Multifarious characteristics of sulfur-oxidizing bacteria residing in rice rhizosphere

Sulfur-oxidizing bacteria (SOB) are versatile microorganisms known for their ability to oxidize various reduced sulfur compounds, namely, elemental sulfur (S0), hydrogen sulfide (H2S), tetrathionate (S4O62-), and trithionate (S3O62-) to sulfate (SO42-). In this study, out of twelve SOB isolates from rice rhizosphere, five were screened based on their sulfur oxidation potential, viz., SOB1, SOB2, SOB3, SOB4, and SOB5, and were identified as Ochrobactrum soli SOB1, Achromobacter xylosoxidans SOB2, Stenotrophomonas maltophilia SOB3, Brucella tritici SOB4, and Stenotrophomonas pavanii SOB5, respectively. All the isolates displayed chemolithotrophic nutritional mode by consuming thiosulfate and accumulating trithionate and tetrathionate in the growth medium which is ultimately oxidized to sulfate. The strains were authenticated with the production of thiosulfate oxidizing enzymes such as rhodanese and sulfite oxidase. Despite their tendency to oxidize reduced sulfur compounds, B. tritici SOB4 and S. pavanii SOB5 were also found to possess phosphate and zinc solubilization potential, acetic acid, and indole acetic acid (IAA) production and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. The presence of sulfanyl (R-SH) groups was noticed in the A. xylosoxidans SOB2. Elemental sulfur conversion into sulfate was noted in the S. maltophilia SOB3, and hydrogen sulfide conversion into sulfate was observed in the Ochromobacter soli SOB1. Sulfur oxidation potential coupled with beneficial properties of the isolates widen the knowledge on SOB.

Genomic and metabolic versatility of Pseudomonas aeruginosa contributes to its inter-kingdom transmission and survival

Pseudomonas aeruginosa is one of the most versatile bacteria with renowned pathogenicity and extensive drug resistance. The diverse habitats of this bacterium include fresh, saline and drainage waters, soil, moist surfaces, taps, showerheads, pipelines, medical implants, nematodes, insects, plants, animals, birds and humans. The arsenal of virulence factors produced by P. aeruginosa includes pyocyanin, rhamnolipids, siderophores, lytic enzymes, toxins and polysaccharides. All these virulent elements coupled with intrinsic, adaptive and acquired antibiotic resistance facilitate persistent colonization and lethal infections in different hosts. To date, treating pulmonary diseases remains complicated due to the chronic secondary infections triggered by hospital-acquired P. aeruginosa. On the contrary, this bacterium can improve plant growth by suppressing phytopathogens and insects. Notably, P. aeruginosa is one of the very few bacteria capable of trans-kingdom transmission and infection. Transfer of P. aeruginosa strains from plant materials to hospital wards, animals to humans, and humans to their pets occurs relatively often. Recently, we have identified that plant-associated P. aeruginosa strains could be pathologically similar to clinical isolates. In this review, we have highlighted the genomic and metabolic factors that facilitate the dominance of P. aeruginosa across different biological kingdoms and the varying roles of this bacterium in plant and human health.

Inhibitory effects of epiphytic Kluyveromyces marxianus from Indian senna (Cassia angustifolia Vahl.) on growth and aflatoxin production of Aspergillus flavus

Aspergillus flavus infection and subsequent aflatoxin contamination are considered the major constraints in senna (Cassia angustifolia Vahl.) export. Using native epiphytic yeast to control phytopathogens is a successful strategy for managing plant diseases. In the present investigation, we exploited the antagonistic potential of epiphytic yeast isolates obtained from senna against A. flavus growth and aflatoxin B1 (AFB1) production. Four Kluyveromyces marxianus strains (YSL3, YSL16, YSP12, and YSF9) exhibited vigorous antagonistic activity with a maximum inhibition of 64 %. In vivo evaluation of senna pods showed that K. marxianus strains effectively reduced A. flavus colonization with a population range of 5.87 to 7.08 log10 CFU/g. In contrast, the untreated senna pods were found to have severe fungal colonization with a population of 7.84 log10 CFU/g. In addition, HPLC analysis showed that aflatoxin B1 in senna pods was drastically reduced upon yeast treatment up to 14 DAI. Furthermore, we demonstrated the antifungal action mechanisms of K. marxianus, such as surface colonizing ability on pods, production of antifungal volatiles (VOCs), siderophores, extracellular lytic enzymes, and cell wall binding ability to AFB1. All four strains of K. marxianus showed rapid colonization on the senna pod, and YSP12 reached the maximum population of 7.18 log10 CFU/pod at 9 days after inoculation (DAI). The exposure of A. flavus to K. marxianus VOCs significantly reduced the growth by up to 99 and 93.2 % at 7 and 14 DAI, respectively. Scanning electron microscopic images demonstrated severe mycelial damage and hyphal deformities of A. flavus. In addition, yeast VOCs can reduce aflatoxin biosynthesis in A. flavus by up to 99 and 93.2 % at 7 and 14 DAI, respectively. Gas chromatography-mass spectrometry analysis confirmed the presence of antimicrobial compounds such as dimethyl trisulfide, ethyl acetate, ethanol, 3-methyl butanal, 2-methyl-1-butanol, and 3-methyl-1-butanol in the volatiles. K. marxianus strains produced siderophores and hydrolytic enzymes such as chitinase and β-1,3-glucanase. A higher AFB1 binding ability was observed in the heat-killed cells (47.5 to 70.65 %) than in the viable cells (43.16 to 60.98 %) of K. marxianus. The current study demonstrated that epiphytic K. marxianus isolated from senna could be a successful biocontrol source to reduce aflatoxin contamination in senna pods.

SCAR marker: A potential tool for authentication of agriculturally important microorganisms

Microbial inoculants are globally recommended for plant growth promotion and control of plant pathogens. These inoculants require stringent quality checks for sustainable field efficacy. Questionable regulatory frameworks constantly deteriorate the reliability of bio-inoculant technology. Existing global regulations do not involve any rapid molecular technique for the routine inspection of microbial preparations. Sequence characterized amplified region (SCAR) marker offers rapid and precise strain-level authentication of target microbes. Such advanced molecular techniques must be exploited to accurately validate the microbial formulations. Besides, the global dissemination of plant pathogenic microbes has always been an alarming threat to food security. SCAR markers could be used at the plant quarantine centers to rapidly detect catastrophic pathogens, thereby circumventing the import and export of contagious plant materials. The current review is focused on promoting the SCAR marker technology to validate commercial bio-inoculants and predict plant pandemics.

Pathogenesis of plant-associated Pseudomonas aeruginosa in Caenorhabditis elegans model

Background

Pseudomonas aeruginosa is a globally dreaded pathogen that triggers fatality in immuno-compromised individuals. The agricultural ecosystem is a massive reservoir of this bacterium, and several studies have recommended P. aeruginosa to promote plant growth. However, there were limited attempts to evaluate the health risks associated with plant-associated P. aeruginosa. The current study hypothesized that agricultural P. aeruginosa strains exhibit eukaryotic pathogenicity despite their plant-beneficial traits.

Results

We have demonstrated that feeding with the plant-associated P. aeruginosa strains significantly affects Caenorhabditis elegans health. Out of the 18 P. aeruginosa strain tested, PPA03, PPA08, PPA10, PPA13, PPA14, PPA17, and PPA18 isolated from cucumber, tomato, eggplant, and chili exhibited higher virulence and pathogenicity. Correlation studies indicated that nearly 40% of mortality in C. elegans was triggered by the P. aeruginosa strains with high levels of pyocyanin (> 9 µg/ml) and biofilm to planktonic ratio (> 8).

Conclusion

This study demonstrated that plant-associated P. aeruginosa could be a potential threat to human health similar to the clinical strains. Pyocyanin could be a potential biomarker to screen the pathogenic P. aeruginosa strains in the agricultural ecosystem.

Non Dysraphic Intramedullary Spinal Cord Lipoma

Among all intramedullary spinal cord lesions, intramedullary spinal cord lipomas account less than 1%. Non-dysraphic intramedullary lipoma is very rare. It is most commonly seen in cervicodorsal region followed by cervico bulbar, lumbar and sometimes multiple. Here we present a 17-year-old female who underwent MRI due to upper dorsal pain followed by progressive bilateral lower limb weakness which showed intramedullary lesion extending from T1-T9, involving eight vertebral segments with distal syrinx and features suggestive of lipoma. Patient underwent surgical decompression of lipoma. Patient had an uneventful post-operative period. Diagnosis confirmed by histopathology.

Plant-associated Pseudomonas aeruginosa strains harbour multiple virulence traits critical for human infection

Introduction. Pseudomonas aeruginosa causes fatal infections in immunocompromised individuals and patients with pulmonary disorders.Gap Statement. Agricultural ecosystems are the vast reservoirs of this dreaded pathogen. However, there are limited attempts to analyse the pathogenicity of P. aeruginosa strains associated with edible plants.Aim. This study aims to (i) elucidate the virulence attributes of P. aeruginosa strains isolated from the rhizosphere and endophytic niches of cucumber, tomato, eggplant and chili;and (ii) compare these phenotypes with that of previously characterized clinical isolates.Methodology. Crystal-violet microtitre assay, swarm plate experiment, gravimetric quantification and sheep blood lysis were performed to estimate the biofilm formation, swarming motility, rhamnolipid production and haemolytic activity, respectively, of P. aeruginosa strains. In addition, their pathogenicity was also assessed based on their ability to antagonize plant pathogens (Xanthomonas oryzae, Pythium aphanidermatum, Rhizoctonia solani and Fusarium oxysporum) and kill a select nematode (Caenorhabditis elegans).Results. Nearly 80 % of the plant-associated strains produced rhamnolipid and exhibited at least one type of lytic activity (haemolysis, proteolysis and lipolysis). Almost 50 % of these strains formed significant levels of biofilm and exhibited swarming motility. The agricultural strains showed significantly higher and lower virulence against the bacterial and fungal pathogens, respectively, compared to the clinical strains. In C. elegans, a maximum of 40 and 100% mortality were induced by the agricultural and clinical strains, respectively.Conclusion. This investigation shows that P. aeruginosa in edible plants isolated directly from the farm express virulence and pathogenicity. Furthermore, clinical and agricultural P. aeruginosa strains antagonized the tested fungal phytopathogens, Pythium aphanidermatum, Rhizoctonia solani and Fusarium oxysporum. Thus, we recommend using these fungi as simple eukaryotic model systems to test P. aeruginosa pathogenicity.

An alternate surgical treatment of giant serpentine aneurysm of the middle cerebral artery: Resection and End-to-End anastomosis

A section of giant intracranial aneurysms can develop serpentine morphology, secondary to a peculiar near-complete intra-aneurysmal thrombosis. The resulting complex angioarchitecture, along with the atypical clinical presentations (mass effect/distal ischemia) seen, makes management of such aneurysms technically challenging. Such aneurysms are notoriously not amenable to endovascular treatment, and hence, the only remaining treatment option is a tailored microsurgical procedure (clipping/parent vessel occlusion or reconstruction/trapping/aneurysmorrhaphy) accompanied by a safety bypass (high-flow/low-flow/in-situ bypass, depending on distal circulation's dependence on proximal trunk with reference to aneurysm). Microsurgical plan can be executed either in a single-stage or in two stages (bypass followed by later-date aneurysm treatment). Superficial temporal artery - middle cerebral artery (STA-MCA) bypass with/followed by aneurysm trapping-decompression is the most routinely performed microsurgical procedure for such aneurysms. We herein present an operative video illustrating an alternate surgical treatment of one such giant serpentine aneurysm of the MCA: Resection and End-to-End anastomosis. A 20-year-old boy underwent microsurgery for a giant right MCA serpentine aneurysm. In view of the poor distal flow in the ipsilateral MCA territory, an STA-MCA bypass with aneurysm trapping-decompression was planned. Intraoperatively, the presence of a stretched and elongated ipsilateral MCA (secondary to aneurysm's mass effect), plus the relatively narrow neck of the thrombosed aneurysm, provided us a rare opportunity to execute the above-mentioned alternate treatment. Intra and postoperative angiography confirmed the anastomosis patency. The patient made an uneventful recovery. This can save operating time, eliminate donor artery-related morbidity, and offer a surgical alternate to the conventional strategy of STA-MCA bypass.

Interaction of water activity and temperature on growth, gene expression, and aflatoxin B1 production in Aspergillus flavus on Indian senna (Cassia angustifolia Vahl.)

Senna (Cassia angustifolia Vahl.) is a medicinal crop with laxative properties, and it has significant demand in the global pharmaceutical market. Senna pods are highly susceptible to aflatoxin contamination, and the successful export of pods is hindered due to the regulatory limits of importing countries. The senna pod water activity (a_w) from harvest to storage is the key factor determining AFB₁ accumulation. The temperature conditions from field to warehouse also interact with pod a_w, which influences fungal growth and AFB₁ production. The determination of an ideal combination of a_w and temperature led to the assessment of the critical control point for AFB₁ synthesis in senna. Hence, this study aimed to evaluate the influence of a_w (0.99, 0.96, 0.93, 0.90, and 0.87 a_w) and temperature (20, 28, and 37 °C) on fungal growth, gene expression (aflR and aflS), and AFB₁ production by A. flavus in senna agar medium. The fungus showed the longest lag time (7.7 days) at 20 °C with 0.87 a_w. We observed that 0.96 a_w (P < 0.01) was optimum for the diametric growth rate at 28 and 37 °C. However, the peak expression of regulatory genes (aflR and aflS) and the maximum AFB₁ production were observed only at 28 °C (0.96 a_w). The highest growth rate occurred at 37 °C, which did not favor the expression of genes and AFB₁ production. However, at 28 °C, it positively correlated with gene expression and AFB₁ production. The suppressed expression of regulatory genes and a trace amount of aflatoxin B₁ were found at 20 °C with all the tested a_w. In our experiments, the low a_w (0.87 and 0.90 a_w) suppressed the fungal growth, gene expression, and AFB₁ production of A. flavus at all of the tested temperatures (20, 28, and 37 °C). The rapid drying of senna pods with a low water activity (≤0.87 a_w) and storage at low temperature (20 °C) are ideal conditions to avoid AFB₁ and ensure the quality of produce for export.

Rhizospheric and endophytic Pseudomonas aeruginosa in edible vegetable plants share molecular and metabolic traits with clinical isolates

AIM

Pseudomonas aeruginosa, a leading opportunistic pathogen causing hospital-acquired infections, is also commonly found in agricultural settings. However, there are minimal attempts to examine the molecular and functional attributes shared by agricultural and clinical strains of P. aeruginosa. This study investigates the presence of P. aeruginosa in edible vegetable plants (including salad vegetables) and analyses the evolutionary and metabolic relatedness of the agricultural and clinical strains.

METHODS AND RESULTS

Eighteen rhizospheric and endophytic P. aeruginosa strains were isolated from cucumber, tomato, eggplant, and chili directly from the farms. The identity of these strains was confirmed using biochemical and molecular assays. The genetic and metabolic traits of these plant-associated P. aeruginosa isolates were compared with clinical strains. DNA fingerprinting and 16S rDNA-based phylogenetic analyses revealed that the plant- and human-associated strains are evolutionarily related. Both agricultural and clinical isolates possessed plant-beneficial properties, including mineral solubilization to release essential nutrients (phosphorous, potassium, and zinc), ammonification, and the ability to release extracellular pyocyanin, siderophore, and indole-3 acetic acid.

CONCLUSION

These findings suggest that rhizospheric and endophytic P. aeruginosa strains are genetically and functionally analogous to the clinical isolates. In addition, the genotypic and phenotypic traits do not correlate with plant sources or ecosystems.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study reconfirms that edible plants are the potential source for human and animal transmission of P. aeruginosa.

Pichia kudriavzevii-a potential soil yeast candidate for improving soil physical, chemical and biological properties

Soil yeasts exhibit an array of beneficial effects to plants viz., plant growth promotion, phosphate solubilization, nitrogen and sulphur oxidation, etc. Yeasts remain as poorly investigated group of microorganisms that represent an abundant and dependable source of bioactive/chemically novel compounds and potential bioinoculants. Hence this study holds the key concept of assessing the performance of soil yeasts with potential plant growth promoting ability in soil quality improvement. Sixteen soil yeast isolates with plant growth promoting traits were assessed for biofilm forming potential and five potential soil yeast isolates were selected and identified through molecular technique. Soil incubation study was performed with these isolates to assess their impact on soil physical, chemical and biological properties. Due to inoculation of soil yeasts, notable changes were observed in soil physical, chemical and biological properties. Among the soil yeast isolates, Pichia kudriavzevii gave better results in soil incubation study.

Harnessing PGPR inoculation through exogenous foliar application of salicylic acid and microbial extracts for improving rice growth

Plant-growth-promoting rhizobacteria (PGPR) should effectively colonize along the plant root to enhance the plant and soil health. The present investigation aims to improve the PGPR-mediated plant health benefits through above-ground foliar management. A green fluorescent protein-tagged PGPR strain, Pseudomonas chlororaphis (ZSB15-M2) was inoculated in a nonautoclaved agricultural soil before rice culturing. Salicylic acid and cell extracts of Corynebacterium glutamicum and Saccharomyces cerevisiae as a supply of hormonal and inducer compounds were applied on the foliage of the 10-days-old rice plants and subsequently observed the colonizing ability of ZSB15-M2. The cell extracts of Corynebacteria and yeast showed a 100-fold increase in the ZSB15-M2 population in the rhizosphere of rice, whereas salicylic acid had a 10-fold increase in relation to mock control. The rice root exudates collected after the spraying of salicylic acid and microbial extracts showed significantly enhanced release of total carbon, total protein, total sugar, total amino nitrogen, total nitrogen, and phenol content. In vitro assays revealed that these root exudates collected after exogenous spray of these chemicals enhanced the chemotactic motility and biofilm formation of ZSB15-M2 compared to the control plant's root exudate. Metabolomic analysis of root exudates collected from these rice plants by gas chromatography-mass spectrometry revealed that the Corynebacteria and yeast cell extracts enhanced the divergence of metabolites of rice root exudate. Further, due to these cumulative effects in the rice rhizosphere, the total chlorophyll, total protein, total nitrogen, and total phosphorus of rice were significantly improved. These observations provide insights into the rhizosphere functioning of rice plants as modulated by above-ground treatments with improved colonization of inoculant strains as well as the plant growth.

Mitigation of drought stress in rice crop with plant growth-promoting abiotic stress-tolerant rice phyllosphere bacteria

In the search of effective drought-alleviating and growth-promoting phyllosphere bacteria, a total of 44 bacterial isolates were isolated from the leaf surface of drought-tolerant rice varieties, Mattaikar, Nootripattu, Anna R(4), and PMK3, and screened for their abiotic stress tolerance by subjecting their growth medium to temperature, salinity, and osmotic stress. Only eight isolates were found to grow and proliferate under different abiotic stress conditions. These isolates were identified using 16S ribosomal DNA gene sequence and submitted to the NCBI database. All the bacterial isolates were identified as Bacillus sp., except PB24, which was identified as Staphylococcus sp., and these isolates were further screened for plant growth-promoting (PGP) traits such as IAA production, GA production, ACC deaminase activity, and exopolysaccharide production under three different osmotic stress conditions adjusted using polyethylene glycol (PEG 6000). Additionally, mineral solubilization was measured under the normal condition. Bacillus endophyticus PB3, Bacillus altitudinis PB46, and Bacillus megaterium PB50 were found to have multifarious PGP traits. Consecutively, the performance of an individual strain to improve the plant growth was investigated under the osmotic stress (25% PEG 6000) and nonstress condition by inoculating them into rice seeds using hydroponics culture. Furthermore, the drought-alleviating potency of bacterial strains was assessed in the rice plants using pot experiment (-1.2 MPa) through bacterial foliar application during the reproductive stage. Finally, as a result of seed inoculation and foliar spray, the application of B. megaterium PB50 significantly improved the plant growth under osmotic stress, protected plants from physical drought through stomatal closure, and improved carotenoid, total soluble sugars, and total protein content. Metabolites of PB50 were profiled under both stress and nonstress conditions using gas chromatography-mass spectroscopy.

Rhizosphere engineering through exogenous growth-regulating small molecules improves the colonizing efficiency of a plant growth-promoting rhizobacterium in rice

Enhancing the rhizosphere colonization and persistence of plant growth-promoting rhizobacteria (PGPR) is necessary for maximizing PGPR-mediated benefits for crop growth and fitness in environmentally friendly agriculture. In the present investigation, we attempted manipulation of the rice rhizosphere by spraying of low molecular weight plant-regulating metabolites on the foliage of rice plants to in turn enhance the colonizing efficiency of soil-inoculated PGPR strain. The green fluorescent protein gene-tagged rhizobacterial strain, Pseudomonas chlororaphis ZSB15-M2, was inoculated in sterile plant growth medium (vermiculite coco peat mixture) and non-autoclaved agricultural soil. We sprayed different plant growth-regulating small molecules on the foliage of rice seedlings and monitored the colonizing efficiency of ZSB15-M2 in the rice rhizosphere. Among the chemicals assessed, salicylic acid (SA) at 1 mM or Corynebacterium glutamicum cell extract (CGCE, 0.2% w/v) or Saccharomyces cerevisiae cell extract (SCCE, 0.2% w/v) showed a tenfold increase in rhizosphere colony-forming units of ZSB15-M2 compared to control with a significant decline in non-rhizosphere bulk soil population. Foliar spray of CGCE enhanced soil organic carbon, microbial biomass carbon and soil protein by 21.86%, 9.68% and 11.57% respectively in the rice rhizosphere as compared to mock control. Additionally, CGCE spray enhanced the key soil enzymes, viz., dehydrogenase and acid- and alkaline phosphatase in the rhizosphere ranging 15-36%. The cumulative effect of this engineered rhizosphere resulted in the elevation of nitrogen, phosphorus, potassium and zinc availability by 21.83%, 28.83%, 23.95% and 61.94%, respectively, in rice rhizosphere as compared to control. On the other hand, SCCE and SA spray had an equal influence on the rhizosphere's biological attributes, which is lower than that of GCGE and higher than that of mock control. From the study, we propose that the aboveground management of rice with microbial-based small molecules will modulate the rice rhizosphere to attract more beneficial PGPR-based inoculants, thus improving the crop and soil health.

Nested and TaqMan® probe based quantitative PCR for the diagnosis of Ca. Phytoplasma in coconut palms

The root (wilt) disease caused by phytoplasma (Ca. Phytoplasma) is one of the major and destructive occurs in coconut gardens of Southern India. As this organism could not be cultured in vitro, the early detection in the palm is very much challenging. Hence, proper early diagnosis and inoculum assessment relay mostly on the molecular techniques namely nested and quantitative PCR (qPCR). So, the present study qPCR assay conjugated with TaqMan^® probe was developed which is a rapid, sensitive method to detect the phytoplasma. For the study, samples from different parts of infected coconut palms viz., spindle leaflets, roots and the insect vector-leaf hopper (Proutista moesta) were collected and assessed by targeting 16S rRNA gene. Further, nested PCR has been carried out using p1/p7 and fU5/rU3 primers and resulted in the amplification product size of 890 bp. From this amplified product, specifically a target of 69 bp from the 16S rRNA gene region has been detected through primers conjugated with Taqman probe in a step one instrument. The results indicated that the concentration of phytoplasma was more in spindle leaflets (8.9 × 10⁵ g of tissue) followed by roots (7.4 × 10⁵ g of tissue). Thus, a qPCR approach for detection and quantification of coconut phytoplasma was more advantageous than other PCR methods in terms of sensitivity and also reduced risk of cross contamination in the samples. Early diagnosis and quantification will pave way for the healthy coconut saplings selection and management under field conditions.

Multiplex and quantitative PCR targeting SCAR markers for strain-level detection and quantification of biofertilizers

Biofertilizers are the eco-friendly bio-input being used to sustain the agriculture by reducing the chemical inputs and improving the soil health. Quality is the major concern of biofertilizer technology which often leads to poor performance in the field and thereby loses the farmers' faith. To authenticate the strain as well as its presumed cell load of a commercial product, sequence characterized amplified region (SCAR) markers were developed for three biofertilizer strains viz., Azospirillum brasilense (Sp7), Bacillus megaterium (Pb1) and Azotobacter chroococcum (Ac1). We evaluated the feasibility of multiplex-PCR and quantitative real-time PCR for SCAR marker-based quality assessment of the product as well as the persistence of the strains during crop growth. We showed that multiplex PCR can concurrently discriminate the strains based on the amplicons' size and detects up to 10⁴ cells per g or per ml of carrier-based or liquid formulation of biofertilizer, respectively. The detection limit of quantitative PCR targeting SCAR markers is 10³  cells per g or ml of biofertilizer. Both the PCR methods detected and quantified them in the maize rhizosphere. Hence SCAR marker-based quality assessment would be a sensitive tool to monitor the biofertilizer production as well as its persistence in the inoculated crop rhizosphere.

Development of sequence-characterized amplified region (SCAR) markers as a quality standard of inoculants based on Azospirillum

An attempt was made in this work to develop a strain-level molecular marker for unambiguous authentication of two Azospirillum inoculants, viz. A. lipoferum (strain Az204) and A. brasilense (strain Sp7). The sequence-characterized amplified region (SCAR) markers obtained from DNA fingerprints were designed for discrete detection of the strains. The SCAR primers could successfully amplify the target strain without cross-reaction with other Azospirillum strains, native isolates and other inoculants. The detection limit of SCAR primer for Az204 was 8.00 pg of DNA (approximately 10(5) cells per mL), and for Sp7, it was 0.49 pg of DNA (equal to 10(4) cells per mL). A simplified Sephadex G100-based crude DNA extraction protocol developed in this study was found suitable for SCAR marker-based strain authentication. Further, SCAR primers were assessed for simultaneous authentication as well as quantification of commercially prepared Azospirillum inoculants by quantitative real-time PCR (RT-PCR) and most-probable-number PCR (MPN-PCR). The RT-PCR assay can be able to quantify the commercial formulations as equal to culturable MPN method, while MPN-PCR failed for Az204. The SCAR marker-based strain authentication and presumptive quantification developed in the present work can contribute to improving the quality standard of commercial inoculants.

Elucidation of rice rhizosphere metagenome in relation to methane and nitrogen metabolism under elevated carbon dioxide and temperature using whole genome metagenomic approach

Carbon (C) and nitrogen (N) mineralization is one of the key processes of biogeochemical cycling in terrestrial ecosystem in general and rice ecology in particular. Rice rhizosphere is a rich niche of microbial diversity influenced by change in atmospheric temperature and concentration of carbon dioxide (CO2). Structural changes in microbial communities in rhizosphere influence the nutrient cycling. In the present study, the bacterial diversity and population dynamics were studied under ambient CO2 (a-CO2) and elevated CO2+temperature (e-CO2T) in lowland rice rhizosphere using whole genome metagenomic approach. The whole genome metagenomic sequence data of lowland rice exhibited the dominance of bacterial communities including Proteobacteria, Firmicutes, Acidobacteria, Actinobacteria and Planctomycetes. Interestingly, four genera related to methane production namely, Methanobacterium, Methanosphaera, Methanothermus and Methanothermococcus were absent in a-CO2 but noticed under e-CO2T. The acetoclastic pathway was found as the predominant pathway for methanogenesis, whereas, the serine pathway was found as the principal metabolic pathway for CH4 oxidation in lowland rice. The abundances of reads of enzymes in the acetoclastic methanogenesis pathway and serine pathways of methanotrophy were much higher in e-CO2T (328 and 182, respectively) as compared with a-CO2 (118 and 98, respectively). Rice rhizosphere showed higher structural diversities and functional activities in relation to N metabolism involving nitrogen fixation, assimilatory and dissimilatory nitrate reduction and denitrification under e-CO2T than that of a-CO2. Among the three pathways of N metabolism, dissimilarity pathways were predominant in lowland rice rhizosphere and more so under e-CO2T. Consequently, under e-CO2T, CH4 emission, microbial biomass nitrogen (MBN) and dehydrogenase activities were 45%, 20% and 35% higher than a-CO2, respectively. Holistically, a high bacterial diversity and abundances of C and N decomposing bacteria in lowland rice rhizosphere were found under e-CO2T, which could be explored further for their specific role in nutrient cycling, sustainable agriculture and environment management.

Expression of Zinc Transporter Genes in Rice as Influenced by Zinc-Solubilizing Enterobacter cloacae Strain ZSB14

Zinc (Zn) deficiency in major food crops has been considered as an important factor affecting the crop production and subsequently the human health. Rice (Oryza sativa) is sensitive to Zn deficiency and thereby causes malnutrition to most of the rice-eating Asian populations. Application of zinc solubilizing bacteria (ZSB) could be a sustainable agronomic approach to increase the soil available Zn which can mitigate the yield loss and consequently the nutritional quality of rice. Understanding the molecular interactions between rice and unexplored ZSB is useful for overcoming Zn deficiency problems. In the present study, the role of zinc solubilizing bacterial strain Enterobacter cloacae strain ZSB14 on regulation of Zn-regulated transporters and iron (Fe)-regulated transporter-like protein (ZIP) genes in rice under iron sufficient and deficient conditions was assessed by quantitative real-time reverse transcription PCR. The expression patterns of OsZIP1, OsZIP4, and OsZIP5 in root and shoot of rice were altered due to the Zn availability as dictated by Zn sources and ZSB inoculation. Fe sufficiency significantly reduced the root and shoot OsZIP1 expression, but not the OsZIP4 and OsZIP5 levels. Zinc oxide in the growth medium up-regulated all the assessed ZIP genes in root and shoot of rice seedlings. When ZSB was inoculated to rice seedlings grown with insoluble zinc oxide in the growth medium, the expression of root and shoot OsZIP1, OsZIP4, and OsZIP5 was reduced. In the absence of zinc oxide, ZSB inoculation up-regulated OsZIP1 and OsZIP5 expressions. Zinc nutrition provided to the rice seedling through ZSB-bound zinc oxide solubilization was comparable to the soluble zinc sulfate application which was evident through the ZIP genes' expression and the Zn accumulation in root and shoot of rice seedlings. These results demonstrate that ZSB could play a crucial role in zinc fertilization and fortification of rice.

Persistence of Pathogenic and Non-Pathogenic Escherichia coli Strains in Various Tropical Agricultural Soils of India

The persistence of Shiga-like toxin producing E. coli (STEC) strains in the agricultural soil creates serious threat to human health through fresh vegetables growing on them. However, the survival of STEC strains in Indian tropical soils is not yet understood thoroughly. Additionally how the survival of STEC strain in soil diverges with non-pathogenic and genetically modified E. coli strains is also not yet assessed. Hence in the present study, the survival pattern of STEC strain (O157-TNAU) was compared with non-pathogenic (MTCC433) and genetically modified (DH5α) strains on different tropical agricultural soils and on a vegetable growing medium, cocopeat under controlled condition. The survival pattern clearly discriminated DH5α from MTCC433 and O157-TNAU, which had shorter life (40 days) than those compared (60 days). Similarly, among the soils assessed, the red laterite and tropical latosol supported longer survival of O157-TNAU and MTCC433 as compared to wetland and black cotton soils. In cocopeat, O157 recorded significantly longer survival than other two strains. The survival data were successfully analyzed using Double-Weibull model and the modeling parameters were correlated with soil physico-chemical and biological properties using principal component analysis (PCA). The PCA of all the three strains revealed that pH, microbial biomass carbon, dehydrogenase activity and available N and P contents of the soil decided the survival of E. coli strains in those soils and cocopeat. The present research work suggests that the survival of O157 differs in tropical Indian soils due to varied physico-chemical and biological properties and the survival is much shorter than those reported in temperate soils. As the survival pattern of non-pathogenic strain, MTCC433 is similar to O157-TNAU in tropical soils, the former can be used as safe model organism for open field studies.

Morpho-typing and molecular diversity of arbuscular mycorrhizal fungi in sub-tropical soils of Coimbatore region, Tamil Nadu, India

The diversity potential of arbuscular mycorrhizal fungi (AMF) in three different tropical soils of southern part of India was assessed by traditional morpho-typing of AMF-spores and by culture-independent nested-PCR of internal transcribed spacer region of ribosomal genes. The population diversity of AMF in soil was strongly correlated with available P2O5 in soil. Among the three different soils, black-cotton soil had more diversified AMF species than alluvial and red sandy soils. Pooled data of morpho-typing and sequence-driven analysis revealed that Glomus, Gigaspora, Scutellospora and Acaulospora are the AMF genera present in these soils. The diversity of AMF in soil differs with the mycorrhiza colonizing the plant roots.

Molecular profiling of rhizosphere bacterial communities associated with Prosopis juliflora and Parthenium hysterophorus

Prosopis juliflora and Parthenium hysterophorus are the two arid, exotic weeds of India that are characterized by distinct, profuse growth even in nutritionally poor soils and environmentally stressed conditions. Owing to the exceptional growth nature of these two plants, they are believed to harbor some novel bacterial communities with wide adaptability in their rhizosphere. Hence, in the present study, the bacterial communities associated with the rhizosphere of Prosopis and Parthenium were characterized by clonal 16S rRNA gene sequence analysis. The culturable microbial counts in the rhizosphere of these two plants were higher than bulk soils, possibly influenced by the root exudates of these two plants. The phylogenetic analysis of V1_V2 domains of the 16S rRNA gene indicated a wider range of bacterial communities present in the rhizosphere of these two plants than in bulk soils and the predominant genera included Acidobacteria, Gammaproteobacteria, and Bacteriodetes in the rhizosphere of Prosopis, and Acidobacteria, Betaproteobacteria, and Nitrospirae in the Parthenium rhizosphere. The diversity of bacterial communities was more pronounced in the Parthenium rhizosphere than in the Prosopis rhizosphere. This culture-independent bacterial analysis offered extensive possibilities of unraveling novel microbes in the rhizospheres of Prosopis and Parthenium with genes for diverse functions, which could be exploited for nutrient transformation and stress tolerance in cultivated crops.

Diversity analysis of pseudomonas in rice rhizosphere for multifaceted plant growth promotion

This investigation was carried out based on the hypothesis that there may be some pseudomonad strains, which could exist in rhizosphere of plant species contributing multifaceted beneficial activities. For this purpose, 21 pseudomonad isolates from the rhizosphere of rice, cultivated in western parts of Tamil Nadu were screened. All the 21 isolates were authenticated as pseudomonads by a genus-specific PCR screening. The molecular diversity of these isolates was investigated by Amplified Ribosomal DNA Restriction Analysis (ARDRA) and the dendrogram obtained from the analysis revealed that all the 21 isolates clustered into seven groups. Further, these isolates were screened for plant growth promoting activities such as diazotrophy (PCR amplification of nifH gene and acetylene reduction assay), Indole acetic acid (IAA) and siderophore production (spectrometrically), 1-Aminocyclopropane-1-carboxylic acid (ACC) deaminase for ethylene regulation (PCR screening), mineral solubilization (biochemically) and antagonistic potential against soil pathogenic fungi (dual culture assay). Based on the results, two elite Pseudomonas isolates (S9 and O3) were chosen as multi-functional plant growth-promoting rhizobacteria, paving way for potential use as bioinoculants in rice.

Genetic and metabolic diversity of pink-pigmented facultative methylotrophs in phyllosphere of tropical plants

Diversity of Pink-Pigmented Facultative Methylotrophs (PPFMs) in phyllosphere of cotton, maize and sunflower was determined based on differential carbon-substrate utilization profile and Random Amplified Polymorphic DNA data. Results indicate that six diversified groups of PPFMs are found in these crops. Sunflower and maize phyllosphere harbor four different groups of methylobacteria while cotton has only two groups.

Endophytic colonization and in planta nitrogen fixation by a diazotrophic Serratia sp. in rice

Nitrogen fixing endophytic Serratia sp. was isolated from rice and characterized. Re-colonization ability of Serratia sp. in the rice seedlings as endophyte was studied under laboratory condition. For detecting the re-colonization potential in the rice seedlings, Serratia sp. was marked with reporter genes (egfp and Kmr) using transposon mutagenesis. The conjugants were screened for re-colonization ability and presence of nif genes using PCR. Further, the influence of flavonoids and growth hormones on the endophytic colonization and in planta nitrogen fixation of Serratia was also investigated. The flavonoids, quercetin (3 microg/ml) and diadzein (2 microg/ml) significantly increased the re-colonization ability of the endophytic Serratia, whereas the growth hormones like IAA and NAA (5 microg/ml) reduced the endophytic colonization ability of Serratia sp. Similarly, the in planta nitrogen fixation by Serratia sp. in rice was significantly increased due to flavonoids. The inoculation of endophytic diazotrophs increased the plant biomass and biochemical constituents.

Mini transposon vector mediated foreign gene expression in Mesorhizobium huakuii subsp. rengei

Among the transposable elements, mini-Tn5 transposon vector has proven to be of greater utility for insertion mutagenesis of variety of Gram negative bacteria. The mini-Tn5 vector containing promoter less egfp gene and gentamycin resistant gene was used for the present study. The transposon vector was introduced to M. huakuii from E. coli S17 by conjugation. The conjugants were screened for stable expression of egfp both in free-living and in nodules of Astragalus sinicus. The result showed that the conjugant #3 showed stable expression of green fluorescent both in free-living and bacteroid stage. The visualization of sym plasmid of wild strain and conjugants showed that conjugant #3 had a fragmentation of large sized plasmid into two but without affecting the nodulating ability. These results clearly indicated that mini-Tn5 vectors (Transposon vectors) the best alternate tools for plasmid vectors for integration of foreign genes in chromosomal DNA or symbiotic plasmid and expression, both in free-living and bacteroid stage of Rhizobium.

Curing of symbiotic plasmid of Mesorhizobium huakuii subsp. rengei isolated from Astragalus sinicus

Astragalus sinicus (Chinese Milk vetch), a green manure leguminous plant, harbors Mesorhizobium huakuii subsp. rengei strain B3 in the root nodules. The visualization of symbiotic plasmid of strain B3 showed the presence of one sym plasmid of about 425 kbp. Curing of sym plasmid by temperature and acrydine orange was studied. Growing rhizobial cells at high temperature (37 degrees C) or treating the cells with acrydine orange at 50 mg/l eliminated sym plasmid of M. huakuii strain B3, which was confirmed by sym plasmid visualization and plant infection test of cured strains.

Agouti signaling protein and other factors modulating differentiation and proliferation of immortal melanoblasts

The melanocyte lineage potentially forms an attractive model system for studies in cell differentiation, developmental genetics, cell signaling, and melanoma, because differentiated cells produce the visible pigment melanin. Immortal lines of murine melanoblasts (melanocyte precursors) have been described previously, but induction of differentiation involved a complex culture system with keratinocyte feeder cells. Here we describe conditions for both growth and induced differentiation of the melanoblast line melb-a, without feeder cells, and analyze factors that directly control proliferation and differentiation of these pure melanoblasts. Several active factors are products of developmental and other coat color genes, including stem cell factor (SCF), melanocyte-stimulating hormone (alphaMSH), and agouti signaling protein (ASP), a natural antagonist at the MSH receptor (melanocortin 1 receptor, MC1R) encoded by the agouti gene. A stable analog of alphaMSH (NDP-MSH) stimulated differentiation and inhibited growth. ASP in excess inhibited both effects of NDP-MSH, that is, ASP could inhibit pigmentation and stimulate growth. These effects provide an explanation for the interactions in mice of melanocyte developmental mutations with yellow agouti and Mc1r alleles, and a role for embryonic expression patterns of ASP.