Comparative genomics of plant growth promoting phosphobacteria isolated from acidic soils.

Despite being one of the most abundant elements in soil, phosphorus (P) often becomes a limiting macronutrient for plants due to its low bioavailability, primarily locked away in insoluble organic and inorganic forms. Phosphate solubilizing and mineralizing bacteria, also called phosphobacteria, isolated from P-deficient soils have emerged as a promising biofertilizer alternative, capable of converting these recalcitrant P forms into plant-available phosphates. Three such phosphobacteria strains-Serratia sp. RJAL6, Klebsiella sp. RCJ4, and Enterobacter sp. 198-previously demonstrated their particular strength as plant growth promoters for wheat, ryegrass, or avocado under abiotic stresses and P deficiency. Comparative genomic analysis of their draft genomes revealed several genes encoding key functionalities, including alkaline phosphatases, isonitrile secondary metabolites, enterobactin biosynthesis and genes associated to the production of indole-3-acetic acid (IAA) and gluconic acid. Moreover, overall genome relatedness indexes (OGRIs) revealed substantial divergence between Serratia sp. RJAL6 and its closest phylogenetic neighbours, Serratia nematodiphila and Serratia bockelmanii. This compelling evidence suggests that RJAL6 merits classification as a novel species. This in silico genomic analysis provides vital insights into the plant growth-promoting capabilities and provenance of these promising PSRB strains. Notably, it paves the way for further characterization and potential application of the newly identified Serratia species as a powerful bioinoculant in future agricultural settings.

Microbiome engineering optimized by Antarctic microbiota to support a plant host under water deficit.

Climate change challenges modern agriculture to develop alternative and eco-friendly solutions to alleviate abiotic and/or biotic stresses. The use of soil microbiomes from extreme environments opens new avenues to discover novel microorganisms and microbial functions to protect plants. In this study we confirm the ability of a bioinoculant, generated by natural engineering, to promote host development under water stress. Microbiome engineering was mediated through three factors i) Antarctic soil donation, ii) water deficit and iii) multigenerational tomato host selection. We revealed that tomato plants growing in soils supplemented with Antarctic microbiota were tolerant to water deficit stress after 10 generations. A clear increase in tomato seedling tolerance against water deficit stress was observed in all soils over generations of Host Mediated Microbiome Engineering, being Fildes mixture the most representatives, which was evidenced by an increased survival time, plant stress index, biomass accumulation, and decreased leaf proline content. Microbial community analysis using 16s rRNA gene amplicon sequencing data suggested a microbiome restructuring that could be associated with increased tolerance of water deficit. Additionally, the results showed a significant increase in the relative abundance of Candidatus Nitrosocosmicus and Bacillus spp. which could be key taxa associated with the observed tolerance improvement. We proposed that in situ microbiota engineering through the evolution of three factors (long-standing extreme climate adaption and host and stress selection) could represent a promising strategy for novel generation of microbial inoculants.

Effect of particle size of nanoscale zero-valent copper on inorganic phosphorus adsorption-desorption in a volcanic ash soil.

Zero-valent copper engineered nanoparticles (Cu-ENPs) released through unintentional or intentional actions into the agricultural soils can alter the availability of inorganic phosphorus (IP) to plants. In this study, we used adsorption-desorption experiments to evaluate the effect of particle size of 1% Cu-ENPs (25 nm and 40-60 nm) on IP availability in Santa Barbara (SB) volcanic ash soil. X-Ray Diffraction results showed that Cu-ENPs were formed by a mixture of Cu metallic and Cu oxides (Cu2O or/and CuO) species, while specific surface area values showed that Cu-ENPs/25 nm could form larger aggregate particles compared to Cu-ENPs/40-60 nm. The kinetic IP adsorption of SB soil without and with 1% Cu-ENPs (25 nm and 40-60 nm) followed the mechanism described by the pseudo-second-order (k2 = 0.45-1.13 x 10-3 kg mmol-1 min-1; r2 ≥ 0.999, and RSS ≤ 0.091) and Elovich (α = 14621.10-3136.20 mmol kg-1 min-1; r2 ≥ 0.984, and RSS ≤ 69) models. Thus, the rate-limiting step for IP adsorption in the studied systems was chemisorption on a heterogeneous surface. Adsorption equilibrium isotherms without Cu-ENPs were fitted well to the Freundlich model, while with 1% Cu-ENPs (25 nm and 40-60 nm), isotherms were described best by the Freundlich and/or Langmuir model. The IP relative adsorption capacity (KF) was higher with 1% Cu-ENPs/40-60 nm (KF = 110.41) than for 1% Cu-ENPs/25 nm (KF = 74.40) and for SB soil (KF = 48.17). This study showed that plausible IP retention mechanisms in the presence of 1% Cu-ENPs in SB soil were: i) ligand exchange, ii) electrostatic attraction, and iii) co-precipitate formation. The desorption study demonstrated that 1% Cu-ENPs/40-60 nm increased the affinity of IP in SB soil with a greater effect than 1% Cu-ENPs/25 nm. Thus, both the studied size ranges of Cu-ENPs could favor an accumulation of IP in volcanic ash soils.

Efficient and selective removal of SeVI and AsV mixed contaminants from aqueous media by montmorillonite-nanoscale zero valent iron nanocomposite.

Nanoscale zero-valent iron (NZVI) and NZVI supported onto montmorillonite (NZVI-Mt) were synthetized and used in this study to remove SeVI and AsV from water in mono- and binary-adsorbate systems. The adsorption kinetics and isotherm data for SeVI and AsV were adequately described by the pseudo-second-order (PSO) (r2>0.94) and Freundlich (r2>0.93) equations. Results from scanning electron microscopy showed that the dimension of the NZVI immobilized on the Mt was smaller than pure NZVI. Using 0.05 g of adsorbent and an initial 200 mg L-1 AsV and SeVI concentration, the maximum adsorption capacity (qmax) and partition coefficient (PC) for AsV on NZVI-Mt in monocomponent system were 54.75 mg g-1 and 0.065 mg g-1·µM-1, which dropped respectively to 49.91 mg g-1 and 0.055 mg g-1·µM-1 under competitive system. For SeVI adsorption on NZVI-Mt in monocomponent system, qmax and PC were 28.63 mg g-1 and 0.024 mg g-1·µM-1, respectively. Values of qmax and PC were higher for NZVI-Mt than NZVI and montmorillonite, indicating that the nanocomposite contained greater adsorption sites for removing both oxyanions, but with a marked preference for AsV. Future research should evaluate the effect of different operational variables on the removal efficiency of both oxyanions by NZVI-Mt.

Expression analysis and functional characterization of two PHT1 family phosphate transporters in ryegrass.

MAIN CONCLUSION: The phosphate transporters LpPHT1;1 and LpPHT1;4 have different roles in phosphate uptake and translocation in ryegrass under P stress condition. The phosphate transporter 1 (PHT1) family are integral membrane proteins that operate in phosphate uptake, distribution and remobilization within plants. In this study, we report on the functional characterization and expression of two PHT1 family members from ryegrass plants (Lolium perenne L.) and determine their roles in the specificity of Pi transport. The expression level of LpPHT1;4 was strongly influenced by phosphorus (P) status, being higher under P-starvation condition. In contrast, the expression level of LpPHT1;1 was not correlated with P supply. Yeast mutant complementation assays showed that LpPHT1;4 can complement the growth defect of the yeast mutant Δpho84 under Pi-deficient conditions, whereas the yeast mutant expressing LpPHT1;1 was not able to restore growth. Phylogenetic and molecular analyses indicated high sequence similarity to previously identified PHT1s from other species in the Poaceae. These results suggest that LpPHT1;1 may function as a low-affinity Pi transporter, whereas LpPHT1;4 could acts as a high-affinity Pi transporter to maintain Pi homeostasis under stress conditions in ryegrass plants. This study will form the basis for the long-term goal of improving the phosphate use efficiency of ryegrass plants.

Understanding the Strategies to Overcome Phosphorus-Deficiency and Aluminum-Toxicity by Ryegrass Endophytic and Rhizosphere Phosphobacteria.

Phosphobacteria, secreting organic acids and phosphatases, usually favor plant performance in acidic soils by increasing phosphorus (P) availability and aluminum (Al) complexing. However, it is not well-known how P-deficiency and Al-toxicity affect the phosphobacteria physiology. Since P and Al problems often co-occur in acidic soils, we have therefore proposed the evaluation of the single and combined effects of P-deficiency and Al-toxicity on growth, organic acids secretion, malate dehydrogenase (mdh) gene expression, and phosphatase activity of five Al-tolerant phosphobacteria previously isolated from ryegrass. These phosphobacteria were identified as Klebsiella sp. RC3, Stenotrophomona sp. RC5, Klebsiella sp. RCJ4, Serratia sp. RCJ6, and Enterobacter sp. RJAL6. The strains were cultivated in mineral media modified to obtain (i) high P in absence of Al-toxicity, (ii) high P in presence of Al-toxicity, (iii) low P in absence of Al-toxicity, and (iv) low P in presence of Al-toxicity. High and low P were obtained by adding KH2PO4 at final concentration of 1.4 and 0.05 mM, respectively. To avoid Al precipitation, AlCl3 × 6H2O was previously complexed to citric acid (sole carbon source) in concentrations of 10 mM. The secreted organic acids were identified and quantified by HPLC, relative mdh gene expression was determined by qRT-PCR and phosphatase activity was colorimetrically determined using p-nitrophenyl phosphate as substrate. Our results revealed that although a higher secretion of all organic acids was achieved under P-deficiency, the patterns of organic acids secretion were variable and dependent on treatment and strain. The organic acid secretion is exacerbated when Al was added into media, particularly in the form of malic and citric acid. The mdh gene expression was significantly up-regulated by the strains RC3, RC5, and RCJ6 under P-deficiency and Al-toxicity. In general, Al-tolerant phosphobacteria under P deficiency increased both acid and alkaline phosphatase activity with respect to the control, which was deepened when Al was present. The knowledge of this bacterial behavior in vitro is important to understand and predict the behavior of phosphobacteria in vivo. This knowledge is essential to generate smart and efficient biofertilizers, based in Al-tolerant phosphobacteria which could be expansively used in acidic soils.

Rhizobacterial Community Structures Associated with Native Plants Grown in Chilean Extreme Environments.

Chile is topographically and climatically diverse, with a wide array of diverse undisturbed ecosystems that include native plants that are highly adapted to local conditions. However, our understanding of the diversity, activity, and role of rhizobacteria associated with natural vegetation in undisturbed Chilean extreme ecosystems is very poor. In the present study, the combination of denaturing gradient gel electrophoresis and 454-pyrosequencing approaches was used to describe the rhizobacterial community structures of native plants grown in three representative Chilean extreme environments: Atacama Desert (ATA), Andes Mountains (AND), and Antarctic (ANT). Both molecular approaches revealed the presence of Proteobacteria, Bacteroidetes, and Actinobacteria as the dominant phyla in the rhizospheres of native plants. Lower numbers of operational taxonomic units (OTUs) were observed in rhizosphere soils from ATA compared with AND and ANT. Both approaches also showed differences in rhizobacterial community structures between extreme environments and between plant species. The differences among plant species grown in the same environment were attributed to the higher relative abundance of classes Gammaproteobacteria and Alphaproteobacteria. However, further studies are needed to determine which environmental factors regulate the structures of rhizobacterial communities, and how (or if) specific bacterial groups may contribute to the growth and survival of native plants in each Chilean extreme environments.

Urea Fertilizer and pH Influence on Sorption Process of Flumetsulam and MCPA Acidic Herbicides in a Volcanic Soil.

The aim of this study was to evaluate the influence of urea fertilizer and pH on the sorption process of two acidic herbicides, flumetsulam (2',6'-difluoro-5-methyl[1,2,4]triazolo[1,5-a]pyrimidine-2-sulfonanilide) and MCPA (4-chloro--tolyloxyacetic acid), on an Andisol. Urea reduced the adsorption of MCPA but not that of flumetsulam. The Freundlich parameter of MCPA decreased from 8.5 to 5.1 mg L kg. This finding could be attributed to an increase in dissolved organic C due to an initial increase in soil pH for urea application. The higher acidic character of MCPA compared with that of flumetsulam produced a greater hydrolysis of urea, leading to a further pH increase. A marked effect of pH on the adsorption of both herbicides was observed. The organic C distribution coefficient () values for flumetsulam were in the range of 74 to 10 L kg, while those of MCPA were in the range of 208 to 45 L kg. In the kinetic studies, the pseudo-second-order model appeared to fit the data best ( > 0.994). The initial adsorption rates () ranged from 20.00 to 4.59 mg kg h for flumetsulam and from 125.00 to 25.60 mg kg hfor MCPA. Both herbicides were adsorbed rapidly during the first stage of the sorption process, and the rates of sorption were dependent on pH. The application of the Elovich and Weber-Morris models led us to conclude that mass transfer through the boundary layer and, to a lesser degree, intraparticle diffusion were influenced by the chemical character of the herbicide. These results suggest that urea application could increase leaching of acid herbicides in soils.

Silicon in vascular plants: uptake, transport and its influence on mineral stress under acidic conditions.

MAIN CONCLUSION: So far, considerable advances have been achieved in understanding the mechanisms of Si uptake and transport in vascular plants. This review presents a comprehensive update about this issue, but also provides the new insights into the role of Si against mineral stresses that occur in acid soils. Such information could be helpful to understand both the differential Si uptake ability as well as the benefits of this mineral element on plants grown under acidic conditions. Silicon (Si) has been widely recognized as a beneficial element for many plant species, especially under stress conditions. In the last few years, great efforts have been made to elucidate the mechanisms involved in uptake and transport of Si by vascular plants and recently, different Si transporters have been identified. Several researches indicate that Si can alleviate various mineral stresses in plants growing under acidic conditions, including aluminium (Al) and manganese (Mn) toxicities as well as phosphorus (P) deficiency all of which are highly detrimental to crop production. This review presents recent findings concerning the influence of uptake and transport of Si on mineral stress under acidic conditions because a knowledge of this interaction provides the basis for understanding the role of Si in mitigating mineral stress in acid soils. Currently, only four Si transporters have been identified and there is little information concerning the response of Si transporters under stress conditions. More investigations are therefore needed to establish whether there is a relationship between Si transporters and the benefits of Si to plants subjected to mineral stress. Evidence presented suggests that Si supply and its subsequent accumulation in plant tissues could be exploited as a strategy to improve crop productivity on acid soils.

Description of mutual interactions between silicon and phosphorus in Andisols by mathematical and mechanistic models.

The Freundlich model and the Constant Capacitance Model (CCM) were used to describe silicon (Si) and phosphorus (P) sorption, both individually and for binary P-Si systems, on two Andisols with different chemical properties: Freire soil (FS) and Piedras Negras soil (PNS). Silicon sorption kinetics were examined through the Elovich equation, revealing that the initial sorption rate was 16 times greater in PNS. The Freundlich equation provides a good fit to the sorption data for both Andisols. When compared with FS, larger Si sorption capacity and lower Si affinity for the surface sites were observed in PNS; nevertheless, Si sorption decreased in both soils as P sorption increased. Slight reductions in P sorption capacity due to the presence of Si were found, whereas there was no apparent effect on P bonding intensity. The CCM was able to describe Si adsorption, and potentiometric titrations support that Si seems to be specifically sorbed mainly onto sites of negative charge. Comparable log KSiint values were obtained for both soils, indicating that Si was bound on similar sites. Phosphorus sorption was well described by the CCM, and log KPint denoted strong interactions of P with the surface sites. For binary systems, log KPint did not vary with increasing Si concentration; comparatively, log KSiint scarcely decreased with increasing P concentration in PNS, but a 28% reduction was found in FS at the highest initial P concentration.

Phytate addition to soil induces changes in the abundance and expression of Bacillus ß-propeller phytase genes in the rhizosphere.

Phytate-mineralizing rhizobacteria (PMR) perform an essential function for the mineralization of organic phosphorus but little is known about their ecology in soils and rhizosphere. In this study, PCR-based methods were developed for detection and quantification of the Bacillus ß-propeller phytase (BPP) gene. Experiments were conducted to monitor the presence and persistence of a phytate-mineralizing strain, Bacillus sp. MQH19, after inoculation of soil microcosms and within the rhizosphere. The occurrence of the BPP gene in natural pasture soils from Chilean Andisols was also examined. The results showed that the Bacillus BPP gene was readily detected in sterile and nonsterile microcosms, and that the quantitative PCR (qPCR) methods could be used to monitor changes in the abundance of the BPP gene over time. Our results also show that the addition of phytate to nonsterile soils induced the expression of the BPP gene in the rhizosphere of ryegrass and the BPP gene was detected in all pasture soils sampled. This study shows that phytate addition soils induced changes in the abundance and expression of Bacillus BPP to genes in the rhizosphere and demonstrates that Bacillus BPP gene is cosmopolitan in pasture soils from Chilean Andisols.

Plant growth-promoting rhizobacteria associated with ancient clones of creosote bush (Larrea tridentata).

Plant growth-promoting rhizobacteria (PGPR) are common components of the rhizosphere, but their role in adaptation of plants to extreme environments is not yet understood. Here, we examined rhizobacteria associated with ancient clones of Larrea tridentata in the Mohave desert, including the 11,700-year-old King Clone, which is oldest known specimen of this species. Analysis of unculturable and culturable bacterial community by PCR-DGGE revealed taxa that have previously been described on agricultural plants. These taxa included species of Proteobacteria, Bacteroidetes, and Firmicutes that commonly carry traits associated with plant growth promotion, including genes encoding aminocyclopropane carboxylate deaminase and ß-propeller phytase. The PGPR activities of three representative isolates from L. tridentata were further confirmed using cucumber plants to screen for plant growth promotion. This study provides an intriguing first view of the mutualistic bacteria that are associated with some of the world's oldest living plants and suggests that PGPR likely contribute to the adaptation of L. tridentata and other plant species to harsh environmental conditions in desert habitats.

Molecular and physiological strategies to increase aluminum resistance in plants.

Aluminum (Al) toxicity is a primary limitation to plant growth on acid soils. Root meristems are the first site for toxic Al accumulation, and therefore inhibition of root elongation is the most evident physiological manifestation of Al toxicity. Plants may resist Al toxicity by avoidance (Al exclusion) and/or tolerance mechanisms (detoxification of Al inside the cells). The Al exclusion involves the exudation of organic acid anions from the root apices, whereas tolerance mechanisms comprise internal Al detoxification by organic acid anions and enhanced scavenging of free oxygen radicals. One of the most important advances in understanding the molecular events associated with the Al exclusion mechanism was the identification of the ALMT1 gene (Al-activated malate transporter) in Triticum aestivum root cells, which codes for a plasma membrane anion channel that allows efflux of organic acid anions, such as malate, citrate or oxalate. On the other hand, the scavenging of free radicals is dependent on the expression of genes involved in antioxidant defenses, such as peroxidases (e.g. in Arabidopsis thaliana and Nicotiana tabacum), catalases (e.g. in Capsicum annuum), and the gene WMnSOD1 from T. aestivum. However, other recent findings show that reactive oxygen species (ROS) induced stress may be due to acidic (low pH) conditions rather than to Al stress. In this review, we summarize recent findings regarding molecular and physiological mechanisms of Al toxicity and resistance in higher plants. Advances have been made in understanding some of the underlying strategies that plants use to cope with Al toxicity. Furthermore, we discuss the physiological and molecular responses to Al toxicity, including genes involved in Al resistance that have been identified and characterized in several plant species. The better understanding of these strategies and mechanisms is essential for improving plant performance in acidic, Al-toxic soils.

Activity stabilization of Aspergillus niger and Escherichia coli phytases immobilized on allophanic synthetic compounds and montmorillonite nanoclays.

The aim of this work was to study the stabilization of the activity of two commercial microbial phytases (Aspergillus niger and Escherichia coli) after immobilization on nanoclays and to establish optimal conditions for their immobilization. Synthetic allophane, synthetic iron-coated allophanes and natural montmorillonite were chosen as solid supports for phytase immobilization. Phytase immobilization patterns at different pH values were strongly dependent on both enzyme and support characteristics. After immobilization, the residual activity of both phytases was higher under acidic conditions. Immobilization of phytases increased their thermal stability and improved resistance to proteolysis, particularly on iron-coated allophane (6% iron oxide), which showed activation energy (E(a)) and activation enthalpy (ΔH(#)) similar to free enzymes. Montmorillonite as well as allophanic synthetic compounds resulted in a good support for immobilization of E. coli phytase, but caused a severe reduction of A. niger phytase activity.

Identification of ß-propeller phytase-encoding genes in culturable Paenibacillus and Bacillus spp. from the rhizosphere of pasture plants on volcanic soils.

Phytate is one of the most abundant sources of organic phosphorus (P) in soils, but must be mineralized by phytase-producing bacteria to release P for plant uptake. Microbial inoculants based on Bacillus spp. have been developed commercially, but few studies have evaluated the ecology of these bacteria in the rhizosphere or the types of enzymes that they produce. Here, we studied the diversity of aerobic endospore-forming bacteria (EFB) with the ability to mineralize phytate in the rhizosphere of pasture plants grown in volcanic soils of southern Chile. PCR methods were used to detect candidate phytase-encoding genes and to identify EFB bacteria that carry these genes. This study revealed that the phytate-degrading EFB populations of pasture plants included species of Paenibacillus and Bacillus, which carried genes encoding ß-propeller phytase (BPP). Assays of enzymatic activity confirmed the ability of these rhizosphere isolates to degrade phytate. The phytase-encoding genes described here may prove valuable as molecular markers to evaluate the role of EFB in organic P mobilization in the rhizosphere.

Effect of liquid cow manure on andisol properties and atrazine adsorption.

Application of animal manure amendments to agricultural soils is a common practice to improve soil fertility through the addition of essential plant nutrients. This practice may increase the potential for atrazine (2-chloro-4-ethylamino-6-isopropylamino-1, 3, 5-triazine) leaching due to competition for adsorption sites between the pesticide and dissolved organic carbon (DOC) added through manure. We evaluated the influence of liquid cow manure (LCM) application on soil properties, atrazine adsorption, and the physicochemical controlling mechanisms in an Andisol. The LCM was applied at rates equivalent to 0, 100,000, 200,000, and 300,000 L ha(-1), resulting in treatments S-0, S-100, S-200, and S-300, respectively. The LCM application increased DOC and pH of the soils immediately on addition, but pH returned to S-0 values 30 d after application. The LCM application did not modify atrazine adsorption with the two lowest application rates (S-100 and S-200), but atrazine adsorption was decreased in S-300 (K(f) = 0.96) compared with the control (S-0) (K(f) = 1.19), possibly due to the competitive adsorption of DOC with the pesticide. The Fourier-transformed infrared analysis showed that LCM increased aliphaticity and presence of N-containing groups and polysaccharide-like groups in amended soils; however, these properties did not modify the atrazine interaction in the studied amended soils. Interestingly the addition of DOC to soil at the high application rate (S-300) reduced atrazine adsorption in this rich OM Andisol despite the LCM not raising the concentration of stable organic matter. The application of high rates of liquid manure containing DOC incurs an increased risk of pesticide leaching.

Current and future biotechnological applications of bacterial phytases and phytase-producing bacteria.

Phytases are a group of enzymes capable of releasing phosphate from phytate, one of the most abundant forms of organic phosphate in the natural environment. Phytases can be found in many organisms; in bacteria, they are particularly described in g-proteobacteria. In recent years, bacterial phytases have been isolated, characterized and proposed as potential tools in biotechnology. Microbial phytases have been applied mainly to animal (swine and poultry) and human foodstuffs in order to improve mineral bioavailability and food processing. Here, we summarize the current knowledge of bacterial phytases and phytase-producing bacteria, as well as their potential biotechnological applications, including new fields poorly explored, such as fish nutrition, environmental protection and plant nutrition. Despite the recognized importance in biotechnology, information on bacterial phytases and phytase-producing bacteria is clearly limited and major efforts are required to improve the knowledge of phytases present in bacteria and their utilization.