen inoculum in individual fields may help producers avoid high-risk fields and select IPM packages that enhance yield stability.

Whole genome analysis of halotolerant and alkalotolerant plant growth-promoting rhizobacterium Klebsiella sp. D5A

This research undertook the systematic analysis of the Klebsiella sp. D5A genome and identification of genes that contribute to plant growth-promoting (PGP) traits, especially genes related to salt tolerance and wide pH adaptability. The genome sequence of isolate D5A was obtained using an Illumina HiSeq 2000 sequencing system with average coverages of 174.7× and 200.1× using the paired-end and mate-pair sequencing, respectively. Predicted and annotated gene sequences were analyzed for similarity with the Kyoto Encyclopedia of Genes and Genomes (KEGG) enzyme database followed by assignment of each gene into the KEGG pathway charts. The results show that the Klebsiella sp. D5A genome has a total of 5,540,009 bp with 57.15% G + C content. PGP conferring genes such as indole-3-acetic acid (IAA) biosynthesis, phosphate solubilization, siderophore production, acetoin and 2,3-butanediol synthesis, and N2 fixation were determined. Moreover, genes putatively responsible for resistance to high salinity including glycine-betaine synthesis, trehalose synthesis and a number of osmoregulation receptors and transport systems were also observed in the D5A genome together with numerous genes that contribute to pH homeostasis. These genes reveal the genetic adaptation of D5A to versatile environmental conditions and the effectiveness of the isolate to serve as a plant growth stimulator.

Differential response of kabuli and desi chickpea genotypes toward inoculation with PGPR in different soils

Pakistan is among top three chickpea producing countries but the crop is usually grown on marginal lands without irrigation and fertilizer application which significantly hampers its yield. Soil fertility and inoculation with beneficial rhizobacteria play a key role in nodulation and yield of legumes. Four kabuli and six desi chickpea genotypes were, therefore, evaluated for inoculation response with IAA-producing Ochrobactrum ciceri Ca-34(T) and nitrogen fixing Mesorhizobium ciceri TAL-1148 in single and co-inoculation in two soils. The soil type 1 was previously unplanted marginal soil having low organic matter, P and N contents compared to soil type 2 which was a fertile routinely legume-cultivated soil. The effect of soil fertility status was pronounced and fertile soil on average, produced 31% more nodules, 62% more biomass and 111% grain yield than marginal soil. Inoculation either with O. ciceri alone or its co-inoculation with M. ciceri produced on average higher nodules (42%), biomass (31%), grains yield (64%) and harvest index (72%) in both chickpea genotypes over non-inoculated controls in both soils. Soil 1 showed maximum relative effectiveness of Ca-34(T) inoculation for kabuli genotypes while soil 2 showed for desi genotypes except B8/02. Desi genotype B8/02 in soil type 1 and Pb-2008 in soil type 2 showed significant yield increase as compared to respective un-inoculated controls. Across bacterial inoculation treatments, grain yield was positively correlated to growth and yield contributing parameters (r = 0.294(*) to 0.838(***) for desi and r = 0.388(*) to 0.857(**) for kabuli). PCA and CAT-PCA analyses clearly showed a site-specific response of genotype x bacterial inoculation. Furthermore, the inoculated bacterial strains were able to persist in the rhizosphere showing colonization on root and within nodules. Present study shows that plant growth promoting rhizobacteria (PGPR) inoculation should be integrated with national chickpea breading program in Pakistan especially for marginal soils. Furthermore, the study shows the potential of phytohormone producing strain Ca-34(T) as promising candidate for development of biofertilizer alongwith nodulating strains to get sustainable yield of kabuli and desi chickpea with minimum inputs at marginal land.

Potential of plant growth promoting traits by bacteria isolated from heavy metal contaminated soils

Rhizobacteria can enhance biomass production and heavy metal tolerance of plants under the stress environment. The aim of this study was to collect soil samples from different industrial sites followed by their heavy metal analysis. After performing the ICP-AES analysis of soil samples from seven different sites, bacterial strains were isolated from the soil samples of most polluted (heavy metal) site. Phylogenetic analysis of isolates based on 16S rDNA sequences showed that the isolates belonged to four species: Bacillus thuringiensis, Azotobacter chroococcum, Paenibacillus ehimensis and Pseudomonas pseudoalcaligenes. Plant growth promoting activities; siderophore production, indole acetic acid production, HCN production, and phosphate solubilisation were assayed in vitro, and statistically analysis done by using ANOVA analysis and Tukey's Honestly Significant Difference test (p ≤ 0.05). Plant growth-promoting characteristics of isolated strains were higher compared to the control Pseudomonas fluorescens (NICM 5096). In vitro study was performed to check resistance against two heavy metals of isolates. It was observed that isolated bacterial strains have higher heavy metal resistance as compared to control E. coli (NICM 2563). These isolates may cause pathogenic effects, so to avoid this risk, their antibacterial susceptibility was checked against eight antibiotics. Among the eight antibiotics, Ciprofloxacin-1 has shown higher inhibition against all the isolated bacterial strains.

The biochemistry behind biopesticide efficacy

Biopesticides have the potential to play an important role in sustainable, environmentally safe pest control. A diverse range of biopesticides employ chemical modes of action. This review explores three such biopesticides: a fungus used in weed control, beneficial bacteria controlling fungal and bacterial disease and a virus active against insect pests. Through these case studies, we demonstrate that biopesticides rely on both chemical and biochemical approaches and complementary biological modalities. Hence, biopesticides are more complex than synthetic pesticides. The latter typically utilize a single chemical with a single mode of action, while the former often have more complex or holistic modes of action. The success of current and future biopesticides could be enhanced through increased research focusing on the chemistry involved.

Bacterial endophytes mediate positive feedback effects of early legume termination times on the yield of subsequent durum wheat crops

Field crops influence the biotic properties of the soil, impacting the health and productivity of subsequent crops. Polymerase chain reaction and 454 GS FLX pyrosequencing of amplicons were used to clarify the legacy of chickpea and pea crops on the quality of the bacterial community colonizing the root endosphere of subsequent crops of wheat, in a replicated field study. Similar communities of root endosphere bacteria were formed in durum wheat grown after pea and chickpea crops when chickpea crops were terminated as early as pea (July). Termination of the chickpea crops in September led to the domination of Firmicutes in wheat root endosphere; Actinobacteria dominated the wheat root endosphere following early pulse crop termination. The architecture of wheat plants was correlated with the composition of its root endosphere community. High grain yield was associated with the production of fewer but larger wheat heads, the abundance of endospheric Actinobacteria and Acidobacteria, and the scarcity of endospheric Firmicutes. Pulse termination time affected wheat root endosphere colonization strongly in 2009 but weakly in 2010, an abnormally wet year. This study improved our understanding of the so-called "crop rotation effect" in pulse-wheat systems and showed how this system can be manipulated through agronomic decisions.

Phytohormone production and colonization of canola (Brassica napus L.) roots by Pseudomonas fluorescens 6-8 under gnotobiotic conditions

Pseudomonas fluorescens 6-8, a rhizosphere isolate previously shown to enhance root elongation of canola ( Brassica napus L.), was characterized for its ability to produce indole-3-acetic acid and cytokinins in pure culture and in the rhizosphere of canola under gnotobiotic conditions in comparison with the cytokinin-producing strain P. fluorescens G20-18 and its mutant CNT2. Strain 6-8 produced isopentenyl adenosine, zeatin riboside, and dihydroxyzeatin riboside at levels similar to those of G20-18, but only very low concentrations of indole-3-acetic acid. In a gnotobiotic assay canola inoculated with 6-8 and G20-18 had higher concentrations of isopentenyl adenosine and zeatin riboside in the rhizosphere and greater root length than the noninoculated control. The ability of strain 6-8 to colonize canola roots was assessed following transformation with the green fluorescent protein and inoculation onto canola seed in a gnotobiotic assay. Higher populations of strain 6-8 were observed on the proximal region of the root closest to the seed than on the mid and distal portions 9 days after seed inoculation. The ability of P. fluorescens 6-8 to produce cytokinins, colonize the roots of canola seedlings, and enhance root elongation may contribute to its ability to survive in the rhizosphere and may benefit seedling growth.

A plant growth-promoting pseudomonad is closely related to the Pseudomonas syringae complex of plant pathogens

Pseudomonas putida GR12-2 is well known as a plant growth-promoting rhizobacterium; however, phylogenetic analysis using the 16S rRNA gene and four housekeeping genes indicated that this strain forms a monophyletic group with the Pseudomonas syringae complex, which is composed of several species of plant pathogens. On the basis of these sequence analyses, we suggest that P. putida GR12-2 be redesignated as P. syringae GR12-2. To compare the ecological roles of P. syringae GR12-2 with its close relatives P. syringae pathovar (pv.) tomato DC3000 and P. syringae pv. syringae B728a, we investigated their ability to cause disease and promote plant growth. When introduced on tobacco or tomato leaves, P. syringae GR12-2 was unable to elicit a hypersensitive response or cause disease, which are characteristic responses of P. syringae DC3000 and B728a, nor were type III secretion system genes required for virulence detected in P. syringae GR12-2 by PCR or DNA hybridization. In contrast to P. syringae GR12-2, neither of the phytopathogens was able to promote root growth when inoculated onto canola seeds. Although commensals and nonpathogens have been reported among the strains of the P. syringae complex, P. syringae GR12-2 is a mutualist and a phytostimulator.