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Arbuscular mycorrhizal fungi (AMF) and beneficial bacteria are found naturally associated with most terrestrial plant roots. While it is now well known that bacteria colonize AMF and can form aggregates and biofilms, little is known about how interactions between bacterial communities and AMF take place under both in situ and in vitro conditions. We investigated the impact of inoculation with AMF-associated bacteria (AABs) of AMF by in vitro recreation of the interaction on synthetic growth media in a two-compartment Petri plate system. The inoculated AABs were found to be associated with the mycorrhizal co-culture and were found to migrate along growing AMF hyphae and to be associated with the spore surface. AABs differentially influenced the growth of the AMF and their functional capability demonstrated by analysis of phosphate solubilization, nitrogen fixation, and biofilm formation. We have thus characterized these important interactions adding to a further understanding of the synergistic relationship between the two cross-kingdom microbial partners. KEY POINTS: • An in vitro assay was utilized to recreate functional biofilms with AMF-associated bacteria. • AMF-associated bacteria formed a biofilm and enhanced sporulation of Rhizophagus irregularis. • AMF-bacterial interactions through biofilm formation influence the functional capability of both partners.

Soil environments are dynamic and the plant rhizosphere harbours a phenomenal diversity of micro-organisms which exchange signals and beneficial nutrients. Bipartite beneficial or symbiotic interactions with host roots, such as mycorrhizae and various bacteria, are relatively well characterized. In addition, a tripartite interaction also exists between plant roots, arbuscular mycorrhizal fungi (AMF) and associated bacteria. Bacterial biofilms exist as a sheet of bacterial cells in association with AMF structures, embedded within a self-produced exopolysaccharide matrix. Such biofilms may play important functional roles within these tripartite interactions. However, the details about such interactions in the rhizosphere and their relevant functional relationships have not been elucidated. This review explores the current understanding of naturally occurring microbial biofilms, and their interaction with biotic surfaces, especially AMF. The possible roles played by bacterial biofilms and the potential for their application for a more productive and sustainable agriculture is discussed in this review.

Graphene has triggered enormous interest in, and exploration of, its applications in diverse areas of science and technology due to its unique properties. While graphene has displayed great potential as a nano-delivery system for drugs and biomolecules in biomedicine, its application as a nanocarrier in agriculture has only begun to be explored. Conventional fertilizers and agricultural delivery systems have a number of disadvantages, such as: fast release of the active ingredient, low delivery efficiency, rapid degradation and low stability that often leads to their over-application and consequent environmental problems. Advanced nano fertilizers with high carrier efficiency and slow and controlled release are now considered the gold standard for promoting agricultural sustainability while protecting the environment. Graphene’s attractive properties include large surface area, chemical stability, mechanical stability, tunable surface chemistry and low toxicity making it a promising material on which to base agricultural delivery systems. Recent research has demonstrated considerable success in the use of graphene for agricultural applications, including its utilization as a delivery vehicle for plant nutrients and crop protection agents, as well as in post-harvest management of crops. This review, therefore, presents a comprehensive overview of the current status of graphene-based nanocarriers in agriculture. Additionally, the review outlines the surface functionalization methods used for effective molecular delivery, various strategies for nano-vehicle design and the underlying features necessary for a graphene-based agro-delivery system. Finally, the review discusses directions for further research in optimization of graphene-based nanocarriers.

Background Application of nanotechnology for crop protection in the form of nanopesticide has attracted significant interest in modern agriculture for the management of devastating polyphagous pests. In the present work, highly stable, ready-to-use water-based nanoformulations of hydrazine-based pesticides were evaluated for their Insect Growth Regulatory potential against the polyphagous insect pest—Spodoptera litura. Also, the nanoformulations were screened for their antifungal behaviour against plant pathogenic fungi; Colletotrichum gloeosporioides, Rhizoctonia solani, Fusarium solani, and Alternaria solani. Results Nanoformulation of sulfonyl acyl hydrazine derivative, NF7, emerged as the best insect growth regulator with GI90 value 0.010 mg L−1 followed by NF4 and NF6 with GI90 0.012 and 0.013 mg L−1, respectively. Results of diet incorporation method showed enhanced efficacy of nanoformulations when compared with topical application method. Antifungal screening showed that many nanoformulations displayed at least 50% growth inhibition for treatment dosage 50–200 mg L−1 against the fungal pathogens tested (C. gloeosporioides, R. solani, F. solani, and A. solani). NF6, NF7, and NF8 were more potent antifungal agents at lower treatment dosages, while at high doses (400 and 800 mg L−1), 100% growth inhibition at concentration was observed against R. solani and F. solani, except NF1 having 64% growth inhibition against F. solani. Conclusion Results presented here are very promising and deliver new nanoformulations of diacyl and sulfonyl acyl hydrazine-based derivatives to be employed as nanopesticide for sustainable crop protection.

Beneficial ecosystem services provided by arbuscular mycorrhizal fungi (AMF) are the outcome of their synergistic actions with diverse bacterial communities (AMF-associated bacteria; AAB) living in strict association with AMF hyphae and spores. Herein, bacterial diversity associated with 6 AMF species from 33 different co-cultures belonging to order Glomerales and Diversisporales were identified, using a combination of culture-dependent functional analyses and amplicon sequencing. Overall, 231 bacterial strains were isolated from the AMF spores and hyphae which covered 30 bacterial genera and 52 species. Hierarchical clustering based on plant growth promoting traits identified 9 clades comprising diverse bacterial genera with clades 7, 8 and 9 representing the most functionally rich AAB. High-throughput amplicon sequencing across a small subset of 8 AMF co-cultures spread across 3 AMF genera identified Operational Taxonomic Units belonging to 118 bacterial genera. The study revealed a greater diversity of AAB from spores of in vitro transformed AMF root co-cultures rather than in situ, pot AMF cultures. Functionally active, culturable AABs with multiple plant growth promoting traits such as phosphate solubilisation, nitrogen fixation, biofilm formation, enzyme and plant growth regulator production along with biocontrol activity were identified. These properties could be utilized individually and/or as consortia with AMF, as biological growth enhancers.

The production of biocontrol factors by Pseudomonads is reported to be controlled at the post-transcriptional level by the GacS/GacA signal transduction pathway. This involves RNA-binding translational repressor proteins, RsmA and RsmE, and the small regulatory RNAs (sRNAs) RsmX, RsmY, and RsmZ. While the former represses genes involved in secondary metabolite production, the latter relieves this repression at the end of exponential growth. We have studied the fluorescent Pseudomonas strain Psd, possessing good biocontrol potential, and confirmed the presence of rsmY and rsmZ by PCR amplification. Gene constructs for all the three small RNAs (RsmX, RsmY and RsmZ) carried on broad host-range plasmid, pME6032 were mobilized into strain Psd. Expression analysis of gacA in the recombinant strains over-expressing rsmX (Psd-pME7320), rsmY (Psd-pME6359) and rsmZ (Psd-pME6918) revealed a significant upregulation of the response regulator. Besides, a remarkable down-regulation of rsmA was also reported in all the strains. The variant strains were found to produce comparatively higher levels of phenazines. Indole acetic acid levels were higher to some extent, and strain Psd-pME6918 also showed elevated production of HCN. The tomato seedlings infected with Fusarium oxysporum and Verticillium dahliae in the presence of culture filtrate of the recombinant strains showed better plant protection response in comparison to the wild-type strain Psd. These results suggest that small RNAs are important determinants in regulation of the biocontrol property of strain Psd.

Background Small RNAs (sRNAs) are non-coding RNAs known to regulate various biological functions such as stress adaptation, metabolism, virulence as well as pathogenicity across a wide range of bacteria, mainly by controlling mRNA stabilization or regulating translation. Identification and functional characterization of sRNAs has been carried out in various plant growth-promoting bacteria and they have been shown to help the cells cope up with environmental stress. No study has been carried out to uncover these regulatory molecules in the diazotrophic alpha-proteobacterium Azospirillum brasilense Sp245 to date. Results Expression-based sRNA identification (RNA-seq) revealed the first list of ~ 468 sRNA candidate genes in A. brasilense Sp245 that were differentially expressed in nitrogen starvation versus non-starved conditions. In parallel, in silico tools also identified 2 of the above as candidate sRNAs. Altogether, putative candidates were stringently curated from RNA-seq data based on known sRNA parameters (size, location, secondary structure, and abundance). In total, ~ 59 significantly expressed sRNAs were identified in this study of which 53 are potentially novel sRNAs as they have no Rfam and BSRD homologs. Sixteen sRNAs were randomly selected and validated for differential expression, which largely was found to be in congruence with the RNA-seq data. Conclusions Differential expression of 468 A. brasilense sRNAs was indicated by RNA-seq data, a subset of which was confirmed by expression analysis. Four of the significantly expressed sRNAs were not observed in nitrogen starvation while 16 sRNAs were found to be exclusively expressed in nitrogen depletion. Putative candidate sRNAs identified have potential mRNA targets primarily involved in stress (abiotic and biotic) adaptability; regulation of bacterial cellular, biological and molecular pathways such as nitrogen fixation, polyhydroxybutyrate synthesis, chemotaxis, biofilm formation and transcriptional regulation. In addition to directly influencing bacteria, some of these sRNAs also have targets influencing plant-microbe interactions through adhesion of bacteria to plant roots directly, suppressing host response, inducing plant defence and signalling.

Detecting microbial life in the soil environment is a goal of space exploration because of its influence not only on the plant growth but also on the human health. In order to identify the soil microbes contributing to the nutrient cycling and sustainable agriculture, various studies have been attempted to capture the microbial activity in vivo and to understand their role individually. However, these attempts have not been successful owing to the presence of nonculturable microbes in abundance. Advances in metagenomics study and sensor-based technology have contributed to a great extent to identify such microbes. Conventional soil microbial detection involving culture-dependent methods have failed to deliver in real time. Nanomaterial incorporation into biosensors can enhance the performance of biosensors due to their unique physicochemical properties. This field has initiated the understanding of the complex interplay between nanomaterials and microbes and the resulting biological consequences. This chapter provides brief insights into the importance of the soil microbiome and biosensors with nanomaterial interventions for bacterial detection. A range of nanomaterials have been investigated for their role in biorecognition. Additionally, the mechanistic aspects of nanomaterial-microbe interaction with implications for microbial detection are touched upon.

Azospirillum brasilense Sp245, a diazotrophic plant growth-promoting bacterium influences host plants via well-known mechanisms, gene interactions and confers abiotic and biotic stress tolerance mediated by signalling molecules. We present here, the functional characterization of a small RNA (sRNA), sSp_p6, identified from the 468 sRNAs identified in A. brasilense Sp245 and confirmed its involvement in nitrogen metabolism in the strain. sSp_p6 expression was found to be modulated in carbon and nitrogen stress while forming an interactive network with the target genes, vnfG (encoding vanadium-dinitrogenase) and σ-54 (sigma factor, interaction region) thereby establishing an essential role of this sRNA in biological nitrogen fixation by the strain. Additionally, upon inoculation with sSp_p6 overexpressing mutant, the host plant Sorghum exhibited increased lateral root formation, which led to improved plant root morphology.

Extracellular pili-like structures (PLS) produced by cyanobacteria have been poorly explored. We have done detailed topographical and electrical characterisation of PLS in Nostoc punctiforme PCC 73120 using transmission electron microscopy (TEM) and conductive atomic force microscopy (CAFM). TEM analysis showed that N. punctiforme produces two separate types of PLS differing in their length and diameter. The first type of PLS are 6-7.5 nm in diameter and 0.5-2 µm in length (short/thin PLS) while the second type of PLS are ~20-40 nm in diameter and more than 10 µm long (long/thick PLS). This is the first study to report long/thick PLS in N. punctiforme. Electrical characterisation of these two different PLS by CAFM showed that both are electrically conductive and can act as microbial nanowires. This is the first report to show two distinct PLS and also identifies microbial nanowires in N. punctiforme. This study paves the way for more detailed investigation of N. punctiforme nanowires and their potential role in cell physiology and symbiosis with plants.

Resistance to quinolone antibiotics has been a serious problem ever since nalidixic acid was introduced into clinical medicine. Over time, resistance of pathogenic microbes to nalidixic acid led to the design of novel variants to revive its potential application. In the present work, a series of eight nanoformulations of nalidixic acid-based diacyl and sulfonyl acyl hydrazine derivatives were prepared. All nanoformulations were found to be stable at different storage temperatures. Antibacterial and anticandida activity of the eight nanoformulations presented encouraging results when compared with their non-nano parent counterparts. The nanoformulations of chloro, furanyl, and sulfonyl acyl substituted derivatives of nalidixic acid displayed most promising results (MIC ranging from 50 to 100 μg mL−1) against the tested bacteria and yeast. Among the screened bacteria, Acinetobacter baumannii displayed maximum sensitivity to the above nanoformulations. Biosafety study on the mammalian model—wax moth, Galleria mellonella—showed that all eight prepared nanoformulations were absolutely nontoxic to the larvae and subsequent pupae and hence may likely have no or low toxicity against mammalian systems. Graphical Abstract Electronic supplementary material The online version of this article (10.1186/s11671-018-2718-8) contains supplementary material, which is available to authorized users.

Figure S1. Synthetic scheme. Figure S2. Particle size distribution of nanoformulations: a) NF 1, b) NF 2, c) NF 3, d) NF 4, d) NF 5, e) NF 6, f) NF 7 and g) NF 8. Figure S3. TEM images of nanoformulation a) NF1, b) NF2, c) NF3, d) NF4 and e) NF5 after 3 months storage at room temperature (representative images shown, scale bar is shown at the bottom left corner of each figure and varied between 20 nm to 100 nm). Figure S4. Antibacterial activity of nanoformulations and non-nano derivatives against bacillus subtilis using CFU per mL. a) 800, b) 400, c) 200, d) 100, e) 50μgmL1 and f) Control. Figure S5. Antibacterial activity of nanoformulations and non-nano derivatives against Acinetobacter baumannii using CFU per mL. a) 800, b) 400, c) 200, d) 100, e) 50μgmL− 1 and f) Control. Figure S6. Anticandida activity of nanoformulations (NF) along with their non-nano derivatives (NN) showing zone of inhibition at each test concentration in μgmL− 1. Table S1a Stability of prepared nanoformulations stored at 4 °C. Table S1b. Stability of prepared nanoformulations stored at 25 °C. Table S2. Net change in OD (average of 3 readings) at 570 nm after 18 h of exposure to nanoformulations on Staphylococcus aureus. Table S3. Net change in OD (average of 3 readings) at 570 nm after 18 h of exposure to nanoformulations on Bacillus subtilis. Table S4. Net change in OD (average of 3 readings) at 570 nm after 18 h of exposure to nanoformulations on Pseudomonas aeruginosa. Table S5. Net change in OD (average of 3 readings) at 570 nm after 18 h of exposure to nanoformulations on Acinetobacter baumannii. (DOCX 14298 kb)

Cosmopolitan plant root symbionts The aboveground lives of plants are only sustainable because of the symbiotic soil fungi that encase their roots. These fungi swap nutrients with plants, defend them from attack, and help them withstand abrupt environmental changes. Out of necessity, fungal symbionts in the soil would appear to be restricted and local to certain plant species. Davison et al. , however, discovered that some taxa are globally distributed. How these underground fungi have dispersed so widely remains a mystery; perhaps human farmers have had something to do with it. Science , this issue p. 970

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.

Bacterial biosynthesis of the phytohormone, indole-3-acetic acid (IAA) is well established and along with the diffusible gaseous molecule, nitric oxide (NO) is known to positively regulate the developmental processes of plant roots. IAA and NO act as signaling molecules in plant-microbe interactions as they modulate the gene expression in both, plants and microorganisms. Although IAA and NO may not be required for essential bacterial physiological processes, numerous studies point towards a crosstalk between IAA and NO in the rhizosphere. In this review, we describe various IAA and NO-responsive or sensing genes/proteins/regulators. There is also growing evidence for the interaction of IAA and NO with other plant growth regulators and the involvement of NO with the quorum sensing system in biofilm formation and virulence. This interactive network can greatly impact the host plant-microbe interactions in the soil. Coupled with this, the specialized σ(54) -dependent transcription observed in some of the IAA and NO-influenced genes can confer inducibility to these traits in bacteria and may allow the expression of IAA and NO-influenced microbial genes in nutrient limiting or changing environmental conditions for the benefit of plants.

Electromicrobiology has gained momentum in the last 10 years with advances in microbial fuel cells and the discovery of microbial nanowires (MNWs). The list of MNW-producing micro-organisms is growing and providing intriguing insights into the presence of such micro-organisms in diverse environments and the potential roles MNWs can perform. This review discusses the MNWs produced by different micro-organisms, including their structure, composition and mechanism of electron transfer through MNWs. Two hypotheses, metallic-like conductivity and an electron hopping model, have been proposed for electron transfer and we present a current understanding of both these hypotheses. MNWs not only are poised to change the way we see micro-organisms but also may impact the fields of bioenergy, biogeochemistry and bioremediation; hence, their potential applications in these fields are highlighted here.

Microbial nanowires (MNWs) can play an important role in the transformation and mobility of toxic metals/metalloids in environment. The potential role of MNWs in cell-arsenic (As) interactions has not been reported in microorganisms and thus we explored this interaction using Synechocystis PCC 6803 as a model system. The effect of half maximal inhibitory concentration (IC50) [~300 mM As (V) and ~4 mM As (III)] and non-inhibitory [4X lower than IC50, i.e., 75 mM As (V) and 1 mM As (III)] of As was studied on Synechocystis cells in relation to its effect on Chlorophyll (Chl) a, type IV pili (TFP)-As interaction and intracellular/extracellular presence of As. In silico analysis showed that subunit PilA1 of electrically conductive TFP, i.e., microbial nanowires of Synechocystis have putative binding sites for As. In agreement with in silico analysis, transmission electron microscopy analysis showed that As was deposited on Synechocystis nanowires at all tested concentrations. The potential of Synechocystis nanowires to immobilize As can be further enhanced and evaluated on a large scale and thus can be applied for bioremediation studies.

Sorghum is known to be intolerant to soil acidity and grows best in the pH range of 5.7–6.4. Consequently, its associations with metabolically versatile plant growth promoting bacterial strains in the rhizosphere are likely to be helpful as they will be able to support the growth of the host plant even under varying rhizospheric conditions by improving root growth. The mechanism of the phytohormones crosstalking with each other and integration of the signaling pathways have been deciphered to a large extent in plants, yet the interrelationship between the bacterial plant growth regulators has not yet been unraveled. In-depth understanding of sorghum genomics is necessary for improving sorghum composition and agronomic behavior. Along with this, innovative strategies and genomics and transcriptomics studies can be designed to understand the microbial communities associated with sorghum. These offer an environmentally sustainable approach to increase sorghum production and health.

Since the 2006 discovery of the Acinetobacter baumannii strain AYE AbaR1 resistance island, similar elements have been reported in numerous members of this species. As AbaR1 is distantly related to Tn 7 , we have renamed it Tn AbaR1 . Tn AbaR transposons are known to carry multiple antibiotic resistance- and efflux-associated genes, although none have been experimentally studied en bloc . We deleted the Tn AbaR transposon in A. baumannii A424, which we have designated Tn AbaR23 , and characterized independent deletion mutants DCO163 and DCO174. The NotI pulsed-field gel electrophoresis (PFGE) profile of strain DCO174 was consistent with targeted deletion of Tn AbaR23 alone, but strain DCO163 apparently harbored a second large genomic deletion. Nevertheless, “subtractive amplification” targeting 52 Tn AbaR and/or resistance-associated loci yielded identical results for both mutants and highlighted genes lost relative to strain A424. PCR mapping and genome sequencing revealed the entire 48.3-kb sequence of Tn AbaR23 . Consistent with Tn AbaR23 carrying two copies of sul1 , both mutants exhibited markedly increased susceptibility to sulfamethoxazole. In contrast, loss of tetAR (A) resulted in only a minor and variable increase in tetracycline susceptibility. Despite not exhibiting a growth handicap, strain DCO163 was more susceptible than strain DCO174 to 9 of 10 antibiotics associated with mutant-to-mutant variation in susceptibility, suggesting impairment of an undefined resistance-associated function. Remarkably, despite all three strains sharing identical gyrA and parC sequences, the ciprofloxacin MIC of DCO174 was >8-fold that of DCO163 and A424, suggesting a possible paradoxical role for Tn AbaR23 in promoting sensitivity to ciprofloxacin. This study highlights the importance of experimental scrutiny and challenges the assumption that resistance phenotypes can reliably be predicted from genotypes alone.

Identification of extracellular conductive pilus-like structures (PLS) i.e. microbial nanowires has spurred great interest among scientists due to their potential applications in the fields of biogeochemistry, bioelectronics, bioremediation etc. Using conductive atomic force microscopy, we identified microbial nanowires in Microcystis aeruginosa PCC 7806 which is an aerobic, photosynthetic microorganism. We also confirmed the earlier finding that Synechocystis sp. PCC 6803 produces microbial nanowires. In contrast to the use of highly instrumented continuous flow reactors for Synechocystis reported earlier, we identified simple and optimum culture conditions which allow increased production of nanowires in both test cyanobacteria. Production of these nanowires in Synechocystis and Microcystis were found to be sensitive to the availability of carbon source and light intensity. These structures seem to be proteinaceous in nature and their diameter was found to be 4.5-7 and 8.5-11 nm in Synechocystis and M. aeruginosa, respectively. Characterization of Synechocystis nanowires by transmission electron microscopy and biochemical techniques confirmed that they are type IV pili (TFP) while nanowires in M. aeruginosa were found to be similar to an unnamed protein (GenBank : CAO90693.1). Modelling studies of the Synechocystis TFP subunit i.e. PilA1 indicated that strategically placed aromatic amino acids may be involved in electron transfer through these nanowires. This study identifies PLS from Microcystis which can act as nanowires and supports the earlier hypothesis that microbial nanowires are widespread in nature and play diverse roles.

Production of nitric oxide (NO) and the presence of NO metabolism genes, nitrous oxide reductase (nosZ), nitrous oxide reductase regulator (nosR) and nitric oxide reductase (norB) were identified in the plant-associated bacterium (PAB) Azospirillum brasilense SM. NO presence was confirmed in all overexpressing strains, while improvement in the plant growth response of these strains was mediated by increased NO and indole-3-acetic acid (IAA) levels in the strains. Electron microscopy showed random distribution to biofilm, with surface colonization of pleiomorphic Azospirilla. Quantitative IAA estimation highlighted a crucial role of nosR and norBC in regulating IAA biosynthesis. The NO quencher and donor reduced/blocked IAA biosynthesis by all strains, indicating their common regulatory role in IAA biosynthesis. Tryptophan (Trp) and l-Arginine (Arg) showed higher expression of NO genes tested, while in the case of ipdC, only Trp and IAA increased expression, while Arg had no significant effect. The highest nosR expression in SMnosR in the presence of IAA and Trp, along with its 2-fold IAA level, confirmed the relationship of nosR overexpression with Trp in increasing IAA. These results indicate a strong correlation between IAA and NO in A. brasilense SM and suggest the existence of cross-talk or shared signaling mechanisms in these two growth regulators.

Bacterial biosynthesis of the phytohormone, indole-3-acetic acid (IAA) is well established and along with the diffusible gaseous molecule, nitric oxide (NO) is known to positively regulate the developmental processes of plant roots. IAA and NO act as signaling molecules in plant-microbe interactions as they modulate the gene expression in both, plants and microorganisms. Although IAA and NO may not be required for essential bacterial physiological processes, numerous studies point towards a crosstalk between IAA and NO in the rhizosphere. In this review, we describe various IAA and NO-responsive or sensing genes/proteins/regulators. There is also growing evidence for the interaction of IAA and NO with other plant growth regulators and the involvement of NO with the quorum sensing system in biofilm formation and virulence. This interactive network can greatly impact the host plant-microbe interactions in the soil. Coupled with this, the specialized σ(54) -dependent transcription observed in some of the IAA and NO-influenced genes can confer inducibility to these traits in bacteria and may allow the expression of IAA and NO-influenced microbial genes in nutrient limiting or changing environmental conditions for the benefit of plants.

The rhizosphere is a hub of immense metabolic activities due to the presence of highly versatile microorganisms. Several rhizosphere-inhabiting microorganisms fulfill important ecological functions, such as nutrient recycling and pathogen control, that often translates into better plant growth and health (Couillerot et al., 2009). Additionally, Q2 this microenvironment is described as a “microbial hot-spot” where diverse interactions between organisms, beneficial as well as pathogenic, take place (Whipps, 2001). The former group of strains comprises the plantgrowth-promoting bacteria (PGPB) that influence plant growth by producing phytohormones or enhancing the availability of nutrients by inducing systemic resistance in plants and by antagonizing pathogenic bacteria (Bashan and de-Bashan, 2005; Lugtenberg and Kamilova, 2009; Raaijmakers et al., 2009; Spaepen et al., 2009a; Upadhyay and Srivastava, 2010a; Sharon et al., 2011). It is also clear that some PGPB are capable of exerting multiple PGP Q3 mechanisms (Upadhyay and Srivastava, 2008, 2010b; Bashan and de-Bashan, 2010). Successful utilization of PGPB in agriculture, therefore, requires a thorough understanding of the mechanisms that enable them to colonize the rhizosphere and of the factors that lead to

Experimental and in silico PCR analysis targeting IS Aba11 and Tn AbaR islands in 196 epidemiologically unrelated Acinetobacter strains representative of ≥19 species were performed. The first two Acinetobacter baumannii IS Aba11 elements identified had been found to map to the same site on Tn AbaR transposons. However, no further evidence of physical linkage between the two elements was demonstrated. Indeed, examination of 25 definite or putative insertion sites suggested limited sequence specificity. Importantly, an aacC1 -tagged version of IS Aba11 was shown to actively transpose in A. baumannii . Similarity searches identified nine iso-IS Aba11 elements in Acinetobacter and one in Enhydrobacter and single representatives of four distant homologs in bacteria belonging to the phyla “ Cyanobacteria ” and Proteobacteria . Phylogenetic, sequence, and structural analyses of IS Aba11 and/or its associated transposase (Tnp IS Aba11 ) suggested that these elements be assigned to a new family. All five homologs encode transposases with a shared extended signature comprising 16 invariant residues within the N2, N3, and C1 regions, four of which constituted the cardinal IS Aba11 family HHEK motif that is substituted for the YREK DNA binding motif conserved in the IS 4 family. Additionally, IS Aba11 family members were associated with either no flanking direct repeat (DR) or an IS Aba11 -typical 5-bp DR and possessed variable-length terminal inverted repeats that exhibited extensive intrafamily sequence identity. Given the limited pairwise identity among Tnp IS Aba11 homologs and the observed restricted distribution of IS Aba11 , we propose that substantial gaps persist in the evolutionary record of IS Aba11 and that this element represents a recent though potentially highly significant entrant into the A. baumannii gene pool.