Genetics of phosphate solubilization and its potential applications for improving plant growth-promoting bacteria

Plant growth-promoting bacteria (PGPB) are soil and rhizosphere bacteria that can benefit plant growth by different mechanisms. The ability of some microorganisms to convert insoluble phosphorus (P) to an accessible form, like orthophosphate, is an important trait in a PGPB for increasing plant yields. In this mini-review, the isolation and characterization of genes involved in mineralization of organic P sources (by the action of enzymes acid phosphatases and phytases), as well as mineral phosphate solubilization, is reviewed. Preliminary results achieved in the engineering of bacterial strains for improving capacity for phosphate solubilization are presented, and application of this knowledge to improving agricultural inoculants is discussed.     

Are drought-resistance promoting bacteria cross-compatible with different plant models?

The association between plant and plant growth promoting bacteria (PGPB) contributes to the successful thriving of plants in extreme environments featured by water shortage. We have recently shown that, with respect to the non-cultivated desert soil, the rhizosphere of pepper plants cultivated under desert farming hosts PGPB communities that are endowed with a large portfolio of PGP traits. Pepper plants exposed to bacterial isolates from plants cultivated under desert farming exhibited a higher tolerance to water shortage, compared with untreated control. This promotion was mediated by a larger root system (up to 40%), stimulated by the bacteria, that enhanced plant ability to uptake water from dry soil. We provide initial evidence that the nature of the interaction can have a limited level of specificity and that PGPB isolates may determine resistance to water stress in plants others than the one of the original isolation. It is apparent that, in relation to plant resistance to water stress, a feature of primary evolutionary importance for all plants, a cross-compatibility between PGPB and different plant models exists at least on a short-term.     

盐胁迫环境下植物促生菌的作用机制研究进展

盐胁迫是限制干旱和半干旱地区作物生产的主要非生物胁迫之一,严重影响作物的生长发育,植物促生菌(Plant growth-promoting bacteria,PGPB)可有效减轻植物的盐胁迫损伤,合理施用PGPB是盐胁迫下促进作物生长的重要途径。本文从盐胁迫环境下PGPB在调节植物激素内稳态、促进养分吸收和诱导植物产生系统耐受性等方面的作用阐述了PGPB提高植物耐盐性、减轻植物胁迫损伤的作用机制。讨论了能够在植物根际稳定定殖并在盐生环境下稳定保持PGP活性的功能菌株对未来农业的可持续发展的重要意义,同时,对该研究方向的重难点和未来的发展趋势作出展望。     

Novel insertion sequence elements associated with genetic heterogeneity and phenotype conversion in Ralstonia solanacearum

Three insertion sequences (IS) elements were isolated from the phytopathogen Ralstonia solanacearum. Southern hybridization using these IS elements as probes revealed hybridization profiles that varied greatly between different strains of the pathogen. During a spontaneous phenotype conversion event, the promoter of the phcA gene was interrupted by one of these IS elements.     

Enhanced Cd extraction of oilseed rape (Brassica napus) by plant growth-promoting bacteria isolated from Cd hyperaccumulator Sedum alfredii Hance

Four plant growth-promoting bacteria (PGPB) were used as study materials, among them two heavy metal-tolerant rhizosphere strains SrN1 (Arthrobacter sp.) and SrN9 (Bacillus altitudinis) were isolated from rhizosphere soil, while two endophytic strains SaN1 (Bacillus megaterium) and SaMR12 (Sphingomonas) were identified from roots of the cadmium (Cd)/zinc (Zn) hyperaccumulator Sedum alfredii Hance. A pot experiment was carried out to investigate the effects of these PGPB on plant growth and Cd accumulation of oilseed rape (Brassica napus) plants grown on aged Cd-spiked soil. The results showed that the four PGPB significantly boosted oilseed rape shoot biomass production, improved soil and plant analyzer development (SPAD) value, enhanced Cd uptake of plant and Cd translocation to the leaves. By fluorescent in situ hybridization (FISH) and green fluorescent protein (GFP), we demonstrated the studied S. alfredii endophytic bacterium SaMR12 were able to colonize successfully in the B. napus roots. However, all four PGPB could increase seed Cd accumulation. Due to its potential to enhance Cd uptake by the plant and to restrict Cd accumulation in the seeds, SaMR12 was selected as the most promising microbial partner of B. napus when setting up a plant–microbe fortified remediation system.     

Physiological and metabolic diversity in the yeast <Emphasis Type="Italic">Kluyveromyces marxianus</Emphasis>

Kluyveromyces marxianus is homothallic hemiascomycete yeast frequently isolated from dairy environments. It possesses phenotypic traits such as enhanced thermotolerance, inulinase production, and rapid growth rate that distinguish it from its closest relative Kluyveromyces lactis. Certain of these traits, notably fermentation of lactose and inulin to ethanol, make this yeast attractive for industrial production of ethanol from inexpensive substrates. There is relatively little known, however, about the diversity in this species, at the genetic, metabolic or physiological levels. This study compared phenotypic traits of 13 K. marxianus strains sourced from two European Culture Collections. A wide variety of responses to thermo, osmotic, and cell wall stress were observed, with some strains showing multi-stress resistance. These traits generally appeared unlinked indicating that, as with other yeasts, multiple resistance/adaptation pathways are present in K. marxianus. The data indicate that it should be possible to identify the molecular basis of traits to facilitate selection or engineering of strains adapted for industrial environments. The loci responsible for mating were also identified by genome sequencing and PCR analysis. It was found that K. marxianus can exist as stable haploid or diploid cells, opening up additional prospects for future strain engineering.     

Mechanisms of action of plant growth promoting bacteria

The idea of eliminating the use of fertilizers which are sometimes environmentally unsafe is slowly becoming a reality because of the emergence of microorganisms that can serve the same purpose or even do better. Depletion of soil nutrients through leaching into the waterways and causing contamination are some of the negative effects of these chemical fertilizers that prompted the need for suitable alternatives. This brings us to the idea of using microbes that can be developed for use as biological fertilizers (biofertilizers). They are environmentally friendly as they are natural living organisms. They increase crop yield and production and, in addition, in developing countries, they are less expensive compared to chemical fertilizers. These biofertilizers are typically called plant growth-promoting bacteria (PGPB). In addition to PGPB, some fungi have also been demonstrated to promote plant growth. Apart from improving crop yields, some biofertilizers also control various plant pathogens. The objective of worldwide sustainable agriculture is much more likely to be achieved through the widespread use of biofertilizers rather than chemically synthesized fertilizers. However, to realize this objective it is essential that the many mechanisms employed by PGPB first be thoroughly understood thereby allowing workers to fully harness the potentials of these microbes. The present state of our knowledge regarding the fundamental mechanisms employed by PGPB is discussed herein.     

Natural occurrence of Azospirillum brasilense in strawberry plants

Azospirillum species are free-living nitrogen-fixing bacteria commonly found in soil and in association with roots of different plant species. For their capacity to stimulate growth they are known as plant growth-promoting bacteria (PGPB). In this work, we demonstrate the natural occurrence and colonization of different parts of strawberry plants by Azospirillum brasilense in the cropping area of Tucumán, Argentina. Although bacteria isolations were carried out from two strawberry cultivars, e.g., Camarosa and Pájaro, attempts were successful only with the cultivar Camarosa. Whereas different strains of Azospirillum were isolated from the root surface and inner tissues of roots and stolons of the cultivar Camarosa, we have not obtained Azospirillum isolates from the cultivar Pájaro. After microbiological and molecular characterization (ARDRA) we determined that the isolates belonged to the species A. brasilense. All isolates showed to have the capacity to fix nitrogen, to produce siderophores and indoles. Local isolates exhibited different yields of indoles production when growing in N-free NFb semisolid media supplemented or not with tryptophan (0.1 mg ml⁻¹). This is the first report on the natural occurrence of A. brasilense in strawberry plants, especially colonizing inner tissues of stolons, as well as roots. The local isolates showed three important characteristics within the PGPB group: N₂-fixation, siderophores, and indoles production.     

Linkage between reovirus-induced apoptosis and inhibition of cellular DNA synthesis: role of the S1 and M2 genes.

The mammalian reoviruses are capable of inhibiting cellular DNA synthesis and inducing apoptosis. Reovirus strains type 3 Abney (T3A) and type 3 Dearing (T3D) inhibit cellular DNA synthesis and induce apoptosis to a substantially greater extent than strain type 1 Lang (T1L). We used T1L x T3A and T1L x T3D reassortant viruses to identify viral genes associated with differences in the capacities of reovirus strains to elicit these cellular responses to viral infection. We found that the S1 and M2 genome segments determine differences in the capacities of both T1L x T3A and T1L x T3D reassortant viruses to inhibit cellular DNA synthesis and to induce apoptosis. These genes encode viral outer-capsid proteins that play important roles in viral attachment and disassembly. To extend these findings, we used field isolate strains of reovirus to determine whether the strain-specific differences in inhibition of cellular DNA synthesis and induction of apoptosis are also associated with viral serotype, a property determined by the S1 gene. In these experiments, type 3 field isolate strains were found to inhibit cellular DNA synthesis and to induce apoptosis to a greater extent than type 1 field isolate strains. Statistical analysis of these data indicate a significant correlation between the capacity of T1L x T3A and T1L x T3D reassortant viruses and field isolate strains to inhibit cellular DNA synthesis and to induce apoptosis. These findings suggest that reovirus-induced inhibition of cellular DNA synthesis and induction of apoptosis are linked and that both phenomena are induced by early steps in the viral replication cycle.     

Phenotype-centric modeling for rational metabolic engineering

Phenotype-centric modeling enables a paradigm shift in the analysis of mechanistic models. It brings the focus to a network's biochemical phenotypes and their relationship with measurable traits (e.g., product yields, system dynamics, signal amplification factors, etc.) and away from computationally intensive simulation-centric modeling. Here, we explore applications of this new modeling strategy in the field of rational metabolic engineering using the amorphadiene biosynthetic network as a case study. This network has previously been studied using a mechanistic model and the simulation-centric strategy, and thus provides an excellent means to compare and contrast results obtained from these two very different strategies. We show that the phenotype-centric strategy, without values for the parameters, not only identifies beneficial intervention strategies obtained with the simulation-centric strategy, but it also provides an understanding of the mechanistic context for the validity of these predictions. Additionally, we propose a set of hypothetical strains with the potential to outperform reported production strains and to enhance the mechanistic understanding of the amorphadiene biosynthetic network. Further, we identify the landscape of possible intervention strategies for the given model. We believe that phenotype-centric modeling can advance the field of rational metabolic engineering by enabling the development of next generation kinetics-based algorithms and methods that do not rely on a priori knowledge of kinetic parameters but allow a structured, global analysis of system design in the parameter space.     

Plant Growth-Promoting Bacteria Facilitate the Growth of Barley and Oats in Salt-Impacted Soil: Implications for Phytoremediation of Saline Soils

Plant growth-promoting bacteria (PGPB) strains that contain the enzyme 1-amino- cyclopropane-1-carboxylate (ACC) deaminase can lower stress ethylene levels and improve plant growth. In this study, ACC deaminase-producing bacteria were isolated from a salt-impacted (～50 dS/m) farm field, and their ability to promote plant growth of barley and oats in saline soil was investigated in pouch assays (1% NaCl), greenhouse trials (9.4 dS/m), and field trials (6–24 dS/m). A mix of previously isolated PGPB strains UW3 (Pseudomonas sp.) and UW4 (P. sp.) was also tested for comparison. Rhizobacterial isolate CMH3 (P. corrugata) and UW3+UW4 partially alleviated plant salt stress in growth pouch assays. In greenhouse trials, CMH3 enhanced root biomass of barley and oats by 200% and 50%, respectively. UW3+UW4, CMH3 and isolate CMH2 also enhanced barley and oat shoot growth by 100%–150%. In field tests, shoot biomass of oats tripled when treated with UW3+UW4 and doubled with CHM3 compared with that of untreated plants. PGPB treatment did not affect salt uptake on a per mass basis; higher plant biomass led to greater salt uptake, resulting in decreased soil salinity. This study demonstrates a method for improving plant growth in marginal saline soils. Associated implications for salt remediation are discussed.     

Characterization of bacterial communities associated with Brassica napus L. growing on a Zn-contaminated soil and their effects on root growth

The interaction between plant growth-promoting bacteria (PGPB) and plants can enhance biomass production and metal tolerance of the host plants. This work aimed at isolating and characterizing the cultivable bacterial community associated with Brassica napus growing on a Zn-contaminated site, for selecting cultivable PGPB that might enhance biomass production and metal tolerance of energy crops. The effects of some of these bacterial strains on root growth of B. napus exposed to increasing Zn and Cd concentrations were assessed. A total of 426 morphologically different bacterial strains were isolated from the soil, the rhizosphere, and the roots and stems of B. napus. The diversity of the isolated bacterial populations was similar in rhizosphere and roots, but lower in soil and stem compartments. Burkoholderia, Alcaligenes, Agrococcus, Polaromonas, Stenotrophomonas, Serratia, Microbacterium, and Caulobacter were found as root endophytes exclusively. The inoculation of seeds with Pseudomonas sp. strains 228 and 256, and Serratia sp. strain 246 facilitated the root development of B. napus at 1,000 µM Zn. Arthrobacter sp. strain 222, Serratia sp. strain 246, and Pseudomonas sp. 228 and 262 increased the root length at 300 µM Cd.     

Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 Pseudomonas syringae isolates

Closely related pathogens may differ dramatically in host range, but the molecular, genetic, and evolutionary basis for these differences remains unclear. In many Gram- negative bacteria, including the phytopathogen Pseudomonas syringae, type III effectors (TTEs) are essential for pathogenicity, instrumental in structuring host range, and exhibit wide diversity between strains. To capture the dynamic nature of virulence gene repertoires across P. syringae, we screened 11 diverse strains for novel TTE families and coupled this nearly saturating screen with the sequencing and assembly of 14 phylogenetically diverse isolates from a broad collection of diseased host plants. TTE repertoires vary dramatically in size and content across all P. syringae clades; surprisingly few TTEs are conserved and present in all strains. Those that are likely provide basal requirements for pathogenicity. We demonstrate that functional divergence within one conserved locus, hopM1, leads to dramatic differences in pathogenicity, and we demonstrate that phylogenetics-informed mutagenesis can be used to identify functionally critical residues of TTEs. The dynamism of the TTE repertoire is mirrored by diversity in pathways affecting the synthesis of secreted phytotoxins, highlighting the likely role of both types of virulence factors in determination of host range. We used these 14 draft genome sequences, plus five additional genome sequences previously reported, to identify the core genome for P. syringae and we compared this core to that of two closely related non-pathogenic pseudomonad species. These data revealed the recent acquisition of a 1 Mb megaplasmid by a sub-clade of cucumber pathogens. This megaplasmid encodes a type IV secretion system and a diverse set of unknown proteins, which dramatically increases both the genomic content of these strains and the pan-genome of the species.     

Effects of plant growth promoting bacteria and mycorrhizal on Capsicum annuum L. var. aviculare ([Dierbach] D’Arcy and Eshbaugh) germination under stressing abiotic conditions

Capsicum annuum var. aviculare to Tarahumara and Papago Indians and farmers of Sonora desert is a promising biological and commercial value as a natural resource from arid and semiarid coastal zones. Traditionally, apply synthetic fertilizers to compensate for soil nitrogen deficiency. However, indiscriminate use of these fertilizers might increase salinity. The inoculation by plant growth promoting bacteria (PGPB) and arbuscular mycorrhizal fungi (AMF) represents an alternative as potential bio fertilizer resources for salty areas. Seeds ecotypes from four areas of Sonora desert (Mazocahui, Baviacora, Arizpe, La Tortuga), in order to inoculate them with one species of PGPB and AMF. Two germination tests were carried out to study the effect of salinity, temperature regime (night/day) and inoculation with PGPB and AMF growth factors measured on germination (percentage and rate), plant height, root length, and produced biomass (fresh and dry matter). The results indicated that from four studied ecotypes, Mazocahui was the most outstanding of all, showing the highest germination under saline and non-saline conditions. However, the PGPB and AMF influenced the others variables evaluated. This study is the first step to obtain an ideal ecotype of C. a. var. aviculare, which grows in the northwest of México and promoting this type of microorganisms as an efficient and reliable biological product. Studies of the association of PGPB and AMF with the C. a. var. aviculare-Mazocahui ecotype are recommended to determine the extent to which these observations can be reproduced under field conditions.     

Metabolic profile and antioxidant responses during drought stress recovery in sugarcane treated with humic acids and endophytic diazotrophic bacteria

Water deficit is the major yield‐limiting factor for sugarcane crop production that can be enhanced by inoculating with plant growth promoting bacteria (PGPB) combined with humic substances. The aim of this work was to examine changes to the metabolic profile and antioxidant enzyme activity of sugarcane treated with PGPB and humic acid (HA) after drought and then rehydration. The drought was imposed by withholding irrigation for 21 days thereby measuring enzyme activity, metabolic profile and photosynthetic rate 1 week after rehydratation. Growth of plants treated with HA, PGPB and with both treatments combined (PGPB + HA) was higher than control plants. The antioxidant enzymes superoxide dismutase (SOD), catalase (CAT) and ascorbate peroxidase (APX) activities remained higher after rehydration only in plants treated with HA. Plants treated with HA and PGPB + HA exhibited increased transpiration, stomatal conductance and net photosynthesis than plants treated with PGPB. The PGPB‐treated plants exhibited drought resistance that resembled ‘delayed stress onset’, which is a new term for preserving water in the plants tissues. Water preservation in plants treated with PGPB was corroborated by higher relative water content (RWC) than control plants at the end of the drought period. Plants treated with HA + PGPB exhibited the highest water potential after rehydration and high RWC. Osmotic adjustment in the other treatments (control, HA and PGPB) was indicated by a new pattern of metabolic response after rehydration, including generally enhanced carbohydrates and proteins and specific changes induced by HA‐enhancing aromatic compounds, whereas PGPB exhibited enhanced fatty acids and other aliphatic H species. Humic acids assist with drought stress recovery by inducing antioxidant enzyme activity whereas PGPB induced preservation of leaf water potential and RWC by closing stomata efficiently, resulting in plant water preservation.     

Hybrid Dysgenesis in DROSOPHILA MELANOGASTER: A Syndrome of Aberrant Traits Including Mutation, Sterility and Male Recombination

A syndrome of associated aberrant traits is described in Drosophila melanogaster. Six of these traits, mutation, sterility, male recombination, transmission ratio distortion, chromosomal aberrations and local increases in female recombination, have previously been reported. A seventh trait, nondisjunction, is described for the first time. All of the traits we have examined are found nonreciprocally in F(1) hybrids. We present evidence that at least four of the traits are not found in nonhybrids. Therefore we have proposed the name hybrid dysgenesis to describe this syndrome.-A partition of tested strains into two types, designated P and M, was made according to the paternal or maternal contribution required to produce hybrid dysgenesis. This classification seems to hold for crosses of strains from within the United States and Australia, as well as for crosses between strains from the two countries. Strains collected recently from natural populations are typically of the P type and those having a long laboratory history are generally of the M type. However, a group of six strains collected from the wild in the 1960's are unambiguously divided equally between the P and M types. The dichotomy of this latter group raises interesting questions concerning possible implications for speciation.-Temperature often has a critical effect on the manifestation of hybrid dysgenesis. High F(1 ) developmental temperatures tend to increase the expression of sterility, sometimes to extreme levels. Conversely, low developmental temperatures tend to inhibit the expression of some dysgenic traits.-There are potentially important practical implications of hybrid dysgenesis for laboratory experimentation. The results suggest that care should be exercised in planning experiments involving strain crosses.     

Peptide inhibitors of appressorium development in Glomerella cingulata

The phytopathogen Glomerella cingulata (anamorph: Colletotrichum gloeosporioides) infects host tissue by means of a specialised infection structure, the appressorium. The Saccharomyces cerevisiae alpha-mating factor pheromone, the Saccharomyces kluyveri alpha-mating factor pheromone and a hendecapeptide produced by G. cingulata inhibit appressorium development. The amino acid sequence of the G. cingulata peptide, GYFSYPHGNLF, is different from that of the mature pheromone peptides of other filamentous fungi. The peptide has sequence similarity with the Saccharomyces alpha-mating factor pheromones, but is unable to elicit growth arrest in S. cerevisiae.     

Plant growth-promoting bacteria as inoculants in agricultural soils

Plant-microbe interactions in the rhizosphere are the determinants of plant health, productivity and soil fertility. Plant growth-promoting bacteria (PGPB) are bacteria that can enhance plant growth and protect plants from disease and abiotic stresses through a wide variety of mechanisms; those that establish close associations with plants, such as the endophytes, could be more successful in plant growth promotion. Several important bacterial characteristics, such as biological nitrogen fixation, phosphate solubilization, ACC deaminase activity, and production of siderophores and phytohormones, can be assessed as plant growth promotion (PGP) traits. Bacterial inoculants can contribute to increase agronomic efficiency by reducing production costs and environmental pollution, once the use of chemical fertilizers can be reduced or eliminated if the inoculants are efficient. For bacterial inoculants to obtain success in improving plant growth and productivity, several processes involved can influence the efficiency of inoculation, as for example the exudation by plant roots, the bacterial colonization in the roots, and soil health. This review presents an overview of the importance of soil-plant-microbe interactions to the development of efficient inoculants, once PGPB are extensively studied microorganisms, representing a very diverse group of easily accessible beneficial bacteria.     

酿酒酵母转化木糖生产化学品的研究进展

木糖的有效利用是木质纤维素生产生物燃料或化学品经济性转化的基础。30年来,通过理性代谢改造和适应性进化等工程策略,显著提高了传统乙醇发酵微生物——酿酒酵母Saccharomyces cerevisiae的木糖代谢能力。因此,近年来在酿酒酵母中利用木糖生产化学品的研究逐步展开。研究发现,酿酒酵母分别以木糖和葡萄糖为碳源时,其转录组和代谢组存在明显差异。与葡萄糖相比,木糖代谢过程中细胞整体呈现出Crabtree-negative代谢特征,如有限的糖酵解途径活性减少了丙酮酸到乙醇的代谢通量,以及增强的胞质乙酰辅酶A合成和呼吸能量代谢等,这都有利于以丙酮酸或乙酰辅酶A为前体的下游产物的有效合成。文中对酿酒酵母木糖代谢途径改造与优化、木糖代谢特征以及以木糖为碳源合成化学品的细胞工厂构建等方面进行了详细综述,并对木糖作为重要碳源在大宗化学品生物合成中存在的困难和挑战以及未来研究方向进行了总结与展望。     

The evolution of genetic architecture. I. Diversification of genetic backgrounds by genetic drift

The genetic architecture of a phenotype plays a critical role in determining phenotypic evolution through its effects on patterns of genetic variation. Genetic architecture is often considered to be constant in evolutionary quantitative genetic models. However, genetic architecture may be variable and itself evolve when there are dominance and epistatic interactions among alleles at the same and different loci, respectively. The evolution of genetic architecture by genetic drift is examined here by testing the breeding value of four standard inbred mouse strains mated across a set of 26 related recombinant quasi-inbred (RqI) lines generated from the intercross of the Large (LG/J) and Small (SM/J) inbred mouse strains. Phenotypes of interest include age-specific body weights, growth, and adult body composition. If the genetic architecture of these traits has differentiated by genetic drift during the production of the RqI strains, we should observe interactions between tester strain and RqI strain. The breeding values of the tester strains will change relative to one another depending on which RqI strain they are crossed to. The study included an average of 15.1 offspring per cross, over a total of 100 different crosses. Multivariate and univariate analyses of variance indicate that there is strongly significant interaction for all traits. Interaction is more pronounced in males than in females and accounted for an average of about 40% of the explained variation in males and 30% in females. These results indicate that the genetic architecture of these traits has differentiated by genetic drift in the RqI strains since their isolation from a common founder population. Further analysis indicates that this differentiation results in changes in the order of tester strain effects so that common patterns of selection in these differentiated populations could result in the fixation of different alleles.