An ipdC gene knock-out of Azospirillum brasilense strain SM and its implications on indole-3-acetic acid biosynthesis and plant growth promotion

Indole-3-acetic acid (IAA) protects Azospirillum brasilense from indole-induced stress

Azospirillum brasilense is plant-growth promoting rhizobacteria that produces the phytohormone indole-3-acetic acid (IAA) to induce changes in plant root architecture. The major pathway for IAA biosynthesis in A. brasilense converts tryptophan into indole-3-pyruvic acid (I3P) and then, through the rate-limiting enzyme, indole-3-pyruvate decarboxylase (IpdC), into IAA. Here, we characterize the potential role for IAA biosynthesis in the physiology of these bacteria by characterizing the expression pattern of the ipdC promoter, analyzing an A. brasilense ipdC mutant using multiple physiological assays and characterizing the effect of I3P, which likely accumulates in the absence of ipdC and affects bacterial physiology. We found that the ipdC mutant derivative has a reduced growth rate and an altered physiology, including reduced translation activity as well as a more depolarized membrane potential compared to the parent strain. Similar effects could be recapitulated in the parent strain by exposing these cells to increasing concentrations of I3P, as well as other indole intermediates of IAA biosynthesis. Our results also indicate a protective role for IAA against the harmful effects of indole derivatives, with exogenous IAA restoring the membrane potential of cells exposed to indole derivatives for prolonged periods. These protective effects appeared to restore cell physiology, including in the wheat rhizosphere. Together, our data suggest that the IAA biosynthesis pathway plays a major role in A. brasilense physiology by maintaining membrane potential homeostasis and regulating translation, likely to mitigate the potential membrane-damaging effects of indoles that accumulate during growth under stressful conditions.IMPORTANCEIAA is widely synthesized in bacteria, particularly in soil and rhizosphere bacteria, where it functions as a phytohormone to modulate plant root architecture. IAA as a secondary metabolite has been shown to serve as a signaling molecule in several bacterial species, but the role of IAA biosynthesis in the physiology of the producing bacterium remains seldom explored. Results obtained here suggest that IAA serves to protect A. brasilense from the toxic effect of indoles, including metabolite biosynthetic precursors of IAA, on membrane potential homeostasis. Given the widespread production of IAA in soil bacteria, this protective effect of IAA may be conserved in diverse soil bacteria.

MibR and LibR are involved in the transcriptional regulation of the ipdC gene in Azospirillum brasilense Sp7

Azospirillum brasilense is a PGPR that produces the phytohormone IAA, a signaling molecule involved in bacteria-plant interaction processes. IAA biosynthesis in Azospirillum is mainly carried out via the IPyA pathway in which the enzyme phenylpyruvate decarboxylase encoded by the ipdC gene is the main. The promoter region of ipdC gene contains cis elements that are highly conserved among different Azospirillum strains. In this work, we identified two proteins that interact with the promoter region of the ipdC gene, named MibR and LibR that belong to the MarR and LuxR transcriptional regulators family, respectively. Both proteins have an HTH domain, and in the case of LibR, it has a REC domain, with aspartic acid residue conserved in positions 7, 8 and 54, this last as a possible phosphorylation target. To explore their participation in the regulation of the ipdC gene, mutants of libR, mibR, and libR-mibR double mutant were generated. The results showed a decrease in IAA biosynthesis that was related to the observed decrease in ipdC gene expression mostly in the doble mutant compared with the wild type. In this work we suggest that ipdC transcription is regulated by LibR and MibR, providing new findings insight into the mechanism employed by A. brasilense to control IAA biosynthesis.

Synthesis and Degradation of the Phytohormone Indole-3-Acetic Acid by the Versatile Bacterium Paraburkholderia xenovorans LB400 and Its Growth Promotion of Nicotiana tabacum Plant

Plant growth-promoting bacteria (PGPB) play a role in stimulating plant growth through mechanisms such as the synthesis of the phytohormone indole-3-acetic acid (IAA). The aims of this study were the characterization of IAA synthesis and degradation by the model aromatic-degrading bacterium Paraburkholderia xenovorans LB400, and its growth promotion of the Nicotiana tabacum plant. Strain LB400 was able to synthesize IAA (measured by HPLC) during growth in the presence of tryptophan and at least one additional carbon source; synthesis of anthranilic acid was also observed. RT-PCR analysis indicates that under these conditions, strain LB400 expressed the ipdC gene, which encodes indole-3-pyruvate decarboxylase, suggesting that IAA biosynthesis proceeds through the indole-3-pyruvate pathway. In addition, strain LB400 degraded IAA and grew on IAA as a sole carbon and energy source. Strain LB400 expressed the iacC and catA genes, which encode the α subunit of the aromatic-ring-hydroxylating dioxygenase in the IAA catabolic pathway and the catechol 1,2-dioxygenase, respectively, which may suggest a peripheral IAA pathway leading to the central catechol pathway. Notably, P. xenovorans LB400 promoted the growth of tobacco seedlings, increasing the number and the length of the roots. In conclusion, this study indicates that the versatile bacterium P. xenovorans LB400 is a PGPB.

Genetic and biochemical determinants in potentially toxic metals resistance and plant growth promotion in Rhizobium sp LBMP-C04

The association of bacteria resistant to potentially toxic metals (PTMs) with plants to remove, transfer, or stabilize these elements from the soil is an appropriate tool for phytoremediation processes in metal-contaminated environments. The objective of this study was to evaluate the potential of Rhizobium sp. LBMP-C04 for phytoremediation processes and plant growth promotion in metal-contaminated soils. Functional annotation allowed us to predict a variety of genes related to PTMs resistance and plant growth promotion in the bacterial genome. Resistance genes are mainly associated with DNA repair, and the import or export of metals in bacterial cells to maintain cell homeostasis. Genes that promote plant growth are related to mechanisms of osmotic stress tolerance, phosphate solubilization, nitrogen metabolism, biological nitrogen fixation, biofilm formation, heat shock responses, indole-3-acetic acid (IAA) biosynthesis, tryptophan, and organic acids metabolism. Biochemical tests indicated that Rhizobium sp. LBMP-C04 can solubilize calcium phosphate and produce siderophores and IAA in vitro in the presence of the PTMs Cd2+,Cu2+,Cr3+,Cr6+, Zn2+, and Ni2+. Results indicate the possibility of using Rhizobium sp. LBMP-C04 as a potentially efficient bacterium in phytoremediation processesin environments contaminated by PTMs and simultaneously promote plant growth.

Complete Genome Sequence of a Novel Azospirillum Strain TA Isolated from Western Siberia Chernevaya Taiga Soil

A whole genome sequence of a new strain of the nitrogen-fixing bacterium Azospirillum doebereinerae, known for its diverse plant growth-promoting bacteria (PGPB), was obtained for the first time. The strain, designated Azospirillum doebereinerae AT, was isolated during a soil analysis in the Chernevaya taiga of Western Siberia, a unique and fertile forest ecosystem known for its diverse plant growth-promoting bacteria (PGPB). The A. doebereinerae genome under study is fully assembled into seven circular molecules, none of which are unequivocally plasmids, with a total length of 6.94 Mb and a G + C content of 68.66%. A detailed phylogenomic analysis confirmed its placement within the genus Azospirillum, specifically closely related to A. doebereinerae GSF71T. Functional annotation revealed genes involved in nitrogen metabolism, highlighting the potential of strain TA as a biofertilizer and plant growth-promoting agent. The findings contribute to our understanding of the genomic diversity and metabolic potential of the Azospirillum genus, and they are of interest for further study in the field of comparative bacterial genomics, given the strain's multi-chromosomal genome structure.

Plant communication with rhizosphere microbes can be revealed by understanding microbial functional gene composition

Understanding rhizosphere microbial ecology is necessary to reveal the interplay between plants and associated microbial communities. The significance of rhizosphere-microbial interactions in plant growth promotion, mediated by several key processes such as auxin synthesis, enhanced nutrient uptake, stress alleviation, disease resistance, etc., is unquestionable and well reported in numerous literature. Moreover, rhizosphere research has witnessed tremendous progress due to the integration of the metagenomics approach and further shift in our viewpoint from taxonomic to functional diversity over the past decades. The microbial functional genes corresponding to the beneficial functions provide a solid foundation for the successful establishment of positive plant-microbe interactions. The microbial functional gene composition in the rhizosphere can be regulated by several factors, e.g., the nutritional requirements of plants, soil chemistry, soil nutrient status, pathogen attack, abiotic stresses, etc. Knowing the pattern of functional gene composition in the rhizosphere can shed light on the dynamics of rhizosphere microbial ecology and the strength of cooperation between plants and associated microbes. This knowledge is crucial to realizing how microbial functions respond to unprecedented challenges which are obvious in the Anthropocene. Unraveling how microbes-mediated beneficial functions will change under the influence of several challenges, requires knowledge of the pattern and composition of functional genes corresponding to beneficial functions such as biogeochemical functions (nutrient cycle), plant growth promotion, stress mitigation, etc. Here, we focus on the molecular traits of plant growth-promoting functions delivered by a set of microbial functional genes that can be useful to the emerging field of rhizosphere functional ecology.

Bacterial indole-3-acetic acid: A key regulator for plant growth, plant-microbe interactions, and agricultural adaptive resilience

Indole-3-acetic acid (IAA), a fundamental phytohormone categorized under auxins, not only influences plant growth and development but also plays a critical role in plant-microbe interactions. This study reviews the role of IAA in bacteria-plant communication, with a focus on its biosynthesis, regulation, and the subsequent effects on host plants. Bacteria synthesize IAA through multiple pathways, which include the indole-3-acetamide (IAM), indole-3-pyruvic acid (IPyA), and several other routes, whose full mechanisms remain to be fully elucidated. The production of bacterial IAA affects root architecture, nutrient uptake, and resistance to various abiotic stresses such as drought, salinity, and heavy metal toxicity, enhancing plant resilience and thus offering promising routes to sustainable agriculture. Bacterial IAA synthesis is regulated through complex gene networks responsive to environmental cues, impacting plant hormonal balances and symbiotic relationships. Pathogenic bacteria have adapted mechanisms to manipulate the host's IAA dynamics, influencing disease outcomes. On the other hand, beneficial bacteria utilize IAA to promote plant growth and mitigate abiotic stresses, thereby enhancing nutrient use efficiency and reducing dependency on chemical fertilizers. Advancements in analytical methods, such as liquid chromatography-tandem mass spectrometry, have improved the quantification of bacterial IAA, enabling accurate measurement and analysis. Future research focusing on molecular interactions between IAA-producing bacteria and host plants could facilitate the development of biotechnological applications that integrate beneficial bacteria to improve crop performance, which is essential for addressing the challenges posed by climate change and ensuring global food security. This integration of bacterial IAA producers into agricultural practice promises to revolutionize crop management strategies by enhancing growth, fostering resilience, and reducing environmental impact.

The role of plant growth promoting rhizobacteria in plant drought stress responses

Climate change has exacerbated the effects of abiotic stresses on plant growth and productivity. Drought is one of the most important abiotic stress factors that interfere with plant growth and development. Plant selection and breeding as well as genetic engineering methods used to improve crop drought tolerance are expensive and time consuming. Plants use a myriad of adaptative mechanisms to cope with the adverse effects of drought stress including the association with beneficial microorganisms such as plant growth promoting rhizobacteria (PGPR). Inoculation of plant roots with different PGPR species has been shown to promote drought tolerance through a variety of interconnected physiological, biochemical, molecular, nutritional, metabolic, and cellular processes, which include enhanced plant growth, root elongation, phytohormone production or inhibition, and production of volatile organic compounds. Therefore, plant colonization by PGPR is an eco-friendly agricultural method to improve plant growth and productivity. Notably, the processes regulated and enhanced by PGPR can promote plant growth as well as enhance drought tolerance. This review addresses the current knowledge on how drought stress affects plant growth and development and describes how PGPR can trigger plant drought stress responses at the physiological, morphological, and molecular levels.

Biosynthetic Pathways and Functions of Indole-3-Acetic Acid in Microorganisms

Indole-3-acetic acid (IAA) belongs to the family of auxin indole derivatives. IAA regulates almost all aspects of plant growth and development, and is one of the most important plant hormones. In microorganisms too, IAA plays an important role in growth, development, and even plant interaction. Therefore, mechanism studies on the biosynthesis and functions of IAA in microorganisms can promote the production and utilization of IAA in agriculture. This mini-review mainly summarizes the biosynthesis pathways that have been reported in microorganisms, including the indole-3-acetamide pathway, indole-3-pyruvate pathway, tryptamine pathway, indole-3-acetonitrile pathway, tryptophan side chain oxidase pathway, and non-tryptophan dependent pathway. Some pathways interact with each other through common key genes to constitute a network of IAA biosynthesis. In addition, functional studies of IAA in microorganisms, divided into three categories, have also been summarized: the effects on microorganisms, the virulence on plants, and the beneficial impacts on plants.

Graphene oxide influence in soil bacteria is dose dependent and changes at osmotic stress: growth variation, oxidative damage, antioxidant response, and plant growth promotion traits of a Rhizobium strain

Climate change events, such as drought, are increasing and soil bacteria can be severely affected. Moreover, the accumulation of emerging pollutants is expected to rapidly increase, and their impact on soil organisms, their interactions, and the services they provide is poorly known. The use of graphene oxide (GO) has been increasing due to its enormous potential for application in several areas and it is expected that concentration in soil will increase in the future, potentially causing disturbances in soil microorganisms not yet identified.Here we show the effects that GO nanosheets can cause on soil bacteria, in particular those that promote plant growth, in control and 10% polyethylene glycol (PEG) conditions. Low concentrations of GO nanosheets did not affect the growth of Rhizobium strain E20-8, but under osmotic stress (PEG) GO decreased bacterial growth even at lower concentrations. GO caused oxidative stress, with antioxidant mechanisms being induced to restrain damage, effectively at lower concentrations, but less effective at higher concentrations, and oxidative damage overcame. Under osmotic stress, alginate and glycine betaine osmoregulated the bacteria. Simultaneous exposure to PEG and GO induced oxidative damage. Plant growth promotion traits (indole acetic acid and siderophores production) were increased by osmotic stress and GO did not disturb these abilities. In the context of climate change, our findings might be relevant as they can form the premises for the implementation of crop production methodologies adapted to the new prevailing conditions, which include the presence of nanoparticles in the soil and more frequent and severe drought.

Enhancing rhizoremediation of petroleum hydrocarbons through bioaugmentation with a plant growth-promoting bacterial consortium

The slow rate of natural attenuation of organic pollutants, together with unwanted environmental impacts of traditional remediation strategies, has necessitated the exploration of plant-microbe systems for enhanced bioremediation applications. The identification of microorganisms capable of promoting rhizoremediation through both plant growth-promoting and hydrocarbon-degrading processes is crucial to the success and adoption of plant-based remediation techniques. In this study, through successive enrichments of soil samples from a historic oil-contaminated site in Wietze, Germany, we isolated a plant growth-promoting and hydrocarbon-degrading bacterial consortium dominated by Alphaproteobacteria. In microcosm experiments involving Medicago sativa L. and the isolated bacterial consortium, we examined the ability of the consortium to enhance rhizoremediation of petroleum hydrocarbons. The inoculation of M. sativa with the consortium resulted in 66% increase in plant biomass, and achieved a 91% reduction in diesel fuel hydrocarbon concentrations in the soil within 60 days. Metagenome analysis led to the identification of genes and taxa putatively involved in these processes. The majority of the coding DNA sequences associated with plant growth promotion and hydrocarbon degradation in this study were affiliated to Acidocella aminolytica and Acidobacterium capsulatum indicating their potential for biotechnological applications in the rhizoremediation of sites contaminated by petroleum-derived organic pollutants.

Plant Growth Promotion Diversity in Switchgrass-Colonizing, Diazotrophic Endophytes

Endophytic nitrogen-fixing (diazotrophic) bacteria are essential members of the microbiome of switchgrass (Panicum virgatum), considered to be an important commodity crop in bioenergy production. While endophytic diazotrophs are known to provide fixed atmospheric nitrogen to their host plant, there are many other plant growth-promoting (PGP) capabilities of these organisms to be demonstrated. The diversity of PGP traits across different taxa of switchgrass-colonizing endophytes is understudied, yet critical for understanding endophytic function and improving cultivation methods of important commodity crops. Here, we present the isolation and characterization of three diazotrophic endophytes: Azospirillum agricola R1C, Klebsiella variicola F10Cl, and Raoultella terrigena R1Gly. Strains R1C and F10Cl were isolated from switchgrass and strain R1Gly, while isolated from tobacco, is demonstrated herein to colonize switchgrass. Each strain exhibited highly diverse genomic and phenotypic PGP capabilities. Strain F10Cl and R1Gly demonstrated the highest functional similarity, suggesting that, while endophyte community structure may vary widely based on host species, differences in functional diversity are not a clearly delineated. The results of this study advance our understanding of diazotrophic endophyte diversity, which will allow us to design robust strategies to improve cultivation methods of many economically important commodity crops.

Characterization of cellular, biochemical and genomic features of the diazotrophic plant growth-promoting bacterium Azospirillum sp. UENF-412522, a novel member of the Azospirillum genus

Given their remarkable beneficial effects on plant growth, several Azospirillum isolates currently integrate the formulations of various commercial inoculants. Our research group isolated a new strain, Azospirillum sp. UENF-412522, from passion fruit rhizoplane. This isolate uses carbon sources that are partially distinct from closely-related Azospirillum isolates. Scanning electron microscopy analysis and population counts demonstrate the ability of Azospirillum sp. UENF-412522 to colonize the surface of passion fruit roots. In vitro assays demonstrate the ability of Azospirillum sp. UENF-412522 to fix atmospheric nitrogen, to solubilize phosphate and to produce indole-acetic acid. Passion fruit plantlets inoculated with Azospirillum sp. UENF-41255 showed increased shoot and root fresh matter by 13,8% and 88,6% respectively, as well as root dry matter by 61,4%, further highlighting its biotechnological potential for agriculture. We sequenced the genome of Azospirillum sp. UENF-412522 to investigate the genetic basis of its plant-growth promotion properties. We identified the key nif genes for nitrogen fixation, the complete PQQ operon for phosphate solubilization, the acdS gene that alleviates ethylene effects on plant growth, and the napCAB operon, which produces nitrite under anoxic conditions. We also found several genes conferring resistance to common soil antibiotics, which are critical for Azospirillum sp. UENF-412522 survival in the rhizosphere. Finally, we also assessed the Azospirillum pangenome and highlighted key genes involved in plant growth promotion. A phylogenetic reconstruction of the genus was also conducted. Our results support Azospirillum sp. UENF-412522 as a good candidate for bioinoculant formulations focused on plant growth promotion in sustainable systems.

Elucidating key plant growth-promoting (PGPR) traits in Burkholderia sp. Nafp2/4-1b (=SARCC-3049) using gnotobiotic assays and whole-genome-sequence analysis

Burkholderia sp. Nafp2/4-1b (=SARCC-3049) is a plant growth-promoting rhizobacteria (PGPR) initially isolated from the rhizosphere of pristine grassland in South Africa, and its ability to enhance growth was previously evaluated on maize (Zea mays L.). Here, the bacterium was tested with the aim of investigating its role in improving the nodulation and growth of the forage legume lucerne (Medicago sativa L.) when it is co-inoculated with the rhizobial symbionts of this legume in the glasshouse. When the co-inoculation resulted in a statistically significant (P = 0·05) increase in the number of nodules and improved plant biomass compared with single inoculation, we sequenced and analysed its genome to gain a better understanding of the genetic determinants responsible for the observed PGPR traits. The Illumina HiSeq 2500-sequenced genome resulted in 92 scaffolds, with an N50 of 322 407 bp, a total draft genome size of 7 788 045 bp and GC content of 66·2%. Analysis of the genome sequence confirmed the presence of a number of essential genes that code for various PGPR traits. The main plant beneficial genes associated with PGPR traits in Burkholderia sp. Nafp2/4-1b include pyoverdine siderophores biosynthesis gene (PvdF); acdS that codes for 1-aminocyclopropane-1-carboxylate (ACC) deaminase; the tryptophan synthase genes involved in auxin biosynthesis (TSA1, TSB1) and the pqqABCDE operon related to phosphate solubilization. This study generated valuable information on the potential of the PGPR Burkholderia sp. strain Nafp2/4-1b as an effective commercial inoculant, which warrants further formulation and field application studies before developing it into a low cost, environmentally safe and effective biofertilizer.

The auxin-producing Bacillus thuringiensis RZ2MS9 promotes the growth and modifies the root architecture of tomato (Solanum lycopersicum cv. Micro-Tom)

Strains of Bacillus thuringiensis (Bt) are commonly commercialized as bioinoculants for insect pest control, but their benefits go beyond their insecticidal property: they can act as plant growth-promoters. Auxins play a major role in the plant growth promotion. However, the mechanism of auxin production by the Bacilli group, and more specifically by Bt strains, is unclear. In previous work, the plant growth-promoting rhizobacterium (PGPR) B. thuringiensis strain RZ2MS9 increased the corn roots. This drew our attention to the strain's auxin production trait, earlier detected in vitro. Here, we demonstrate that in its genome, RZ2MS9 harbours the complete set of genes required in two pathways that are used for Indole acetic acid (IAA) production. We also detected that the strain produces almost five times more IAA during the stationary phase. The bacterial application increased the shoot dry weight of the Micro-Tom (MT) tomato by 24%. The application also modified MT root architecture, with an increase of 26% in the average lateral root length and inhibition of the axial root. At the cellular level, RZ2MS9-treated MT plants presented elongated root cortical cells with intensified mitotic activity. Altogether, these are the best characterized auxin-associated phenotypes. Besides that, no growth alteration was detected in the auxin-insensitive diageotropic (dgt) plants either with or without the RZ2MS9 inoculation. Our results suggest that auxins play an important role in the ability of B. thuringiensis RZ2MS9 to promote MT growth and provide a better understanding of the auxin production mechanism by a Bt strain.

Beneficial Plant-Associated Microorganisms From Semiarid Regions and Seasonally Dry Environments: A Review

Semiarid regions are apparently low biodiversity environments; however, these environments may host a phylogenetically diverse microbial community associated with plants. Their microbial inhabitants are often recruited to withstand stressful settings and improve plant growth under harsh conditions. Thus, plant-associated microorganisms isolated from semiarid and seasonally dry environments will be detailed in the present review, focusing on plant growth promotion potential and the microbial ability to alleviate plant abiotic stress. Initially, we explored the role of microbes from dry environments around the world, and then, we focused on seasonally dry Brazilian biomes, the Caatinga and the Cerrado. Cultivable bacteria from semiarid and seasonally dry environments have demonstrated great plant growth promotion traits such as plant hormone production, mobilization of insoluble nutrients, and mechanisms related to plant abiotic stress alleviation. Several of these isolates were able to improve plant growth under stressful conditions commonly present in typical semiarid regions, such as high salinity and drought. Additionally, we highlight the potential of plants highly adapted to seasonal climates from the Caatinga and Cerrado biomes as a suitable pool of microbial inoculants to maintain plant growth under abiotic stress conditions. In general, we point out the potential for the exploitation of new microbial inoculants from plants growing in dry environments to ensure a sustainable increase in agricultural productivity in a future climate change scenario.

Transcriptome Profiles Reveal the Growth-Promoting Mechanisms of Paenibacillus polymyxa YC0136 on Tobacco (Nicotiana tabacum L.)

Paenibacillus polymyxa is an important member of the plant growth-promoting rhizobacteria. P. polymyxa YC0136 inoculation had beneficial effect on growth promotion and biological control of tobacco (Nicotiana tabacum L.) under field conditions. This study aimed to reveal the growth-promoting mechanisms of strain YC0136. In growth-promotion assays, tobacco plant height was increased by 8.42% and 8.25% at 60 and 90 days, respectively, after inoculation with strain YC0136. Strain YC0136 also promoted the accumulation of tobacco biomass in varying degrees. Following inoculation with strain YC0136, 3,525 and 4,368 tobacco genes were up-regulated and down-regulated, respectively. Strain YC0136 induced the expression of plant hormone-related genes in tobacco, including auxin, cytokinin, and gibberellin, as well as transcription factors related to stress resistance such as WRKY and MYB. In addition, strain YC0136 induced the up-regulation of genes in the phenylpropanoid biosynthesis pathway by 1.51-4.59 times. Interaction with tobacco also induced gene expression changes in strain YC0136, with 286 and 223 genes up-regulated and down-regulated, respectively. Tobacco interaction induced up-regulation of the ilvB gene related to auxin biosynthesis in strain YC0136 by 1.72 times and induced expression of some nutrient transport genes. This study contributes to our understanding of the growth-promoting mechanisms of strain YC0136 on tobacco and provides a theoretical basis for the application of P. polymyxa YC0136 as a biological fertilizer.

Indole-3-acetic acid biosynthesis and its regulation in plant-associated bacteria

Numerous studies have reported the stimulation of plant growth following inoculation with an IAA-producing PGPB. However, the specific mode of IAA production by the PGPB is rarely elucidated. In part, this is due to the overwhelming complexity of IAA biosynthesis and regulation. The promiscuity of the enzymes implicated in IAA biosynthesis adds another element of complexity when attempting to decipher their role in IAA biosynthesis. To date, the majority of research on IAA biosynthesis describes three separate pathways classified in terms of their intermediates-indole acetonitrile (IAN), indole acetamide (IAM), and indole pyruvic acid (IPA). Each of these pathways is mediated by a set of enzymes, many of which are traditionally assumed to exist for that specific catalytic role. This lends the possibility of missing other, novel, enzymes that may also incidentally serve that function. Some of these pathways are constitutively expressed, while others are inducible. Some enzymes involved in IAA biosynthesis are known to be regulated by IAA or by IAA precursors, as well as by a multitude of environmental cues. This review aims to provide an update to our current understanding of the biosynthesis and regulation of IAA in bacteria. KEY POINTS: • IAA produced by PGPB improves bacterial stress tolerance and promotes plant growth. • Bacterial IAA biosynthesis is convoluted; multiple interdependent pathways. • Biosynthesis of IAA is regulated by IAA, IAA-precursors, and environmental factors.

Indole-3-Acetic Acid in Burkholderia pyrrocinia JK-SH007: Enzymatic Identification of the Indole-3-Acetamide Synthesis Pathway

Burkholderia pyrrocinia JK-SH007 is a plant growth-promoting bacteria (PGPB), that can promote the growth of poplar and other trees, and, production of the plant hormone indole-3-acetic acid (IAA) is one of the reasons for this effect. Therefore, the aims of this study were to evaluate the effect of the external environment on the synthesis of IAA by B. pyrrocinia JK-SH007 and to perform a functional analysis of its IAA synthesis pathway. In this study, IAA and its synthetic intermediates indole-3-acetamide (IAM), indole-3-pyruvic acid (IPyA), tryptamine (TAM), and indole-3-acetonitrile (IAN) were detected in B. pyrrocinia JK-SH007 fermentation broth by high-performance liquid chromatography and tandem mass spectrometry (HPLC-MS/MS), and these indolic compounds were also found in the cell-free extraction of B. pyrrocinia JK-SH007, but the genomic analysis of B. pyrrocinia JK-SH007 indicated that IAA biosynthesis was mainly through the IAM and TAM pathways. The effects of L-tryptophan (L-Trp), temperature and pH on the synthesis of IAA were investigated, and the results showed that L-Trp exerted a significant effect on IAA synthesis and that 37°C and pH 7 were the optimal conditions IAA production by B. pyrrocinia JK-SH007. In addition, the protein expression of tryptophan 2-monooxygenase and indoleacetamide hydrolase, which are the key enzymes of the indole acetamide-mediated IAA synthesis pathway, was analyzed, and their activity was verified by substrate feeding experiments. The results revealed the existence of an IAA synthesis pathway mediated by IAM and indicated that this pathway plays a role in B. pyrrocinia JK-SH007. This study lays the foundation for further exploration of the specific pathway and mechanism of IAA synthesis in B. pyrrocinia JK-SH007.

Genome sequencing and assessment of plant growth-promoting properties of a Serratia marcescens strain isolated from vermicompost

Background

Plant-bacteria associations have been extensively studied for their potential in increasing crop productivity in a sustainable manner. Serratia marcescens is a species of Enterobacteriaceae found in a wide range of environments, including soil.

Results

Here we describe the genome sequencing and assessment of plant growth-promoting abilities of S. marcescens UENF-22GI, a strain isolated from mature cattle manure vermicompost. In vitro, S. marcescens UENF-22GI is able to solubilize P and Zn, to produce indole compounds (likely IAA), to colonize hyphae and counter the growth of two phytopathogenic fungi. Inoculation of maize with this strain remarkably increased seedling growth and biomass under greenhouse conditions. The S. marcescens UENF-22GI genome has 5 Mb, assembled in 17 scaffolds comprising 4662 genes (4528 are protein-coding). No plasmids were identified. S. marcescens UENF-22GI is phylogenetically placed within a clade comprised almost exclusively of non-clinical strains. We identified genes and operons that are likely responsible for the interesting plant-growth promoting features that were experimentally described. The S. marcescens UENF-22GI genome harbors a horizontally-transferred genomic island involved in antibiotic production, antibiotic resistance, and anti-phage defense via a novel ADP-ribosyltransferase-like protein and possible modification of DNA by a deazapurine base, which likely contributes to its competitiveness against other bacteria.

Conclusions

Collectively, our results suggest that S. marcescens UENF-22GI is a strong candidate to be used in the enrichment of substrates for plant growth promotion or as part of bioinoculants for agriculture.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5130-y) contains supplementary material, which is available to authorized users.

Players over the Surface: Unraveling the Role of Exopolysaccharides in Zinc Biosorption by Fluorescent Pseudomonas Strain Psd

Fluorescent Pseudomonas strain Psd is a soil isolate, possessing multiple plant growth promoting (PGP) properties and biocontrol potential. In addition, the strain also possesses high Zn²⁺ biosorption capability. In this study, we have investigated the role exopolysaccharides (EPS) play in Zn²⁺ biosorption. We have identified that alginates are the prime components contributing to Zn²⁺ biosorption. Deletion of the alg8 gene, which codes for a sub-unit of alginate polymerase, led to a significant reduction in EPS production by the organism. We have also demonstrated that the increased alginate production in response to Zn²⁺ exposure leads to improved biofilm formation by the strain. In the alg8 deletion mutant, however, biofilm formation was severely compromised. Further, we have studied the functional implications of Zn²⁺ biosorption by Pseudomonas strain Psd by demonstrating the effect on the PGP and biocontrol potential of the strain.

Low nitrogen stress stimulating the indole-3-acetic acid biosynthesis of Serratia sp. ZM is vital for the survival of the bacterium and its plant growth-promoting characteristic

Serratia sp. ZM is a plant growth-promoting (PGP) bacterial strain isolated from the rhizospheric soil of Populus euphratica in northwestern China. In this study, low nitrogen supply significantly stimulated the production of indole-3-acetic acid (IAA) in Serratia sp.ZM. The inoculation of the bacterium to wheat seedlings improved plant growth compared with the uninoculated group, and the stimulating effect was more prominent under low nitrogen stress. Inactivation of the predicted key gene in the IAA biosynthesis pathway impaired IAA production and significantly hampered mutant growth in poor medium. Furthermore, the IAA-deficient mutant lost the PGP effect under either normal or low nitrogen conditions in plant experiments. This study revealed the significant impact of environmental nitrogen levels on IAA production in the PGP strain and the vital effect of IAA on resistance physiology of both the bacterium and host plant. The characteristics of Serratia sp. ZM also indicated its application potential as a biofertilizer for plants, especially those suffering from poor nitrogen soil.

Mitogen-Activated Protein Kinase 6 and Ethylene and Auxin Signaling Pathways Are Involved in Arabidopsis Root-System Architecture Alterations by Trichoderma atroviride

Trichoderma atroviride is a symbiotic fungus that interacts with roots and stimulates plant growth and defense. Here, we show that Arabidopsis seedlings cocultivated with T. atroviride have an altered root architecture and greater biomass compared with axenically grown seedlings. These effects correlate with increased activity of mitogen-activated protein kinase 6 (MPK6). The primary roots of mpk6 mutants showed an enhanced growth inhibition by T. atroviride when compared with wild-type (WT) plants, while T. atroviride increases MPK6 activity in WT roots. It was also found that T. atroviride produces ethylene (ET), which increases with l-methionine supply to the fungal growth medium. Analysis of growth and development of WT seedlings and etr1, ein2, and ein3 ET-related Arabidopsis mutants indicates a role for ET in root responses to the fungus, since etr1 and ein2 mutants show defective root-hair induction and enhanced primary-root growth inhibition when cocultivated with T. atroviride. Increased MPK6 activity was evidenced in roots of ctr1 mutants, which correlated with repression of primary root growth, thus connecting MPK6 signaling with an ET response pathway. Auxin-inducible gene expression analysis using the DR5:uidA reporter construct further revealed that ET affects auxin signaling through the central regulator CTR1 and that fungal-derived compounds, such as indole-3-acetic acid and indole-3-acetaldehyde, induce MPK6 activity. Our results suggest that T. atroviride likely alters root-system architecture modulating MPK6 activity and ET and auxin action.

Bacterial cellular engineering by genome editing and gene silencing

Genome editing is an important technology for bacterial cellular engineering, which is commonly conducted by homologous recombination-based procedures, including gene knockout (disruption), knock-in (insertion), and allelic exchange. In addition, some new recombination-independent approaches have emerged that utilize catalytic RNAs, artificial nucleases, nucleic acid analogs, and peptide nucleic acids. Apart from these methods, which directly modify the genomic structure, an alternative approach is to conditionally modify the gene expression profile at the posttranscriptional level without altering the genomes. This is performed by expressing antisense RNAs to knock down (silence) target mRNAs in vivo. This review describes the features and recent advances on methods used in genomic engineering and silencing technologies that are advantageously used for bacterial cellular engineering.

Indole-3-acetic acid in plant-microbe interactions

Indole-3-acetic acid (IAA) is an important phytohormone with the capacity to control plant development in both beneficial and deleterious ways. The ability to synthesize IAA is an attribute that many bacteria including both plant growth-promoters and phytopathogens possess. There are three main pathways through which IAA is synthesized; the indole-3-pyruvic acid, indole-3-acetamide and indole-3-acetonitrile pathways. This chapter reviews the factors that effect the production of this phytohormone, the role of IAA in bacterial physiology and in plant-microbe interactions including phytostimulation and phytopathogenesis.

Biotechnological applications of mobile group II introns and their reverse transcriptases: gene targeting, RNA-seq, and non-coding RNA analysis

Mobile group II introns are bacterial retrotransposons that combine the activities of an autocatalytic intron RNA (a ribozyme) and an intron-encoded reverse transcriptase to insert site-specifically into DNA. They recognize DNA target sites largely by base pairing of sequences within the intron RNA and achieve high DNA target specificity by using the ribozyme active site to couple correct base pairing to RNA-catalyzed intron integration. Algorithms have been developed to program the DNA target site specificity of several mobile group II introns, allowing them to be made into ‘targetrons.’ Targetrons function for gene targeting in a wide variety of bacteria and typically integrate at efficiencies high enough to be screened easily by colony PCR, without the need for selectable markers. Targetrons have found wide application in microbiological research, enabling gene targeting and genetic engineering of bacteria that had been intractable to other methods. Recently, a thermostable targetron has been developed for use in bacterial thermophiles, and new methods have been developed for using targetrons to position recombinase recognition sites, enabling large-scale genome-editing operations, such as deletions, inversions, insertions, and ‘cut-and-pastes’ (that is, translocation of large DNA segments), in a wide range of bacteria at high efficiency. Using targetrons in eukaryotes presents challenges due to the difficulties of nuclear localization and sub-optimal magnesium concentrations, although supplementation with magnesium can increase integration efficiency, and directed evolution is being employed to overcome these barriers. Finally, spurred by new methods for expressing group II intron reverse transcriptases that yield large amounts of highly active protein, thermostable group II intron reverse transcriptases from bacterial thermophiles are being used as research tools for a variety of applications, including qRT-PCR and next-generation RNA sequencing (RNA-seq). The high processivity and fidelity of group II intron reverse transcriptases along with their novel template-switching activity, which can directly link RNA-seq adaptor sequences to cDNAs during reverse transcription, open new approaches for RNA-seq and the identification and profiling of non-coding RNAs, with potentially wide applications in research and biotechnology.

Plant growth-promoting rhizobacteria and root system functioning

The rhizosphere supports the development and activity of a huge and diversified microbial community, including microorganisms capable to promote plant growth. Among the latter, plant growth-promoting rhizobacteria (PGPR) colonize roots of monocots and dicots, and enhance plant growth by direct and indirect mechanisms. Modification of root system architecture by PGPR implicates the production of phytohormones and other signals that lead, mostly, to enhanced lateral root branching and development of root hairs. PGPR also modify root functioning, improve plant nutrition and influence the physiology of the whole plant. Recent results provided first clues as to how PGPR signals could trigger these plant responses. Whether local and/or systemic, the plant molecular pathways involved remain often unknown. From an ecological point of view, it emerged that PGPR form coherent functional groups, whose rhizosphere ecology is influenced by a myriad of abiotic and biotic factors in natural and agricultural soils, and these factors can in turn modulate PGPR effects on roots. In this paper, we address novel knowledge and gaps on PGPR modes of action and signals, and highlight recent progress on the links between plant morphological and physiological effects induced by PGPR. We also show the importance of taking into account the size, diversity, and gene expression patterns of PGPR assemblages in the rhizosphere to better understand their impact on plant growth and functioning. Integrating mechanistic and ecological knowledge on PGPR populations in soil will be a prerequisite to develop novel management strategies for sustainable agriculture.

Microbial inoculants and their impact on soil microbial communities: a review

The knowledge of the survival of inoculated fungal and bacterial strains in field and the effects of their release on the indigenous microbial communities has been of great interest since the practical use of selected natural or genetically modified microorganisms has been developed. Soil inoculation or seed bacterization may lead to changes in the structure of the indigenous microbial communities, which is important with regard to the safety of introduction of microbes into the environment. Many reports indicate that application of microbial inoculants can influence, at least temporarily, the resident microbial communities. However, the major concern remains regarding how the impact on taxonomic groups can be related to effects on functional capabilities of the soil microbial communities. These changes could be the result of direct effects resulting from trophic competitions and antagonistic/synergic interactions with the resident microbial populations, or indirect effects mediated by enhanced root growth and exudation. Combination of inoculants will not necessarily produce an additive or synergic effect, but rather a competitive process. The extent of the inoculation impact on the subsequent crops in relation to the buffering capacity of the plant-soil-biota is still not well documented and should be the focus of future research.

A targetron system for gene targeting in thermophiles and its application in Clostridium thermocellum

Background

Targetrons are gene targeting vectors derived from mobile group II introns. They consist of an autocatalytic intron RNA (a “ribozyme”) and an intron-encoded reverse transcriptase, which use their combined activities to achieve highly efficient site-specific DNA integration with readily programmable DNA target specificity.

Methodology/Principal Findings

Here, we used a mobile group II intron from the thermophilic cyanobacterium Thermosynechococcus elongatus to construct a thermotargetron for gene targeting in thermophiles. After determining its DNA targeting rules by intron mobility assays in Escherichia coli at elevated temperatures, we used this thermotargetron in Clostridium thermocellum, a thermophile employed in biofuels production, to disrupt six different chromosomal genes (cipA, hfat, hyd, ldh, pta, and pyrF). High integration efficiencies (67–100% without selection) were achieved, enabling detection of disruptants by colony PCR screening of a small number of transformants. Because the thermotargetron functions at high temperatures that promote DNA melting, it can recognize DNA target sequences almost entirely by base pairing of the intron RNA with less contribution from the intron-encoded protein than for mesophilic targetrons. This feature increases the number of potential targetron-insertion sites, while only moderately decreasing DNA target specificity. Phenotypic analysis showed that thermotargetron disruption of the genes encoding lactate dehydrogenase (ldh; Clo1313_1160) and phosphotransacetylase (pta; Clo1313_1185) increased ethanol production in C. thermocellum by decreasing carbon flux toward lactate and acetate.

Conclusions/Significance

Thermotargetron provides a new, rapid method for gene targeting and genetic engineering of C. thermocellum, an industrially important microbe, and should be readily adaptable for gene targeting in other thermophiles.

Activity, distribution and function of indole-3-acetic acid biosynthetic pathways in bacteria

The capacity to produce the phytohormone indole-3-acetic acid (IAA) is widespread among bacteria that inhabit diverse environments such as soils, fresh and marine waters, and plant and animal hosts. Three major pathways for bacterial IAA synthesis have been characterized that remove the amino and carboxyl groups from the α-carbon of tryptophan via the intermediates indolepyruvate, indoleacetamide, or indoleacetonitrile; the oxidized end product IAA is typically secreted. The enzymes in these pathways often catabolize a broad range of substrates including aromatic amino acids and in some cases the branched chain amino acids. Moreover, expression of some of the genes encoding key IAA biosynthetic enzymes is induced by all three aromatic amino acids. The broad distribution and substrate specificity of the enzymes suggests a role for these pathways beyond plant-microbe interactions in which bacterial IAA has been best studied.

The ethylene pathway contributes to root hair elongation induced by the beneficial bacteria Phyllobacterium brassicacearum STM196

In Arabidopsis roots, some epidermal cells differentiate into root hair cells. Auxin regulates root hair positioning, while ethylene controls cell elongation. Phyllobacterium brassicacearum STM196, a beneficial strain of plant growth promoting rhizobacteria (PGPR) isolated from the roots of field-grown oilseed rape, stimulates root hair elongation in Arabidopsis thaliana seedlings. We investigated the role of ethylene in the response of root hair cells to STM196 inoculation. While we could not detect a significant increase in ethylene biosynthesis, we could detect a slight activation of the ethylene signalling pathway. Consistent with this, an exhaustive survey of the root hair elongation response of mutants and transgenic lines affected in the ethylene pathway showed contrasting root hair sensitivities to STM196. We propose that local ethylene emission contributes to STM196-induceed root hair elongation.

Characterization of nitrogen-fixing bacteria isolated from field-grown barley, oat, and wheat

Diazotrophic bacteria were isolated from the rhizosphere of field-grown Triticum aestivum, Hordeum vulgare, and Avena sativa grown in various regions of Greece. One isolate, with the highest nitrogen-fixation ability from each of the eleven rhizospheres, was selected for further characterisation. Diazotrophic strains were assessed for plant-growth-promoting traits such as indoleacetic acid production and phosphate solubilisation. The phylogenies of 16S rRNA gene of the selected isolates were compared with those based on dnaK and nifH genes. The constructed trees indicated that the isolates were members of the species Azospirillum brasilense, Azospirillum zeae, and Pseudomonas stutzeri. Furthermore, the ipdC gene was detected in all A. brasilence and one A. zeae isolates. The work presented here provides the first molecular genetic evidence for the presence of culturable nitrogen-fixing P. stutzeri and A. zeae associated with field-grown A. sativa and H. vulgare in Greece.

Genomic insights into the versatility of the plant growth-promoting bacterium Azospirillum amazonense

BACKGROUND

The species Azospirillum amazonense belongs to a well-known genus of plant growth-promoting bacteria. This bacterium is found in association with several crops of economic importance; however, there is a lack of information on its physiology. In this work, we present a comprehensive analysis of the genomic features of this species.

RESULTS

Genes of A. amazonense related to nitrogen/carbon metabolism, energy production, phytohormone production, transport, quorum sensing, antibiotic resistance, chemotaxis/motility and bacteriophytochrome biosynthesis were identified. Noteworthy genes were the nitrogen fixation genes and the nitrilase gene, which could be directly implicated in plant growth promotion, and the carbon fixation genes, which had previously been poorly investigated in this genus. One important finding was that some A. amazonense genes, like the nitrogenase genes and RubisCO genes, were closer phylogenetically to Rhizobiales members than to species of its own order.

CONCLUSION

The species A. amazonense presents a versatile repertoire of genes crucial for its plant-associated lifestyle.

The genetic diversity of culturable nitrogen-fixing bacteria in the rhizosphere of wheat

A total of 17 culturable nitrogen-fixing bacterial strains associated with the roots of wheat growing in different regions of Greece were isolated and characterized for plant-growth-promoting traits such as auxin production and phosphate solubilization. The phylogenetic position of the isolates was first assessed by the analysis of the PCR-amplified 16S rRNA gene. The comparative sequence analysis and phylogenetic analysis based on 16S rRNA gene sequences show that the isolates recovered in this study are grouped with Azospirillum brasilense, Azospirillum zeae, and Pseudomonas stutzeri. The diazotrophic nature of all isolates was confirmed by amplification of partial nifH gene sequences. The phylogenetic tree based on nifH gene sequences is consistent with 16S rRNA gene phylogeny. The isolates belonging to Azospirillum species were further characterized by examining the partial dnaK gene phylogenetic tree. Furthermore, it was demonstrated that the ipdC gene was present in all Azospirillum isolates, suggesting that auxin is mainly synthesized via the indole-3-pyruvate pathway. Although members of P. stutzeri and A. zeae are known diazotrophic bacteria, to the best of our knowledge, this is the first report of isolation and characterization of strains belonging to these bacterial genera associated with wheat.

Phenazine-1-carboxylic acid is a more important contributor to biocontrol Fusarium oxysporum than pyrrolnitrin in Pseudomonas fluorescens strain Psd

Phenazines and pyrrolnitrin (Prn) are broad spectrum antibiotics, produced by bacteria, more so by the biocontrol strains to kill the phytopathogens in soil. We have studied a rhizospheric soil isolate of Pseudomonas fluorescens strain Psd producing both phenazine-1-carboxylic acid (PCA) and Prn. In order to study the contribution of these antibiotics, the phzD and prnC genes involved in PCA and Prn biosynthesis, were disrupted in a site-specific manner using a group II intron-based Targetron gene-knockout system, and gene disruption followed by allelic exchange through homologous recombination, respectively. The resulting knockout strains Psdphz122s-34 and PsdprnC::gen did not produce PCA and Prn, respectively. In fact, by combining these two strategies, a Psdphz122s-34prnC::gen double mutant could also be generated. Identification and lack of PCA production was corroborated by HPLC/APCI-MS analysis, and TLC detection for both the antibiotics in these mutants. Loss of antifungal activity against the phytopathogenic fungus Fusarium oxysporum was observed using in vitro growth assays on plates or growth chamber experiments with tomato seedling on an artificial substrate. Based on the characterization of these gene knockout mutants, we propose that PCA and Prn have a major role in antifungal activity of strain Psd.

Targeted gene disruption in Francisella tularensis by group II introns

Francisella tularensis is a highly infectious Gram-negative bacterium that is the causative agent of tularemia. Very little is known about the molecular mechanisms responsible for F. tularensis virulence, in part due to the paucity of genetic tools available for the study of F. tularensis. We have developed a gene knockout system for F. tularensis that utilizes retargeted mobile group II introns, or "targetrons". These targetrons disrupt both single and duplicated target genes at high efficiency in three different F. tularensis subspecies. Here we describe in detail the targetron-based method for insertional mutagenesis of F. tularensis genes, which should facilitate a better understanding of F. tularensis pathogenesis. Group II introns can be adapted to inactivate genes in bacteria for which few genetic tools exist, thus providing a powerful tool to study the genetic basis of bacterial pathogenesis.

EcI5, a group IIB intron with high retrohoming frequency: DNA target site recognition and use in gene targeting

We find that group II intron EcI5, a subclass CL/IIB1 intron from an Escherichia coli virulence plasmid, is highly active in retrohoming in E. coli. Both full-length EcI5 and an EcI5-DeltaORF intron with the intron-encoded protein expressed separately from the same donor plasmid retrohome into a recipient plasmid target site at substantially higher frequencies than do similarly configured Lactococcus lactis Ll.LtrB introns. A comprehensive view of DNA target site recognition by EcI5 was obtained from selection experiments with donor and recipient plasmid libraries in which different recognition elements were randomized. These experiments suggest that EcI5, like other mobile group II introns, recognizes DNA target sequences by using both the intron-encoded protein and base-pairing of the intron RNA, with the latter involving EBS1, EBS2, and EBS3 sequences characteristic of class IIB introns. The intron-encoded protein appears to recognize a small number of bases flanking those recognized by the intron RNA, but their identity is different than in previously characterized group II introns. A computer algorithm based on the empirically determined DNA recognition rules enabled retargeting of EcI5 to integrate specifically at 10 different sites in the chromosomal lacZ gene at frequencies up to 98% without selection. Our findings provide insight into modes of DNA target site recognition used by mobile group II introns. More generally, they show how the diversity of mobile group II introns can be exploited to provide a large variety of different target specificities and potentially other useful properties for gene targeting.

Organization of the ipdC region regulates IAA levels in different Azospirillum brasilense strains: molecular and functional analysis of ipdC in strain SM

Presence of the indole-3-pyruvic acid pathway (IPyA) of indole-3-acetic acid (IAA) biosynthesis was demonstrated by identifying the ipdC gene encoding indole-3-pyruvate decarboxylase (IPDC) in Azospirillum brasilense strain SM. Comparison with other A. brasilense strains, Sp7 and Sp245, revealed homology in the gene and its 5' regulatory region. The 3' region of strain SM carries a truncated iaaC gene implicated in controlling IAA biosynthesis in strain Sp245. While the ipdC transcript could be visualized by reverse transcription polymerase chain reaction (RT-PCR), truncated iaaC was non-functional. Strain SM derivatives carrying higher copy number of ipdC and P(ipdC) showed improved IAA biosynthesis. P(ipdC) showed sequence elements that are part of composite auxin-responsive promoters. Expression of ipdC was upregulated by IAA, other auxins, temperature and nutrient stress, and an increase in pH. Heterologous overexpression of a functional iaaC gene from strain Sp245 in strain SM confirmed its role in controlling IAA biosynthesis and lowering ipdC expression which may be effected by dissociating IAA-transcriptional regulator interactions in the 5' region. However, the effect of the introduced iaaC was overcome when both ipdC and iaaC were expressed from similar plasmid background. This analysis confirmed that strain-based differences in IAA biosynthesis could be explained by differential regulation of ipdC expression.