Impact of antagonistic endophytic bacteria on productivity of some economically important legumes

Understanding the interactions within and between endophytes and their hosts is still obscure. Investigating endophytic bacterial plant growth-promoting (PGP) traits and co-inoculation effects on legumes' performance is a candidate. Endophytic bacteria were isolated from Vicia sativa root nodules. Such endophytes were screened for their PGP traits, hydrolytic enzymes, and antifungal activities. Sterilized Vicia faba and Pisum sativum seedlings were co-inoculated separately with seven different endophytic bacterial combinations before being planted under sterilized conditions. Later on, several growth-related traits were measured. Eleven endophytes (six rhizobia, two non-rhizobia, and three actinomycetes) could be isolated, and all of them were indole-acetic-acid (IAA) producers, while seven isolates could solubilize phosphorus, whereas three, five, five, and four isolates could produce protease, cellulase, amylase, and chitinase, respectively. Besides, some of these isolates possessed powerful antifungal abilities against six soil-borne pathogenic fungi. Co-inoculation of tested plants with endophytic bacterial mixes (Rhizobiamix+Actinomix+non-Rhizobiamix), (Rhizobiamix+Actinomix), or (Rhizobiamix+non-Rhizobiamix) significantly improved the studied growth parameters (shoot, root fresh and dry weights, length and yield traits) compared to controls, whereas co-inoculated plants with (Rhizobiaalone), (non-Rhizobiamix), or (Actinomix) significantly recorded lower growth parameters. Five efficient endophytes were identified: Rhizobium leguminosarum bv. Viciae, Rhizobium pusense, Brevibacterium frigoritolerans, Streptomyces variabilis, and Streptomyces tendae. Such results suggested that these isolates could be utilized as biocontrols and biofertilizers to improve legumes productivity. Also, co-inoculation with different endophytic mixes is better than single inoculation, a strategy that should be commercially exploited.

The man, the plant, and the insect: shooting host specificity determinants in Serratia marcescens pangenome

Introduction

Serratia marcescens is most commonly known as an opportunistic pathogen causing nosocomial infections. It, however, was shown to infect a wide range of hosts apart from vertebrates such as insects or plants as well, being either pathogenic or growth-promoting for the latter. Despite being extensively studied in terms of virulence mechanisms during human infections, there has been little evidence of which factors determine S. marcescens host specificity. On that account, we analyzed S. marcescens pangenome to reveal possible specificity factors.

Methods

We selected 73 high-quality genome assemblies of complete level and reconstructed the respective pangenome and reference phylogeny based on core genes alignment. To find an optimal pipeline, we tested current pangenomic tools and obtained several phylogenetic inferences. The pangenome was rich in its accessory component and was considered open according to the Heaps' law. We then applied the pangenome-wide associating method (pan-GWAS) and predicted positively associated gene clusters attributed to three host groups, namely, humans, insects, and plants.

Results

According to the results, significant factors relating to human infections included transcriptional regulators, lipoproteins, ABC transporters, and membrane proteins. Host preference toward insects, in its turn, was associated with diverse enzymes, such as hydrolases, isochorismatase, and N-acetyltransferase with the latter possibly exerting a neurotoxic effect. Finally, plant infection may be conducted through type VI secretion systems and modulation of plant cell wall synthesis. Interestingly, factors associated with plants also included putative growth-promoting proteins like enzymes performing xenobiotic degradation and releasing ammonium irons. We also identified overrepresented functional annotations within the sets of specificity factors and found that their functional characteristics fell into separate clusters, thus, implying that host adaptation is represented by diverse functional pathways. Finally, we found that mobile genetic elements bore specificity determinants. In particular, prophages were mainly associated with factors related to humans, while genetic islands-with insects and plants, respectively.

Discussion

In summary, functional enrichments coupled with pangenomic inferences allowed us to hypothesize that the respective host preference is carried out through distinct molecular mechanisms of virulence. To the best of our knowledge, the presented research is the first to identify specific genomic features of S. marcescens assemblies isolated from different hosts at the pangenomic level.

LC-MS/MS method for proline-glycine-proline and acetylated proline-glycine-proline in human plasma

The extracellular cellular matrix (ECM) maintains tissue structure and regulates signaling functions by continuous degradation and remodeling. Inflammation or other disease conditions activate proteases including matrix metalloproteinases (MMPs) that degrade ECM proteins and in particular generate fragments of collagen and elastin, some of which are biologically active ECM peptides or matrikines. Stepwise degradation of collagen by MMP 8, 9 and prolyl endopeptidase release the matrikine proline-glycine-proline (PGP) and its product acetyl-PGP (AcPGP). These peptides are considered as potential biomarkers and therapeutic targets for many disease conditions such as chronic lung disease, heart disease, and cancer. However, there is no published, validated method for the measurement of PGP and AcPGP in plasma and therefore, we developed a sensitive, selective and reliable, isotope dilution LC-multiple reaction monitoring MS method for their determination in human plasma. The chromatographic separation of PGP and AcPGP was achieved in 3 min using Jupiter column with a gradient consisting of acidified acetonitrile and water at a flow rate of 0.5 ml/min. The limit of detection (LOD) for PGP and AcPGP was 0.01 ng/ml and the limit of quantification (LOQ) was 0.05 ng/ml and 0.1 ng/ml, respectively. Precision and accuracy values for all analytes were within 20 % except for the lowest QC of 0.01 ng/ml. The mean extraction recoveries of these analytes were > 90 % using a Phenomenex Phree cartridge and the matrix effect was < 15 % for all the QCs for PGP and AcPGP except the lowest QC. The stability of PGP and AcPGP was > 90 % in several tested conditions including autosampler use, storage at -80 °C, and after 6 times freeze-thaw cycles. Using this method, we successfully extracted and determined PGP levels in human plasma from healthy and COPD subjects. Therefore, this method is suitable for quantification of these peptides in the clinical setting.

Isolation and Characterization of Bacterial Endophytes from Small Nodules of Field-Grown Peanut

It is evident that legume root nodules can accommodate rhizobial and non-rhizobial bacterial endophytes. Our recent nodule microbiome study in peanuts described that small nodules can harbor diverse bacterial endophytes. To understand their functional role, we isolated 87 indigenous endophytes from small nodules of field-grown peanut roots and characterized them at molecular, biochemical, and physiological levels. The amplified 16S rRNA genes and phylogenetic analysis of these isolates revealed a wide variety of microorganisms related to the genera Bacillus, Burkholderia, Enterobacter, Herbaspirillum, Mistsuaria, Pantoea, Pseudomonas, and Rhizobia. It was observed that 37% (100% identity) and 56% (>99% identity) of the isolates matched with the amplified sequence variants (ASVs) from our previous microbiome study. All of these isolates were tested for stress tolerance (high temperature, salinity, acidic pH) and phosphate (P) solubilization along with ammonia (NH3), indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylate deaminase (ACCD), and siderophore production. The majority (78%) of the isolates were found to be halotolerant, thermotolerant, and acidophilic, and a few of them showed a significant positive response to the production of IAA, NH3, siderophore, ACCD, and P-solubilization. To evaluate the plant growth promotion (PGP) activity, plant and nodulation assays were performed in the growth chamber conditions for the selected isolates from both the non-rhizobial and rhizobial groups. However, these isolates appeared to be non-nodulating in the tested conditions. Nonetheless, the isolates 2 (Pantoea), 17 (Burkholderia), 21 (Herbaspirillum), 33o (Pseudomonas), and 77 (Rhizobium sp.) showed significant PGP activity in terms of biomass production. Our findings indicate that these isolates have potential for future biotechnological applications through the development of biologicals for sustainable crop improvement.

Genetic polymorphism and plant growth promotion traits of potent fungal entomopathogens of rice leaf folder

Entomopathogenic fungal biocides are preferred for environment friendly sustainable management of insect pests due to their host specificity and harmlessness to non-target insects. Plant growth promotion (PGP) functions of the entomofungi are also important attributes but hitherto insignificantly explored. Therefore, virulence of 17 natural fungal entomocides (Cordyceps, Beauveria, Metarhizium, Nomuraea, Fusarium, Verticillium, Trichoderma and Paecilomyces spp.) were evaluated for pathogenicity against five rice pests (brown plant hopper (Nilaparvata lugens) and green leaf hopper (Nephotettix virescens) nymphs, leaf folder (Cnaphalocrosis medinalis) and yellow stem borer (Scirpophaga incertulas) larvae and swarming caterpillar (Spodoptera mauritia), respectively), and PGP traits of the potent leaf folder pathogens. Among the fungi, only the leaf folder pathogens (3 isolates each of Beauveria and Metarhizium spp.) infected > 50% (80-90%) larvae but other fungi were ineffective as infected < 50% (0-47%) insects. Besides, the leaf folder pathogens exhibited diverse PGP traits such as organic/inorganic phosphate solubilization (104.7-236.4 µg/ml), and siderophore, ammonia, hydrogen cyanide (HCN), indole production etc. Restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD), simple sequences repeat (SSR) and internal transcribed spacers (ITS) analysis ascertained strain identity and genetic (inter and intra-specific) diversity among the potent biocides Beauveria and Metarhizium spp. The virulent natural fungal pathogens of rice pests with polyvalent PGP traits may be prospected for rice growth promotion and biocontrol of leaf folder.

Kadereit

The Earth is undergoing alterations at a high speed, which causes problems such as environmental pollution and difficulty in food production. This is where halophytes are interesting, due to their high potential in different fields, such as remediation of the environment and agriculture. For this reason, it is necessary to deepen the knowledge of the development of halophytes and how plant growth-promoting bacteria (PGP) can play a fundamental role in this process. Therefore, in this work were tested the effects of five PGP bacteria on its rhizosphere and other endophytic bacteria at different concentrations of NaCl on seed germination, plant growth (0 and 171 mM) and cutting growth (0 mM) of Arthrocaulon macrostachyum. The growth promotion in this strict halophyte is highlighted due to the presence of PGP bacteria and the fact that no salt is needed. Thus, without salt, the bacterial strains Kocuria polaris Hv16, Pseudarthrobacter psychrotolerans C58, and Rahnella aceris RTE9 enhanced the biomass production by more than 60% in both stems and roots. Furthermore, germination was encouraged by more than 30% in the presence of both R. aceris RTE9 and K. polaris Hv16 at 171 mM NaCl; the latter also had a biocontrol effect on the fungi that grew on the seeds. Additionally, for the first time in cuttings of this perennial species, the root biomass was improved thanks to the consortium of K. polaris Hv16 and P. psychrotolerans C58. Finally, this study demonstrates the potential of PGPs for optimising the development of halophytes, either for environmental or agronomic purposes.

Characterization of actinobacteria from wheat seeds for plant growth promoting traits and protection against fungal pathogens

Seeds harbor naturally occurring microbial endophytes that proliferate during seedling development; playing crucial roles in seedling growth, establishment, and protection against fungal pathogens. Resilient actinobacteria of wheat seeds have been explored in this study for their beneficial traits. Ten actinobacteria isolated from the surface-sterilized seeds of wheat variety HD3117 were identified as nine species of Streptomyces and one of Nocardiopsis. Most isolates could grow at 42°C, 5% NaCl, and 10% poly ethylene glycol (PEG); exhibited variable hydrolytic enzyme production for amylase, cellulase, and protease. Few isolates produced indole acetic acid (9.0-18.9 µg ml^-1 ) and could solubilize P (11.3-85.2 µg ml^-1 ). The isolates were antagonistic against one or more fungal pathogens under test (Fusarium graminearum, Bipolaris sorokiniana, Alternaria sp., and Tilletia indica), of which Streptomyces sampsonii WSA20 inhibited all in dual culture assay. Priming of wheat seeds with the efficient isolate WSA20 led to effective colonization in the root zone and significantly improved germination, shoot and root length in seed germination assay. Significant protection was recorded in microcosm experiment where no symptoms of disease were observed. This study shows the significance of actinobacterial endophytes of wheat seeds in influencing seed germination and seedling growth while protecting from soil-borne pathogens. It is original and suggests that the seed inhabiting efficient actinobacteria may be developed as efficient bioinoculant for sustainable farming system.

Effects of Bacterial and Fungal Inocula on Biomass, Ecophysiology, and Uptake of Metals of Alyssoides utriculata (L.) Medik

The inoculation of plants with plant-growth-promoting microorganisms (PGPM) (i.e., bacterial and fungal strains) is an emerging approach that helps plants cope with abiotic and biotic stresses. However, knowledge regarding their synergic effects on plants growing in metal-rich soils is limited. Consequently, the aim of this study was to investigate the biomass, ecophysiology, and metal accumulation of the facultative Ni-hyperaccumulator Alyssoides utriculata (L.) Medik. inoculated with single or mixed plant-growth-promoting (PGP) bacterial strain Pseudomonas fluorescens Migula 1895 (SERP1) and PGP fungal strain Penicillium ochrochloron Biourge (SERP03 S) on native serpentine soil (n = 20 for each treatment). Photosynthetic efficiency (Fv/Fm) and performance indicators (PI) had the same trends with no significant differences among groups, with Fv/Fms > 1 and PI up to 12. However, the aboveground biomass increased 4-5-fold for single and mixed inoculated plants. The aboveground/belowground dry biomass ratio was higher for plants inoculated with fungi (30), mixed (21), and bacteria (17). The ICP-MS highlighted that single and mixed inocula were able to double the aboveground biomass' P content. Mn metal accumulation significantly increased with both single and mixed PGP inocula, and Zn accumulation increased only with single PGP inocula, whereas Cu accumulation increased twofold only with mixed PGP inocula, but with a low content. Only Ni metal accumulation approached the hyperaccumulation level (Ni > 1000 mg/kg DW) with all treatments. This study demonstrated the ability of selected single and combined PGP strains to significantly increase plant biomass and plant tolerance of metals present in the substrate, resulting in a higher capacity for Ni accumulation in shoots.

Insight into Glyproline Peptides' Activity through the Modulation of the Inflammatory and Neurosignaling Genetic Response Following Cerebral Ischemia-Reperfusion

Glyprolines are Gly-Pro (GP)- or Pro-Gly (PG)-containing biogenic peptides. These peptides can act as neutrophil chemoattractants, or atheroprotective, anticoagulant, and neuroprotective agents. The Pro-Gly-Pro (PGP) tripeptide is an active factor of resistance to the biodegradation of peptide drugs. The synthetic Semax peptide, which includes Met-Glu-His-Phe (MEHF) fragments of adrenocorticotropic hormone and the C-terminal tripeptide PGP, serves as a neuroprotective drug for the treatment of ischemic stroke. Previously, we revealed that Semax mostly prevented the disruption of the gene expression pattern 24 h after a transient middle cerebral artery occlusion (tMCAO) in a rat brain model. The genes of this pattern were grouped into an inflammatory cluster (IC) and a neurotransmitter cluster (NC). Here, using real-time RT-PCR, the effect of other PGP-containing peptides, PGP and Pro-Gly-Pro-Leu (PGPL), on the expression of a number of genes in the IC and NC was studied 24 h after tMCAO. Both the PGP and PGPL peptides showed Semax-unlike effects, predominantly without changing gene expression 24 h after tMCAO. Moreover, there were IC genes (iL1b, iL6, and Socs3) for PGP, as well as IC (iL6, Ccl3, Socs3, and Fos) and NC genes (Cplx2, Neurod6, and Ptk2b) for PGPL, that significantly changed in expression levels after peptide administration compared to Semax treatment under tMCAO conditions. Furthermore, gene enrichment analysis was carried out, and a regulatory gene network was constructed. Thus, the spectra of the common and unique effects of the PGP, PGPL, and Semax peptides under ischemia-reperfusion were distinguished.

The effect of gestational diabetes mellitus on occurrence of the pelvic girdle pain and symptom severity in pregnant women

The primary objective of this study was to examine the effect of gestational diabetes mellitus (GDM) on pelvic girdle pain (PGP) occurrence and symptom severity. Pregnant women who were with/without GDM, 20-40 years of age, and also in the second and third trimesters of pregnancy were included in the study. PGP provocation tests were administered to 187 pregnant women to determine the presence and severity of PGP. Based on the test results, the study subjects were divided into two groups; Group 1 (GDM+, PGP+; n:32) and Group 2 (GDM-, PGP+; n:35). Both groups were asked to fill in the Pelvic Girdle Questionnaire (PGQ). The relationship between the presence of GDM and the presence of PGP was found to be significant (p = .043). It was found the groups were similar in view of pain, and also in PGQ total/subscale scores (p > .05). Although GDM has no effect on symptom severity, it has been determined that it may relate to the development of PGP. Therefore, early interventions (nutrition, exercise, belt using, etc.) are recommended to prevent the development of PGP in pregnant women with a family history of diabetes, with a previous diagnosis of diabetes and/or with GDM detected in their previous pregnancies. Clinical Trial Number: 04769375Impact of StatementWhat is already known on this subject? Gestational diabetes mellitus and pelvic girdle pain are pathologies that develops secondary to pregnancy-related systemic and biomechanical changes.What do results on this study add? GDM may related the development of PGP.What are the implications of these findings for clinical practice and/or further research? Early interventions (nutrition, exercise, belt using, etc.) and strict control of pregnant women in view of PGP is recommended to prevent the development of PGP in pregnant women with a family history of diabetes, with previous diagnosis of diabetes and/or with GDM detected in their previous pregnancies. The evaluation of pregnant women for PGP before administering interventions, such as exercise and diet (both decrease the pro-inflammatory markers), following the diagnosis of GDM and the measurement of plasma anti- and pro-inflammatory marker values in the same time period will further reveal the relationship between GDM and PGP.

An Isolated Arthrobacter sp. Enhances Rice (Oryza sativa L.) Plant Growth

Rice is a symbol of life and a representation of prosperity in South Korea. However, studies on the diversity of the bacterial communities in the rhizosphere of rice plants are limited. In this study, four bundles of root samples were collected from the same rice field located in Goyang, South Korea. These were systematically analyzed to discover the diversity of culturable bacterial communities through culture-dependent methods. A total of 504 culturable bacteria were isolated and evaluated for their plant growth-promoting abilities in vitro. Among them, Arthrobacter sp. GN70 was selected for inoculation into the rice plants under laboratory and greenhouse conditions. The results showed a significantly positive effect on shoot length, root length, fresh plant weight, and dry plant weight. Moreover, scanning electron microscopic (SEM) images demonstrated the accumulation of bacterial biofilm networks at the junction of the primary roots, confirming the root-colonizing ability of the bacterium. The strain also exhibited a broad spectrum of in vitro antimicrobial activities against bacteria and fungi. Here, we first report the rice plant growth-promoting ability of the Arthrobacter species with the biofilm-producing and antimicrobial activities against plant and human pathogens. Genome analyses revealed features attributable to enhance rice plant growth, including the genes involved in the synthesis of plant hormones, biofilm production, and secondary metabolites. This study revealed that the rhizobacteria isolated from the roots of rice plants have dual potential to be utilized as a plant growth promoter and antimicrobial agent.

Deciphering Genomes: Genetic Signatures of Plant-Associated Micromonospora

Understanding plant-microbe interactions with the possibility to modulate the plant's microbiome is essential to design new strategies for a more productive and sustainable agriculture and to maintain natural ecosystems. Therefore, a key question is how to design bacterial consortia that will yield the desired host phenotype. This work was designed to identify the potential genomic features involved in the interaction between Micromonospora and known host plants. Seventy-four Micromonospora genomes representing diverse environments were used to generate a database of all potentially plant-related genes using a novel bioinformatic pipeline that combined screening for microbial-plant related features and comparison with available plant host proteomes. The strains were recovered in three clusters, highly correlated with several environments: plant-associated, soil/rhizosphere, and marine/mangrove. Irrespective of their isolation source, most strains shared genes coding for commonly screened plant growth promotion features, while differences in plant colonization related traits were observed. When Arabidopsis thaliana plants were inoculated with representative Micromonospora strains selected from the three environments, significant differences were in found in the corresponding plant phenotypes. Our results indicate that the identified genomic signatures help select those strains with the highest probability to successfully colonize the plant and contribute to its wellbeing. These results also suggest that plant growth promotion markers alone are not good indicators for the selection of beneficial bacteria to improve crop production and the recovery of ecosystems.

Phylogenetic affiliation of endophytic actinobacteria associated with selected orchid species and their role in growth promotion and suppression of phytopathogens

Endophytic actinobacteria aid in plant development and disease resistance by boosting nutrient uptake or producing secondary metabolites. For the first time, we investigated the culturable endophytic actinobacteria associated with ten epiphytic orchid species of Assam, India. 51 morphologically distinct actinobacteria were recovered from surface sterilized roots and leaves of orchids and characterized based on different PGP and antifungal traits. According to the 16S rRNA gene sequence, these isolates were divided into six families and eight genera, where Streptomyces was most abundant (n=29, 56.86%), followed by Actinomadura, Nocardia, Nocardiopsis, Nocardioides, Pseudonocardia, Microbacterium, and Mycolicibacterium. Regarding PGP characteristics, 25 (49.01%) isolates demonstrated phosphate solubilization in the range of 61.1±4.4 - 289.7±11.9 µg/ml, whereas 27 (52.94%) isolates biosynthesized IAA in the range of 4.0 ± 0.08 - 43.8 ± 0.2 µg/ml, and 35 (68.62%) isolates generated ammonia in the range of 0.9 ± 0.1 - 5.9 ± 0.2 µmol/ml. These isolates also produced extracellular enzymes, viz. protease (43.13%), cellulase (23.52%), pectinase (21.56%), ACC deaminase (27.45%), and chitinase (37.25%). Out of 51 isolates, 27 (52.94%) showed antagonism against at least one test phytopathogen. In molecular screening, most isolates with antifungal and chitinase producing traits revealed the presence of 18 family chitinase genes. Two actinobacterial endophytes, Streptomyces sp. VCLA3 and Streptomyces sp. RVRA7 were ranked as the best strains based on PGP and antifungal activity on bonitur scale. GC-MS examination of ethyl acetate extract of these potent strains displayed antimicrobial compound phenol, 2,4-bis-(1,1-dimethylethyl) as the major metabolite along with other antifungal and plant growth beneficial bioactive chemicals. SEM analysis of fungal pathogen F. oxysporum (MTCC 4633) affected by Streptomyces sp. VCLA3 revealed significant destruction in the spore structure. An in vivo plant growth promotion experiment with VCLA3 and RVRA7 on chili plants exhibited statistically significant (p<0.05) improvements in all of the evaluated vegetative parameters compared to the control. Our research thus gives insight into the diversity, composition, and functional significance of endophytic actinobacteria associated with orchids. This research demonstrates that isolates with multiple plant development and broad-spectrum antifungal properties are beneficial for plant growth. They may provide a viable alternative to chemical fertilizers and pesticides and a sustainable solution for chemical inputs in agriculture.

Root-Derived Endophytic Diazotrophic Bacteria Pantoea cypripedii AF1 and Kosakonia arachidis EF1 Promote Nitrogen Assimilation and Growth in Sugarcane

Excessive, long-term application of chemical fertilizers in sugarcane crops disrupts soil microbial flora and causes environmental pollution and yield decline. The role of endophytic bacteria in improving crop production is now well-documented. In this study, we have isolated and identified several endophytic bacterial strains from the root tissues of five sugarcane species. Among them, eleven Gram-negative isolates were selected and screened for plant growth-promoting characteristics, i.e., production of siderophores, indole-3-acetic acid (IAA), ammonia, hydrogen cyanide (HCN), and hydrolytic enzymes, phosphorus solubilization, antifungal activity against plant pathogens, nitrogen-fixation, 1-aminocyclopropane-1-carboxylic acid deaminase activity, and improving tolerance to different abiotic stresses. These isolates had nifH (11 isolates), acdS (8 isolates), and HCN (11 isolates) genes involved in N-fixation, stress tolerance, and pathogen biocontrol, respectively. Two isolates Pantoea cypripedii AF1and Kosakonia arachidis EF1 were the most potent strains and they colonized and grew in sugarcane plants. Both strains readily colonized the leading Chinese sugarcane variety GT42 and significantly increased the activity of nitrogen assimilation enzymes (glutamine synthetase, NADH glutamate dehydrogenase, and nitrate reductase), chitinase, and endo-glucanase and the content of phytohormones gibberellic acid, indole-3-acetic acid, and abscisic acid. The gene expression analysis of GT42 inoculated with isolates of P. cypripedii AF1 or K. arachidis EF1 showed increased activity of nifH and nitrogen assimilation genes. Also, the inoculated diazotrophs significantly increased plant nitrogen content, which was corroborated by the 15N isotope dilution analysis. Collectively, these findings suggest that P. cypripedii and K. arachidis are beneficial endophytes that could be used as a biofertilizer to improve plant nitrogen nutrition and growth of sugarcane. To the best of our knowledge, this is the first report of sugarcane growth enhancement and nitrogen fixation by Gram-negative sugarcane root-associated endophytic bacteria P. cypripedii and K. arachidis. These strains have the potential to be utilized as sugarcane biofertilizers, thus reducing nitrogen fertilizer use and improving disease management.

Differential Protein Expression Analysis of Two Sugarcane Varieties in Response to Diazotrophic Plant Growth-Promoting Endophyte Enterobacter roggenkampii ED5

Plant endophytic bacteria have many vital roles in plant growth promotion (PGP), such as nitrogen (N) fixation and resistance to biotic and abiotic stresses. In this study, the seedlings of sugarcane varieties B8 (requires a low concentration of nitrogen for growth) and GT11 (requires a high concentration of nitrogen for growth) were inoculated with endophytic diazotroph Enterobacter roggenkampii ED5, which exhibits multiple PGP traits, isolated from sugarcane roots. The results showed that the inoculation with E. roggenkampii ED5 promoted the growth of plant significantly in both sugarcane varieties. ¹⁵N detection at 60 days post-inoculation proved that the inoculation with strain ED5 increased the total nitrogen concentration in the leaf and root than control in both sugarcane varieties, which was higher in B8. Biochemical parameters and phytohormones in leaf were analyzed at 30 and 60 days after the inoculation. The results showed that the inoculation with E. roggenkampii ED5 improved the activities of superoxide dismutase (SOD), catalase (CAT), NADH-glutamate dehydrogenase (NADH-GDH), glutamine synthetase (GS), and endo-β-1,4-glucanase, and the contents of proline and indole acetic acid (IAA) in leaf, and it was generally more significant in B8 than in GT11. Tandem Mass Tags (TMT) labeling and liquid chromatography-tandem mass spectrometry (LC-MS/MS) were used to perform comparative proteomic analysis in the sugarcane leaves at 30 days after inoculation with strain ED5. A total of 27,508 proteins were detected, and 378 differentially expressed proteins (DEPs) were found in the treated sugarcane variety B8 (BE) as compared to control (BC), of which 244 were upregulated and 134 were downregulated. In contrast, a total of 177 DEPs were identified in the treated sugarcane variety GT11 (GE) as compared to control (GC), of which 103 were upregulated and 74 were downregulated. The DEPs were associated with nitrogen metabolism, photosynthesis, starch, sucrose metabolism, response to oxidative stress, hydrolase activity, oxidative phosphorylation, glutathione metabolism, phenylpropanoid metabolic process, and response to stresses in Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database. To the best of our knowledge, this is the first proteomic approach to investigate the molecular basis of the interaction between N-fixing endophytic strain E. roggenkampii ED5 and sugarcane.

Modulating Drought Stress Response of Maize by a Synthetic Bacterial Community

Plant perception and responses to environmental stresses are known to encompass a complex set of mechanisms in which the microbiome is involved. Knowledge about plant physiological responses is therefore critical for understanding the contribution of the microbiome to plant resilience. However, as plant growth is a dynamic process, a major hurdle is to find appropriate tools to effectively measure temporal variations of different plant physiological parameters. Here, we used a non-invasive real-time phenotyping platform in a one-to-one (plant–sensors) set up to investigate the impact of a synthetic community (SynCom) harboring plant-beneficial bacteria on the physiology and response of three commercial maize hybrids to drought stress (DS). SynCom inoculation significantly reduced yield loss and modulated vital physiological traits. SynCom-inoculated plants displayed lower leaf temperature, reduced turgor loss under severe DS and a faster recovery upon rehydration, likely as a result of sap flow modulation and better water usage. Microbiome profiling revealed that SynCom bacterial members were able to robustly colonize mature plants and recruit soil/seed-borne beneficial microbes. The high-resolution temporal data allowed us to record instant plant responses to daily environmental fluctuations, thus revealing the impact of the microbiome in modulating maize physiology, resilience to drought, and crop productivity.

Usability of End-to-End Encryption in E-Mail Communication

This paper presents the results of a usability study focused on three end-to-end encryption technologies for securing e-mail traffic, namely PGP, S/MIME, and Pretty Easy Privacy (pEp). The findings of this study show that, despite of existing technology, users seldom apply them for securing e-mail communication. Moreover, this study helps to explain why users hesitate to employ encryption technology in their e-mail communication. For this usability study, we have combined two methods: 1) an online survey, 2) and user testing with 12 participants who were enrolled in tasks requiring e-mail encryption. We found that more than 60% of our study participants (in both methods) are unaware of the existence of encryption technologies and thus never tried to use one. We observed that above all, users 1) are overwhelmed with the management of public keys and 2) struggle with the setup of encryption technology in their e-mail software. Nonetheless, 66% of the participants consider secure e-mail communication as important or very important. Particularly, we found an even stronger concern about identity theft among e-mail users, as 78% of the participants want to make sure that no other person is able to write e-mail on their behalf.

Suppression of HIV-1 Viral Replication by Inhibiting Drug Efflux Transporters in Activated Macrophages

BACKGROUND

Ethanol has been shown to increase oxidative stress, drug efflux transporter expression, and promote HIV progression. Macrophages, which express drug efflux transporters, serve as an essential sanctuary site for HIV. The antiretroviral drug lopinavir, a protease inhibitor, is a substrate of the drug efflux transporters P-glycoprotein and multidrug resistance-associated protein 1. The NF-κB signaling pathway is associated with inflammation and drug efflux transporter expression.

OBJECTIVE

To examine the effects of ethanol on drug efflux transporters and HIV replication of macrophages and develop strategies to increase the efficacy of the protease inhibitor.

METHODS

The expression of PGP and MRP1 was examined with western blot. The NF- κB inhibition was assessed with nuclear western blot. LC-MS/MS and p24 ELISA were used to assess intracellular LPV and viral replication.

RESULTS

Ethanol at 40mM slightly increased drug efflux transporter PGP and MRP1 expression in activated macrophages. IKK-16, an NF- κB inhibitor, counteracted the increased transporter expression caused by ethanol exposure. MK571, an MRP1 inhibitor, and IKK-16 significantly increased intracellular LPV concentration with or without ethanol treatment. MK571 significantly increased LPV efficacy in suppressing viral replication with or without ethanol treatment. A decreasing trend and a significant decrease were observed with IKK-16+LPV treatment compared with LPV alone in the no ethanol treatment and ethanol treatment groups, respectively.

CONCLUSION

In activated macrophages, inhibiting drug efflux transporter MRP1 activity and reducing its expression may represent a promising approach to suppress viral replication by increasing intracellular antiretroviral concentrations. However, different strategies may be required for ethanolrelated vs. untreated groups.

Transfer of rhodamine-123 into the brain and cerebrospinal fluid of fetal, neonatal and adult rats

Background

Adenosine triphosphate binding cassette transporters such as P-glycoprotein (PGP) play an important role in drug pharmacokinetics by actively effluxing their substrates at barrier interfaces, including the blood-brain, blood-cerebrospinal fluid (CSF) and placental barriers. For a molecule to access the brain during fetal stages it must bypass efflux transporters at both the placental barrier and brain barriers themselves. Following birth, placental protection is no longer present and brain barriers remain the major line of defense. Understanding developmental differences that exist in the transfer of PGP substrates into the brain is important for ensuring that medication regimes are safe and appropriate for all patients.

Methods

In the present study PGP substrate rhodamine-123 (R123) was injected intraperitoneally into E19 dams, postnatal (P4, P14) and adult rats. Naturally fluorescent properties of R123 were utilized to measure its concentration in blood-plasma, CSF and brain by spectrofluorimetry (Clariostar). Statistical differences in R123 transfer (concentration ratios between tissue and plasma ratios) were determined using Kruskal-Wallis tests with Dunn’s corrections.

Results

Following maternal injection the transfer of R123 across the E19 placenta from maternal blood to fetal blood was around 20 %. Of the R123 that reached fetal circulation 43 % transferred into brain and 38 % into CSF. The transfer of R123 from blood to brain and CSF was lower in postnatal pups and decreased with age (brain: 43 % at P4, 22 % at P14 and 9 % in adults; CSF: 8 % at P4, 8 % at P14 and 1 % in adults). Transfer from maternal blood across placental and brain barriers into fetal brain was approximately 9 %, similar to the transfer across adult blood-brain barriers (also 9 %). Following birth when placental protection was no longer present, transfer of R123 from blood into the newborn brain was significantly higher than into adult brain (3 fold, p < 0.05).

Conclusions

Administration of a PGP substrate to infant rats resulted in a higher transfer into the brain than equivalent doses at later stages of life or equivalent maternal doses during gestation. Toxicological testing of PGP substrate drugs should consider the possibility of these patient specific differences in safety analysis.

Plant growth promoting and antifungal asset of indigenous rhizobacteria secluded from saffron (Crocus sativus L.) rhizosphere

Saffron (Crocus sativus L.) is an important plant in medicine. The Kashmir Valley (J&K, India) is one of the world's largest and finest saffron producing regions. However, over the past decade, there has been a strong declining trend in saffron production in this area. Plant Growth Promoting Rhizobacteria (PGPR) are free living soil bacteria that have ability to colonize the surfaces of the roots and ability to boost plant growth and development either directly or indirectly. Using the efficient PGPR as a bio-inoculant is another sustainable agricultural practice to improve soil health, grain yield quality, and biodiversity conservation. In the present study, a total of 13 bacterial strains were isolated from rhizospheric soil of saffron during the flowering stage of the tubers and were evaluated for various plant growth promoting characteristics under in vitro conditions such as the solubilization of phosphate, production of indole acetic acid, siderophore, hydrocyanic acid, and ammonia production and antagonism by dual culture test against Sclerotium rolfsii and Fusarium oxysporum. All the isolates were further tested for the production of hydrolytic enzymes such as protease, lipase, amylase, cellulase, and chitinase. The maximum proportions of bacterial isolates were gram-negative bacilli. About 77% of the bacterial isolates showed IAA production, 46% exhibited phosphate solubilization, 46% siderophore, 61% HCN, 100% ammonia production, 69% isolates showed protease activity, 62% lipase, 46% amylase, 85% cellulase, and 39% showed chitinase activity. Three isolates viz., AIS-3, AIS-8 and AIS-10 were found to have the most plant growth properties and effectively control the growth of Sclerotium rolfsii and Fusarium oxysporum. The bacterial isolates were identified as Brevibacterium frigoritolerans (AIS-3), Alcaligenes faecalis subsp. Phenolicus (AIS-8) and Bacillus aryabhattai (AIS-10) respectively by 16S rRNA sequence analysis. Therefore, these isolated rhizobacterial strains could be a promising source of plant growth stimulants to increase cormlets growth and increase saffron production.

Rice-Associated Rhizobacteria as a Source of Secondary Metabolites against Burkholderia glumae

Various diseases, including bacterial panicle blight (BPB) and sheath rot, threaten rice production. It has been established that Burkholderia glumae (B. glumae) is the causative agent of the above mentioned pathologies. In the present study, antagonistic activity, growth promotion, and the metabolite profiles of two rhizobacteria, isolated in different paddy fields, were assessed against B. glumae. Strains were identified based on 16S rRNA gene sequences, and the phylogenetic analyses showed that both strains belong to the genus Enterobacter, with high similarity to the strain Enterobacter tabaci NR146667.2 (99%). The antagonistic activity was assessed with the disc diffusion method. Active fractions were isolated through a liquid/liquid extraction with ethyl acetate (EtOAc) from the fermentation media, and their antibacterial activities were evaluated following the Clinical and Laboratory Standards Institute (CLSI) guidelines. The Pikovskaya modified medium was used to test the ability of in vitro inorganic phosphorus solubilization, and BSB1 proved to be the best inorganic phosphorus solubilizer, with a solubilization index (SI) of 4.5 ± 0.2. The glass-column fractionation of the EtOAc extracted from BCB11 produced an active fraction (25.9 mg) that inhibited the growth of five B. glumae strains by 85-95%. Further, metabolomic analysis, based on GC-MS, showed 3-phenylpropanoic acid (3-PPA) to be the main compound both in this fraction (46.7%), and in the BSB1 extract (28.6%). This compound showed antibacterial activity against all five strains of B. glumae with a minimum inhibitory concentration (MIC) of 1000 mg/L towards all of them. The results showed that rice rhizosphere microorganisms are a source of compounds that inhibit B. glumae growth and are promising plant growth promoters (PGP).

Zinc solubilizing bacteria (Bacillus megaterium) with multifarious plant growth promoting activities alleviates growth in Capsicum annuum L

The present study was designed to isolate an array of zinc solubilizing bacteria (ZSB) and to characterize them for plant growth promotion (PGP) attributes with respect to Capsicum annuum L. For this purpose, seventy bacteria were procured from cow dung and screened for zinc solubilization (ZnO and ZnCO₃). Where, isolate CDK25 was found to be the most potent owing to its maximum zinc solubilization (ZnO) ability (5.0 cm). For quantitative assay, atomic absorption spectroscopy (AAS) was used, where CDK25 showed markedly higher solubilization of ZnO (20.33 ppm). It was investigated that CDK25 also endowed with multiple PGP attributes viz., Phosphate solubilization, Phytase production, Indole acetic acid (IAA) and Siderophore production. Quantitative study revealed isolate CDK25 to solubilize and produce maximum quantity of phosphate (281.59 μg/ml) and IAA (13.8 μg/ml) respectively. ZSB was applied in different treatments under pot culture assay, where T3 (seeds + CDK25) showed significant impact on plant growth parameters, besides showing maximum zinc content in fruit (0.25 mg/100 g). Hence, isolate CDK25 expresses highest potential throughout the experiments; as zinc solubilizer, PGP strain, and based on 16S rRNA gene sequencing identified as Bacillus megaterium. Therefore, meticulous use of this bacterium could aid in providing adequate amount of soluble zinc along with enhanced plants growth, nutrient uptake and yield in sustainable manner.

ABC efflux transporters at blood-central nervous system barriers and their implications for treating spinal cord disorders

The barriers present in the interfaces between the blood and the central nervous system form a major hurdle for the pharmacological treatment of central nervous system injuries and diseases. The family of ATP-binding cassette (ABC) transporters has been widely studied regarding efflux of medications at blood-central nervous system barriers. These efflux transporters include P-glycoprotein (abcb1), 'breast cancer resistance protein' (abcg2) and the various 'multidrug resistance-associated proteins' (abccs). Understanding which efflux transporters are present at the blood-spinal cord, blood-cerebrospinal fluid and cerebrospinal fluid-spinal cord barriers is necessary to determine their involvement in limiting drug transfer from blood to the spinal cord tissue. Recent developments in the blood-brain barrier field have shown that barrier systems are dynamic and the profile of barrier defenses can alter due to conditions such as age, disease and environmental challenge. This means that a true understanding of ABC efflux transporter expression and localization should not be one static value but instead a range that represents the complex patient subpopulations that exist. In the present review, the blood-central nervous system barrier literature is discussed with a focus on the impact of ABC efflux transporters on: (i) protecting the spinal cord from adverse effects of systemically directed drugs, and (ii) limiting centrally directed drugs from accessing their active sites within the spinal cord.

Endophytic Bacillus megaterium BM18-2 mutated for cadmium accumulation and improving plant growth in Hybrid Pennisetum

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The endophytic Bacillus megaterium isolated from Hybrid Pennisetum is promising isolate for Cd bioremediation.

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The mutated strain BM18-2 showed higher capacity to resist Cd until 70 μM and improving plant growth.

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Six different genes of BM18-2 are involved in Cd resistance mechanism.

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Hybrid Pennisetum inoculated with BM18-2 showed higher amount of growth and toleranc to Cd toxicity than uninoculated plants.

Hybrid Pennisetum (Pennisetum americanum × P. purpureum Schumach L.) is a tall and rapidly growing perennial C₄ bunch grass. It has been considered as a promising plant for phytoremediation of heavy metal-contaminated soil due to its high biomass, high resistance to environmental stress, pests and diseases. Heavy metal bioavailability level is the most important parameter for measurement of the phytoremediation efficiency. Endophytic bacteria were used to further enhance phytoremediation of heavy metals through bioaccumulation or bioabsorption process. In the present study, the endophytic Bacillus megaterium strain ‘BM18’ isolated from hybrid Pennisetum was screened under 10-70 μM cadmium (Cd) stress for Cd-resistant mutant colonies. And one such mutant colony‘BM18-2’ was obtained from the screen. Comparably, ‘BM18-2’ was more Cd-tolerant and had higher Cd removal ability than the original strain‘BM18’. The amount of IAA and ammonia production, and phosphate solubilization were 1.09, 1.23 and 1.24 times in ‘BM18-2’ than those of ‘BM18’, respectively. Full genome sequencing of these two strains revealed 6 different genes: BM18GM000901, BM18GM005669 and BM18GM005870 encoding heavy metal efflux pumps, BM18GM003487 and BM18GM005818 encoding transcriptional regulators for metal stress biosensor and BM18GM001335 encoding a replication protein. Inoculation with ‘BM18-2’ or ‘BM18’ both significantly reduced the toxic effect of Cd on hybrid Pennisetum, while the effect of ‘BM18-2’ on plant growth promotion in the presence of Cd was significantly better that of ‘BM18’. Therefore, the mutated strain ‘BM18-2’ could be used as a potential agent for Cd bioremediation, improving growth and Cd absorption of hybrid Pennisetum in Cd contaminated soil.

Erythrobacter aureus sp. nov., a plant growth-promoting bacterium isolated from sediment in the Yellow Sea, China

The application of plant growth-promoting (PGP) bacterium in agriculture is expanding rapidly in recent years. With the development of microbial technology, new bacterial species effective in promoting plant growth have been identified. In this study, a PGP bacterium was isolated from marine sediments of the Yellow Sea in China. The confrontation culture test and pot experiments showed that strain YH-07T inhibited the growth of Fusarium oxysporum f. sp. lycopersici (a plant pathogenic fungus), benefiting plant growth and reducing disease incidence of tomato wilt. We used polyphasic approaches including phenotypic, chemotaxonomic and phylogenetic information to determine its taxonomic status. In addition to profiling general features of the YH-07T genome, we identified genes related to PGP traits and genes involved in environmental stress tolerance. Metabolic assays showed that strain YH-07T could produce siderophores, solubilize phosphate, resist to salinity, and grow well within a wide range of temperature and pH, which is a promising PGP bacterium for future agricultural applications. These results provide evidence that strain YH-07T is a novel species of the genus Erythrobacter, for which the name Erythrobacter aureus sp. nov. is proposed. The type strain is YH-07T (= CGMCC 1.16784T = DSM 107319T).

Selection of an Endophytic Streptomyces sp. Strain DEF09 From Wheat Roots as a Biocontrol Agent Against Fusarium graminearum

Selection of biological control agents (BCA) profits from an integrated study of the tripartite interactions occurring among the BCA, the plant and the pathogen. The environment plays a crucial role in the efficacy of BCA, therefore, the selection process shall utmost mimic naturally occurring conditions. To identify effective biocontrol strains against Fusarium graminearum, the major cause of Fusarium head blight (FHB) in wheat and deoxynivalenol (DON) accumulation in grains, a workflow consisting of in vitro and in vivo assays was set up. Twenty-one Streptomyces strains, 16 of which were endophytes of different plants, were analyzed. In vitro and in vivo tests characterized their plant growth promoting (PGP) traits. Biocontrol activity against F. graminearum was firstly assessed with a dual culture assay. An in vivo germination blotter assay measured Fusarium foot rot and root rot symptoms (FFR-FRR) reduction as well as growth parameters of the plant treated with the Streptomyces strains. A selected subset of Streptomyces spp. strains was then assessed in a growth chamber measuring FFR symptoms and growth parameters of the wheat plant. The approach led to the identification of an effective Streptomyces sp. strain, DEF09, able to inhibit FHB on wheat in controlled conditions by blocking the spread of the pathogen at the infection site. The results were further confirmed in field conditions on both bread and durum wheat, where DEF09 decreased disease severity up to 60%. This work confirms that FRR and FFR pathosystems can be used to identify BCA effective against FHB.

Benzyloxycarbonyl-proline-prolinal (ZPP): Dual complementary roles for neutrophil inhibition

Neutrophil influx and activation contributes to organ damage in several major lung diseases. This inflammatory influx is initiated and propagated by both classical chemokines such as interleukin-8 and by downstream mediators such as the collagen fragment cum neutrophil chemokine Pro-Gly-Pro (PGP), which share use of the ELR + CXC receptor family. Benzyloxycarbonyl-proline-prolinal (ZPP) is known to suppress the PGP pathway via inhibition of prolyl endopeptidase (PE), the terminal enzyme in the generation of PGP from collagen. However, the structural homology of ZPP and PGP suggests that ZPP might also directly affect classical glutamate-leucine-arginine positive (ELR+) CXC chemokine signaling. In this investigation, we confirm that ZPP inhibits PE in vitro, demonstrate that ZPP inhibits both ELR + CXC and PGP-mediated chemotaxis in human and murine neutrophils, abrogates neutrophil influx induced by murine intratracheal challenge with LPS, and attenuates human neutrophil chemotaxis to sputum samples of human subjects with cystic fibrosis. Cumulatively, these data demonstrate that ZPP has dual, complementary inhibitory effects upon neutrophil chemokine/matrikine signaling which make it an attractive compound for clinical study of neutrophil inhibition in conditions (such as cystic fibrosis and chronic obstructive pulmonary disease) which evidence concurrent harmful increases of both chemokine and matrikine signaling.

Genomic insights into plant growth promoting rhizobia capable of enhancing soybean germination under drought stress

BACKGROUND

The role of soil microorganisms in plant growth, nutrient utilization, drought tolerance as well as biocontrol activity cannot be over-emphasized, especially in this era when food crisis is a global challenge. This research was therefore designed to gain genomic insights into plant growth promoting (PGP) Rhizobium species capable of enhancing soybean (Glycine max L.) seeds germination under drought condition.

RESULTS

Rhizobium sp. strain R1, Rhizobium tropici strain R2, Rhizobium cellulosilyticum strain R3, Rhizobium taibaishanense strain R4 and Ensifer meliloti strain R5 were found to possess the entire PGP traits tested. Specifically, these rhizobial strains were able to solubilize phosphate, produce exopolysaccharide (EPS), 1-aminocyclopropane-1-carboxylate (ACC), siderophore and indole-acetic-acid (IAA). These strains also survived and grew at a temperature of 45 °C and in an acidic condition with a pH 4. Consequently, all the Rhizobium strains enhanced the germination of soybean seeds (PAN 1532 R) under drought condition imposed by 4% poly-ethylene glycol (PEG); nevertheless, Rhizobium sp. strain R1 and R. cellulosilyticum strain R3 inoculations were able to improve seeds germination more than R2, R4 and R5 strains. Thus, genomic insights into Rhizobium sp. strain R1 and R. cellulosilyticum strain R3 revealed the presence of some genes with their respective proteins involved in symbiotic establishment, nitrogen fixation, drought tolerance and plant growth promotion. In particular, exoX, htrA, Nif, nodA, eptA, IAA and siderophore-producing genes were found in the two rhizobial strains.

CONCLUSIONS

Therefore, the availability of the whole genome sequences of R1 and R3 strains may further be exploited to comprehend the interaction of drought tolerant rhizobia with soybean and other legumes and the PGP ability of these rhizobial strains can also be harnessed for biotechnological application in the field especially in semiarid and arid regions of the globe.

Metal tolerant bacteria enhanced phytoextraction of lead by two accumulator ornamental species

Microbially enhanced availability and phytoextraction is a promising technique for phytoremediation of lead (Pb). In this study, Pb resistant strains were isolated and investigated for potential effects on plant growth and Pb phytoextraction. Incubation experiments were carried for inoculated and un-inoculated soil containing different levels of Pb. Results revealed that 20% of the isolated bacteria could tolerate Pb up to 800 mg L^-1. Five Pb resistant strains with plant growth promoting (PGP) abilities were evaluated for possible influence on water soluble Pb through soil incubation experiments and significant increase i.e. 1.85- and 1.49-folds in water soluble Pb was observed for NCCP-1848 and NCCP-1862 strains, respectively. Pot experiments indicated significantly higher uptake by Pelargonium hortorum than that by Mesembryanthemum criniflorrum at all levels of soil Pb concentrations with the highest increase (1.9-folds) in plants inoculated with NCCP-1848 followed by NCCP-1862 (1.8-folds increase) compared to the control (Pb and without bacterial strain). The strains NCCP-1848 and NCCP-1862 were identified by 16S rRNA gene sequencing as Microbacterium sp. and Klebsiella sp. The results of present study suggest that Pb resistant plant growth promoting bacteria can serve as an effective bio-inoculant through wide action spectrum for maximizing efficiency of phytoremediation system.

Soil Bacterial Communities From the Chilean Andean Highlands: Taxonomic Composition and Culturability

The Atacama Desert is a highly complex, extreme ecosystem which harbors microorganisms remarkable for their biotechnological potential. Here, a soil bacterial prospection was carried out in the high Altiplano region of the Atacama Desert (>3,800 m above sea level; m a.s.l.), where direct anthropogenic interference is minimal. We studied: (1) soil bacterial community composition using high-throughput sequencing of the 16S rRNA gene and (2) bacterial culturability, by using a soil extract medium (SEM) under a factorial design of three factors: temperature (15 and 30°C), nutrient content (high and low nutrient disposal) and oxygen availability (presence and absence). A total of 4,775 OTUs were identified and a total of 101 isolates were selected for 16S rRNA sequencing, 82 of them corresponded to unique or non-redundant sequences. To expand our view of the Altiplano landscape and to obtain a better representation of its microbiome, we complemented our Operational Taxonomic Units (OTUs) and isolate collection with data from other previous data from our group and obtained a merged set of OTUs and isolates that we used to perform our study. Taxonomic comparisons between culturable microbiota and metabarcoding data showed an overrepresentation of the phylum Firmicutes (44% of isolates vs. 2% of OTUs) and an underrepresentation of Proteobacteria (8% of isolates vs. 36% of OTUs). Within the Next Generation Sequencing (NGS) results, 33% of the OTUs were unknown up to genus, revealing an important proportion of putative new species in this environment. Biochemical characterization and analysis extracted from the literature indicated that an important number of our isolates had biotechnological potential. Also, by comparing our results with similar studies on other deserts, the Altiplano highland was most similar to a cold arid desert. In summary, our study contributes to expand the knowledge of soil bacterial communities in the Atacama Desert and complements the pipeline to isolate selective bacteria that could represent new potential biotechnological resources.

The neutrophil chemoattractant peptide proline-glycine-proline is associated with acute respiratory distress syndrome

Acute respiratory distress syndrome (ARDS) is characterized by unrelenting polymorphonuclear neutrophil (PMN) inflammation and vascular permeability. The matrikine proline-glycine-proline (PGP) and acetylated PGP (Ac-PGP) have been shown to induce PMN inflammation and endothelial permeability in vitro and in vivo. In this study, we investigated the presence and role of airway PGP peptides in acute lung injury (ALI)/ARDS. Pseudomonas aeruginosa-derived lipopolysaccharide (LPS) was instilled intratracheally in mice to induce ALI, and increased Ac-PGP with neutrophil inflammation was noted. The PGP inhibitory peptide, arginine-threonine-arginine (RTR), was administered (it) 30 min before or 6 h after LPS injection. Lung injury was evaluated by detecting neutrophil infiltration and permeability changes in the lung. Pre- and posttreatment with RTR significantly inhibited LPS-induced ALI by attenuating lung neutrophil infiltration, pulmonary permeability, and parenchymal inflammation. To evaluate the role of PGP levels in ARDS, minibronchoalveolar lavage was collected from nine ARDS, four cardiogenic edema, and five nonlung disease ventilated patients. PGP levels were measured and correlated with Acute Physiology and Chronic Health Evaluation (APACHE) score, P a O 2 to F I O 2 (P/F), and ventilator days. PGP levels in subjects with ARDS were significantly higher than cardiogenic edema and nonlung disease ventilated patients. Preliminary examination in both ARDS and non-ARDS populations demonstrated PGP levels significantly correlated with P/F ratio, APACHE score, and duration on ventilator. These results demonstrate an increased burden of PGP peptides in ARDS and suggest the need for future studies in ARDS cohorts to examine correlation with key clinical parameters.

Collagen Hydrolysis Products Reduce the Formation of Stress-Induced Ulcers by Regulating Stress-Associated Activation of the Neuroendocrine and Immune Systems

We studied the effect of collagen fragments (PGP and AcPGP) on serum content of epinephrine, corticosterone, and IL-1β in rats subjected to water-immersion stress. The degree of local inflammation accompanying ulceration was assessed by IL-1β production by ln. gastricus caudalis cells. In 1 h, the sharp increase in hormone concentrations in the blood of stressed animals reflected the high stress intensity. Intranasal administration of PGP reduced the area of stress-induced ulcers by 63%, prevented the increase in the levels of stress hormones and the main proinflammatory cytokine in rat blood. The concentrations of IL-1β in cell culture from regional lymph node of experimental animals returned to normal in 24 and 48 h after the stress. Acetylation of PGP prevents with gastroprotection, but does not abrogate other properties of the peptide.

Direct Macromolecular Drug Delivery to Cerebral Ischemia Area using Neutrophil-Mediated Nanoparticles

Delivery of macromolecular drugs to the brain is impeded by the blood brain barrier. The recruitment of leukocytes to lesions in the brain, a typical feature of neuroinflammation response which occurs in cerebral ischemia, offers a unique opportunity to deliver drugs to inflammation sites in the brain. In the present study, cross-linked dendrigraft poly-L-lysine (DGL) nanoparticles containing cis-aconitic anhydride-modified catalase and modified with PGP, an endogenous tripeptide that acts as a ligand with high affinity to neutrophils, were developed to form the cl PGP-PEG-DGL/CAT-Aco system. Significant binding efficiency to neutrophils, efficient protection of catalase enzymatic activity from degradation and effective transport to receiver cells were revealed in the delivery system. Delivery of catalase to ischemic subregions and cerebral neurocytes in MCAO mice was significantly enhanced, which obviously reducing infarct volume in MCAO mice. Thus, the therapeutic outcome of cerebral ischemia was greatly improved. The underlying mechanism was found to be related to the inhibition of ROS-mediated apoptosis. Considering that neuroinflammation occurs in many neurological disorders, the strategy developed here is not only promising for treatment of cerebral ischemia but also an effective approach for various CNS diseases related to inflammation.

Anti-allergic and anti-inflammatory activity of Phellinus linteus grown on Panax ginseng

Panax ginseng (PG) or Phellinus linteus (PL) have been widely used as traditional medicine owing to their many biological activities, including anti-inflammatory and anti-allergic activities. Previously, our group produced PL that was grown on PG media (PGP) to enhance anti-cancer activities of PGP. Here we studied the anti-allergic activity of PGP and its mechanism of action. The ethyl acetate fraction of PGP exhibited the anti-allergic activity by suppressing β-hexosaminidase release, a marker of degranulation, from antigen/immunoglobulin E (IgE)-stimulated RBL-2H3 cells. Exposure to PGP inhibited the level of antigen/IgE-induced TNF-alpha in RBL-2H3 cells. It markedly suppressed the phosphorylation of spleen associated tyrosine kinase, GRB2-associated-binding protein 2 (Gab2) and extracellular signal-regulated kinases proteins, which are required for the degranulation and production of pro-inflammatory cytokines. Its anti-inflammatory activity was observed in lipopolysaccharide-stimulated RAW 264.7 cells. In addition, PGP contained higher contents of Rg1 than PG. Our findings suggest that PGP might be developed as a therapeutic agent for IgE-mediated allergic diseases.

Hydrogen Cyanide in the Rhizosphere: Not Suppressing Plant Pathogens, but Rather Regulating Availability of Phosphate

Plant growth promoting rhizobacteria produce chemical compounds with different benefits for the plant. Among them, HCN is recognized as a biocontrol agent, based on its ascribed toxicity against plant pathogens. Based on several past studies questioning the validity of this hypothesis, we have re-addressed the issue by designing a new set of in vitro experiments, to test if HCN-producing rhizobacteria could inhibit the growth of phytopathogens. The level of HCN produced by the rhizobacteria in vitro does not correlate with the observed biocontrol effects, thus disproving the biocontrol hypothesis. We developed a new concept, in which HCN does not act as a biocontrol agent, but rather is involved in geochemical processes in the substrate (e.g., chelation of metals), indirectly increasing the availability of phosphate. Since this scenario can be important for the pioneer plants living in oligotrophic alpine environments, we inoculated HCN producing bacteria into sterile mineral sand together with germinating plants and showed that the growth of the pioneer plant French sorrel was increased on granite-based substrate. No such effect could be observed for maize, where plantlets depend on the nutrients stored in the endosperm. To support our concept, we used KCN and mineral sand and showed that mineral mobilization and phosphate release could be caused by cyanide in vitro. We propose that in oligotrophic alpine environments, and possibly elsewhere, the main contribution of HCN is in the sequestration of metals and the consequential indirect increase of nutrient availability, which is beneficial for the rhizobacteria and their plant hosts.

The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes

Background

Since the completion of the Human Genome Project in 2003, it is estimated that more than 200,000 individual whole human genomes have been sequenced. A stunning accomplishment in such a short period of time. However, most of these were sequenced without experimental haplotype data and are therefore missing an important aspect of genome biology. In addition, much of the genomic data is not available to the public and lacks phenotypic information.

Findings

As part of the Personal Genome Project, blood samples from 184 participants were collected and processed using Complete Genomics’ Long Fragment Read technology. Here, we present the experimental whole genome haplotyping and sequencing of these samples to an average read coverage depth of 100X. This is approximately three-fold higher than the read coverage applied to most whole human genome assemblies and ensures the highest quality results. Currently, 114 genomes from this dataset are freely available in the GigaDB repository and are associated with rich phenotypic data; the remaining 70 should be added in the near future as they are approved through the PGP data release process. For reproducibility analyses, 20 genomes were sequenced at least twice using independent LFR barcoded libraries. Seven genomes were also sequenced using Complete Genomics’ standard non-barcoded library process. In addition, we report 2.6 million high-quality, rare variants not previously identified in the Single Nucleotide Polymorphisms database or the 1000 Genomes Project Phase 3 data.

Conclusions

These genomes represent a unique source of haplotype and phenotype data for the scientific community and should help to expand our understanding of human genome evolution and function.

Electronic supplementary material

The online version of this article (doi:10.1186/s13742-016-0148-z) contains supplementary material, which is available to authorized users.

Exploring plant growth-promotion actinomycetes from vermicompost and rhizosphere soil for yield enhancement in chickpea

The main objective of the present study was to isolate and characterize actinomycetes for their plant growth-promotion in chickpea. A total of 89 actinomycetes were screened for their antagonism against fungal pathogens of chickpea by dual culture and metabolite production assays. Four most promising actinomycetes were evaluated for their physiological and plant growth-promotion properties under in vitro and in vivo conditions. All the isolates exhibited good growth at temperatures from 20 °C to 40 °C, pH range of 7–11 and NaCl concentrations up to 8%. These were also found highly tolerant to Bavistin, slightly tolerant to Thiram and Captan (except VAI-7 and VAI-40) but susceptible to Benlate and Ridomil at field application levels and were found to produce siderophore, cellulase, lipase, protease, chitinase (except VAI-40), hydrocyanic acid (except VAI-7 and VAI-40), indole acetic acid and β-1,3-glucanase. When the four actinomycetes were evaluated for their plant growth-promotion properties under field conditions on chickpea, all exhibited increase in nodule number, shoot weight and yield. The actinomycetes treated plots enhanced total N, available P and organic C over the un-inoculated control. The scanning electron microscope studies exhibited extensive colonization by actinomycetes on the root surface of chickpea. The expression profiles for indole acetic acid, siderophore and β-1,3-glucanase genes exhibited up-regulation for all three traits and in all four isolates. The actinomycetes were identified as Streptomyces but different species in the 16S rDNA analysis. It was concluded that the selected actinomycetes have good plant growth-promotion and biocontrol potentials on chickpea.

In vitro biocontrol activity of halotolerant Streptomyces aureofaciens K20: A potent antagonist against Macrophomina phaseolina (Tassi) Goid

A halotolerant actinobacterial strain isolated from salinity affected soil of Eastern Indo-Gangetic plains (IGP), Uttar Pradesh, India, was characterised for its antagonistic potential against Macrophomina phaseolina by dual-culture assay. It was shown to effectively inhibit the growth of M. phaseolina with an inhibition zone of 27 ± 1.33 mm. Further the actinobacterial strain was evaluated for its plant growth promoting (PGP) properties and its ability to produce biocontrol related extracellular enzymes viz. amylase, protease, cellulase, chitinase, gelatinase and urease. The results revealed that the actinobacterial strain had PGP potential along with positive assay for amylase, chitinase and urease. The interaction study between antagonist strain and fungal pathogen, performed by scanning electron microscopy technique revealed that the actinobacterium was able to damage fungal mycelia may be due to chitinase, establishing its role as a potential antagonist against M. phaseolina. The actinobacterial isolate was characterised by 16S rDNA gene sequencing, and was identified as Streptomyces genera. The identified gene sequence was deposited to NCBI GenBank with an accession number KP331758.

Studying the Impact of Presence of Alpha Acid Glycoprotein and Protein Glycoprotein in Chronic Myeloid Leukemia Patients Treated with Imatinib Mesylate in the State of Qatar

Despite the efficacy of imatinib mesylate (IM) in treating chronic myeloid leukemia (CML), there is a high degree of resistance. Alpha- 1-acid glycoprotein may reduce drug efficacy through its ability to interact with IM and blocks it from reaching its target, while protein glycoprotein (PGP) may reduce the intracellular concentration of the drug via an active pump mechanism. We thus investigated the correlation between AGP and PGP levels and the resistance/response to treatment. A total of 26 CML patients were investigated for AGP and PGP levels at diagnosis and during treatment. There was no significant difference or correlation between AGP levels and the different groups of patients. There was also no significant difference in the fluorescence intensities of PGP levels among the different patient groups. The resistance observed in our CML patient population could not be correlated with AGP and PGP levels. There was no significant pattern of AGP and PGP expression, irrespective of the response or resistance to treatment.

An aberrant leukotriene A4 hydrolase-proline-glycine-proline pathway in the pathogenesis of chronic obstructive pulmonary disease

RATIONALE

Chronic neutrophilic inflammation is a hallmark in the pathogenesis of chronic obstructive pulmonary disease (COPD) and persists after cigarette smoking has stopped. Mechanisms involved in this ongoing inflammatory response have not been delineated.

OBJECTIVES

We investigated changes to the leukotriene A4 hydrolase (LTA4H)-proline-glycine-proline (PGP) pathway and chronic inflammation in the development of COPD.

METHODS

A/J mice were exposed to air or cigarette smoke for 22 weeks followed by bronchoalveolar lavage and lung and cardiac tissue analysis. Two human cohorts were used to analyze changes to the LTA4H-PGP pathway in never smokers, control smokers, COPD smokers, and COPD former smokers. PGP/AcPGP and LTA4H aminopeptidase activity were detected by mass spectroscopy, LTA4H amounts were detected by ELISA, and acrolein was detected by Western blot.

MEASUREMENTS AND MAIN RESULTS

Mice exposed to cigarette smoke developed emphysema with increased PGP, neutrophilic inflammation, and selective inhibition of LTA4H aminopeptidase, which ordinarily degrades PGP. We recapitulated these findings in smokers with and without COPD. PGP and AcPGP are closely associated with cigarette smoke use. Once chronic inflammation is established, changes to LTA4H aminopeptidase remain, even in the absence of ongoing cigarette use. Acrolein modifies LTA4H and inhibits aminopeptidase activity to the same extent as cigarette smoke.

CONCLUSIONS

These results demonstrate a novel pathway of aberrant regulation of PGP/AcPGP, suggesting this inflammatory pathway may be intimately involved in disease progression in the absence of ongoing cigarette smoke exposure. We highlight a mechanism by which acrolein potentiates neutrophilic inflammation through selective inhibition of LTA4H aminopeptidase activity. Clinical trial registered with www.clinicaltrials.gov (NCT 00292552).

Sputum PGP is reduced by azithromycin treatment in patients with COPD and correlates with exacerbations

RATIONALE

Proline-glycine-proline (PGP), a neutrophil chemoattractant derived from the enzymatic breakdown of collagen, is elevated in sputum of patients with chronic obstructive pulmonary disease (COPD) and may contribute to disease progression. Whether sputum levels of PGP respond to therapy for COPD or predict outcomes is unknown.

OBJECTIVES

We conducted a study ancillary to a multicenter trial of the efficacy of azithromycin treatment for 1 year in preventing COPD exacerbations to test whether sputum levels of PGP were altered by treatment or associated with exacerbation frequency.

METHODS

We collected remnant sputa from trial participants and assayed them in a blinded fashion for PGP, myeloperoxidase and matrix metalloproteinase (MMP)-9 and for the ability to generate PGP from collagen ex vivo. Once the parent trial was unblinded, the results were correlated with use of azithromycin or placebo and exacerbations in participants.

RESULTS

Azithromycin treatment significantly reduced sputum levels of PGP and myeloperoxidase in patients with COPD, particularly with increased duration of therapy. We found no difference in sputum MMP-9 or PGP generation between participants taking azithromycin or placebo. Sputum PGP levels were highest around the time of an exacerbation and declined with successful treatment.

CONCLUSIONS

These data support a role for PGP in the airway and parenchymal neutrophilic inflammation that drives COPD progression and exacerbations, and provide new information on the anti-inflammatory properties of macrolides. PGP may have potential as a target for novel anti-inflammatory therapies in COPD and as a biomarker for clinical trials.

Proteomic analysis for testis of mice exposed to carbon ion radiation

This paper investigates the mechanism of action of heavy ion radiation (HIR) on mouse testes. The testes of male mice subjected to whole body irradiation with carbon ion beam (0.5 and 4Gy) were analyzed at 7days after irradiation. A two-dimensional gel electrophoresis approach was employed to investigate the alteration of protein expression in the testes. Spot detection and matching were performed using the PDQuest 8.0 software. A difference of more than threefold in protein quantity (normalized spot volume) is the standard for detecting differentially expressed protein spots. A total of 11 differentially expressed proteins were found. Protein identification was performed using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-TOF-TOF). Nine specific proteins were identified by searching the protein sequence database of the National Center for Biotechnology Information. These proteins were found involved in molecular chaperones, metabolic enzymes, oxidative stress, sperm function, and spermatogenic cell proliferation. HIR decreased glutathione activity and increased malondialdehyde content in the testes. Given that Pin1 is related to the cell cycle and that proliferation is affected by spermatogenesis, we analyzed testicular histological changes and Pin1 protein expression through immunoblotting and immunofluorescence. Alterations of multiple pathways may be associated with HIR toxicity to the testes. Our findings are essential for studies on the development, biology, and pathology of mouse testes after HIR in space or radiotherapy.

Lipid synthesis in protozoan parasites: a comparison between kinetoplastids and apicomplexans

Lipid metabolism is of crucial importance for pathogens. Lipids serve as cellular building blocks, signalling molecules, energy stores, posttranslational modifiers, and pathogenesis factors. Parasites rely on a complex system of uptake and synthesis mechanisms to satisfy their lipid needs. The parameters of this system change dramatically as the parasite transits through the various stages of its life cycle. Here we discuss the tremendous recent advances that have been made in the understanding of the synthesis and uptake pathways for fatty acids and phospholipids in apicomplexan and kinetoplastid parasites, including Plasmodium, Toxoplasma, Cryptosporidium, Trypanosoma and Leishmania. Lipid synthesis differs in significant ways between parasites from both phyla and the human host. Parasites have acquired novel pathways through endosymbiosis, as in the case of the apicoplast, have dramatically reshaped substrate and product profiles, and have evolved specialized lipids to interact with or manipulate the host. These differences potentially provide opportunities for drug development. We outline the lipid pathways for key species in detail as they progress through the developmental cycle and highlight those that are of particular importance to the biology of the pathogens and/or are the most promising targets for parasite-specific treatment.

Inventory and general analysis of the ATP-binding cassette (ABC) gene superfamily in maize (Zea mays L.)

The metabolic functions of ATP-binding cassette (or ABC) proteins, one of the largest families of proteins presented in all organisms, have been investigated in many protozoan, animal and plant species. To facilitate more systematic and complicated studies on maize ABC proteins in the future, we present the first complete inventory of these proteins, including 130 open reading frames (ORFs), and provide general descriptions of their classifications, basic structures, typical functions, evolution track analysis and expression profiles. The 130 ORFs were assigned to eight subfamilies based on their structures and homological features. Five of these subfamilies consist of 109 proteins, containing transmembrane domains (TM) performing as transporters. The rest three subfamilies contain 21 soluble proteins involved in various functions other than molecular transport. A comparison of ABC proteins among nine selected species revealed either convergence or divergence in each of the ABC subfamilies. Generally, plant genomes contain far more ABC genes than animal genomes. The expression profiles and evolution track of each maize ABC gene were further investigated, the results of which could provide clues for analyzing their functions. Quantitative real-time polymerase chain reaction experiments (PCR) were conducted to detect induced expression in select ABC genes under several common stresses. This investigation provides valuable information for future research on stress tolerance in plants and potential strategies for enhancing maize production under stressful conditions.

The function of ABCB transporters in auxin transport

Plant ATP-binding cassette (ABC) transporters consist of largest family members among many other membrane transporters and have been implicated in various functions such as detoxification, disease resistance and transport of diverse substrates. Of the ABC-B/multi-drug resistance/P-glycoprotein (ABCB/MDR/PGP) subfamily, at least five members have been reported to mediate cellular transport of auxin or auxin derivatives. Although single mutant phenotypes of these genes are milder than PIN-FORMED (PIN) mutants, those ABCBs significantly contribute for the directional auxin movement in the tissue-level auxin-transporting assay. Uniformly localized ABCB proteins in the plasma membrane (PM) are generaly found in different plant species and stably retained regardless of internal and external signals. This implies that these ABCB proteins may play as basal auxin transporters.