Unraveling the effect of arsenic on the model Medicago-Ensifer interaction: a transcriptomic meta-analysis

The potential of plant growth-promoting bacteria isolated from arid heavy metal contaminated environments in alleviating salt and water stresses in alfalfa

Co-evolution of plant beneficial microbes in contaminated environments enhances plant growth and mitigates abiotic stress. However, few studies on heavy metal (HM) tolerant plant growth-promoting bacteria (PGPB) promoting crop growth in Morocco's farming areas affected by drought and salinity are available. Plant associated bacteria tolerant to HM and able to produce indole acetic acid and siderophores, display ACC-deaminase activity and solubilize phosphate, were isolated from long-term metal exposed environments. Tolerance to HM and biofilms formation in the absence or presence of HM were assessed. A consortium including two Ensifer meliloti strains (RhOL6 and RhOL8), one Pseudomonas sp. strain (DSP17), and one Proteus sp. strain (DSP1), was used to inoculate alfalfa (Medicago sativa) seedlings under various conditions, namely, salt stress (85 mM) and water stress (30% water holding capacity). Shoot and root dry weights of alfalfa were measured 60 days after sowing. In the presence of HM, DSP17 showed the greatest auxin production, whereas RhOL8 had the highest ACC-deaminase activity and DSP17 formed the densest biofilm. Root dry weight increased 138% and 195% in salt and water stressed plants, respectively, regarding non-inoculated controls. Our results confirm the improvement of alfalfa growth and mitigation of salt and drought stress upon inoculation.

Arsenic-enhanced plant growth in As-hyperaccumulator Pteris vittata: Metabolomic investigations and molecular mechanisms

The first-known As-hyperaccumulator Pteris vittata is efficient in As uptake and translocation, which can be used for phytoremediation of As-contaminated soils. However, the underlying mechanisms of As-enhanced plant growth are unknown. We used untargeted metabolomics to investigate the potential metabolites and associated metabolic pathways regulating As-enhanced plant growth in P. vittata. After 60 days of growth in an MS-agar medium containing 15 mg kg-1 As, P. vittata biomass was 33-34 % greater than the no-As control. Similarly, the As contents in P. vittata roots and fronds were 272 and 1300 mg kg-1, considerably greater than the no-As control. Univariate and multivariate analyses based on electrospray ionization indicate that As exposure changed the expression of 1604 and 1248 metabolites in positive and negative modes. By comparing with the no-As control, As exposure significantly changed the expression of 14 metabolites including abscisic acid, d-glucose, raffinose, stachyose, chitobiose, xylitol, gibberellic acids, castasterone, citric acid, riboflavin-5-phosphate, ubiquinone, ubiquinol, UDP-glucose, and GDP-glucose. These metabolites are involved in phytohormone synthesis, energy metabolism, and sugar metabolism and may all potentially contribute to regulating As-enhanced plant growth in P. vittata. Our data provide clues to understanding the metabolic regulations of As-enhanced plant growth in P. vittata, which helps to enhance its phytoremediation efficiency of As-contaminated soils.

Targeting redox metabolism of the maize-Azospirillum brasilense interaction exposed to arsenic-affected groundwater

Arsenic in groundwater constitutes an agronomic problem due to its potential accumulation in the food chain. Among the agro-sustainable tools to reduce metal(oid)s toxicity, the use of plant growth-promoting bacteria (PGPB) becomes important. For that, and based on previous results in which significant differences of As translocation were observed when inoculating maize plants with Az39 or CD Azospirillum strains, we decided to decipher the redox metabolism changes and the antioxidant system response of maize plants inoculated when exposed to a realistic arsenate (As^V ) dose. Results showed that As^V caused morphological changes in the root exodermis. Photosynthetic pigments decreased only in CD inoculated plants, while oxidative stress evidence was detected throughout the plant, regardless of the assayed strain. The antioxidant response was strain-differential since only CD inoculated plants showed an increase in superoxide dismutase, glutathione S-transferase (GST), and glutathione reductase (GR) activities while other enzymes showed the same behavior irrespective of the inoculated strain. Gene expression assays reported that only GST23 transcript level was upregulated by arsenate, regardless of the inoculated strain. As^V diminished the glutathione (GSH) content of roots inoculated with the Az39 strain, and CD inoculated plants showed a decrease of oxidized GSH (GSSG) levels. We suggest a model in which the antioxidant response of the maize-diazotrophs system is modulated by the strain and that GSH plays a central role acting mainly as a substrate for GST. These findings generate knowledge for a suitable PGPB selection, and its scaling to an effective bioinoculant formulation for maize crops exposed to adverse environmental conditions.

Unraveling the role of plant growth-promoting rhizobacteria in the alleviation of arsenic phytotoxicity: A review

The toxic metalloid arsenic (As), is a major pollutant of soil and water, imposing severe health concerns on human lives. It enters the food chain mainly through As-contaminated crops. The uptake, translocation and accumulation of As in plant tissue are often controlled by certain soil-inhabiting microbial communities. Among them, indigenous, free-living As-resistant plant growth-promoting rhizobacteria (PGPR) plays a pivotal role in As-immobilization. Besides, the plant's inability to withstand As after a threshold level is actively managed by these PGPR increasing As-tolerance in host plants by a synergistic plant-microbe interaction. The dual functionality of As-resistant PGPR i.e., phytostimulation and minimization of As-induced phytotoxic damages are one of the main focal points of this review article. It is known that such PGPR having the functional arsenic-resistant genes (in ars operon) including As-transporters, As-transforming genes contributed to the As accumulation and detoxification/transformation respectively. Apart from assisting in nutrient acquisition and modulating phytohormone levels, As-resistant PGPR also influences the antioxidative defense system in plants by maneuvering multiple enzymatic and non-enzymatic antioxidants. Furthermore, they are effective in reducing membrane damage and electrolyte leakage in plant cells. As-induced photosynthetic damage is also found to be salvaged by As-resistant PGPR. Briefly, the eco-physiological, biochemical and molecular mechanisms of As-resistant PGPR are thus elaborated here with regard to the As-exposed crops.

Arsenate-reducing bacteria affect As accumulation and tolerance in Salix atrocinerea

Arsenic (As)-reducing bacteria are able to influence As-speciation and, in this way, change As bio-availability. In consequence, this has an impact on As uptake by plants growing on polluted soil and on the effectiveness of the phytoremediation process. To be able to efficiently utilize these bacteria for As-phytoremediation in the field, a better understanding of the plant-bacterial interactions involved in As-tolerance or toxicity is needed. In this work, seedlings of a clone of Salix atrocinerea derived from a specimen naturally growing on an As-polluted brownfield were grown under gnotobiotic conditions exposed to As, and in the presence or absence of two of its field-associated and in vitro characterized plant growth-promoting (PGP) bacteria. The inoculation with Pantoea sp., induced a moderate reduction of AsV to AsIII in the exposure medium that, together with a coordinated plant response of As uptake, chelation and sequestration, increased As accumulation in roots; which is reflected into a higher phytostabilization. However, inoculation with Rhodococcus erythropolis due to a higher disproportionate reduction of AsV to AsIII in the medium caused less As accumulation in roots that non-bioaugmented plants and despite the lower As content, the concentrations of AsIII present in the medium and the damage suffered in roots and leaves, indicated that As tolerance mechanisms (such as prevention of AsIII uptake and efflux) did not occur in time to avoid physical disturbance and plants growth reduction. Interestingly, by two different metabolic pathways -coordinated by different key transporters mediating As uptake, tolerance, distribution and vacuolar accumulation at the roots- both bacteria limited As accumulation in Salix shoots. Our results provide for the first time a detailed insight in the plant-bacterial responses and physiological changes contributing to As tolerance in S. atrocinerea, that will facilitate the design of effective strategies for exploitation of plant-associated microorganisms for phytoremediation.

The Fungicide Tetramethylthiuram Disulfide Negatively Affects Plant Cell Walls, Infection Thread Walls, and Symbiosomes in Pea (Pisum sativum L.) Symbiotic Nodules

In Russia, tetramethylthiuram disulfide (TMTD) is a fungicide widely used in the cultivation of legumes, including the pea (Pisum sativum). Application of TMTD can negatively affect nodulation; nevertheless, its effect on the histological and ultrastructural organization of nodules has not previously been investigated. In this study, the effect of TMTD at three concentrations (0.4, 4, and 8 g/kg) on nodule development in three pea genotypes (laboratory lines Sprint-2 and SGE, and cultivar 'Finale') was examined. In SGE, TMTD at 0.4 g/kg reduced the nodule number and shoot and root fresh weights. Treatment with TMTD at 8 g/kg changed the nodule color from pink to green, indicative of nodule senescence. Light and transmission electron microscopy analyses revealed negative effects of TMTD on nodule structure in each genotype. 'Finale' was the most sensitive cultivar to TMTD and Sprint-2 was the most tolerant. The negative effects of TMTD on nodules included the appearance of a senescence zone, starch accumulation, swelling of cell walls accompanied by a loss of electron density, thickening of the infection thread walls, symbiosome fusion, and bacteroid degradation. These results demonstrate how TMTD adversely affects nodules in the pea and will be useful for developing strategies to optimize fungicide use on legume crops.

Unraveling the impact of arsenic on the redox response of peanut plants inoculated with two different Bradyrhizobium sp. strains

Arsenic (As) can be present naturally in groundwater from peanut fields, constituting a serious problem, as roots can accumulate and mobilize the metalloid to their edible parts. Understanding the redox changes in the legume exposed to As may help to detect potential risks to human health and recognize tolerance mechanisms. Thirty-days old peanut plants inoculated with Bradyrhizobium sp. strains (SEMIA6144 or C-145) were exposed to a realistic arsenate concentration, in order to unravel the redox response and characterize the oxidative stress indexes. Thus, root anatomy, reactive oxygen species detection by fluorescence microscopy and, ROS histochemical staining along with the NADPH oxidase activity were analyzed. Besides, photosynthetic pigments and damage to lipids and proteins were determined as oxidative stress indicators. Results showed that at 3 μM As^V, the cross-section areas of peanut roots were augmented; NADPH oxidase activity was significantly increased and O₂˙¯and H₂O₂ accumulated in leaves and roots. Likewise, an increase in the lipid peroxidation and protein carbonyls was also observed throughout the plant regardless the inoculated strain, while chlorophylls and carotenes were increased only in those inoculated with Bradyrhizobium sp. C-145. Interestingly, the oxidative burst, mainly induced by the NADPH oxidase activity, and the consequent oxidative stress was strain-dependent and organ-differential. Additionally, As modifies the root anatomy, acting as a possibly first defense mechanism against the metalloid entry. All these findings allowed us to conclude that the redox response of peanut is conditioned by the rhizobial strain, which contributes to the importance of effectively formulating bioinoculants for this crop.

Pioneer trees of Betula pendula at a red gypsum landfill harbour specific structure and composition of root-associated microbial communities

The study of root-associated microbial communities is important to understand the natural processes involved in plant recolonisation at degraded areas. Root associated bacterial and fungal communities of woody species colonising a red gypsum landfill (a metal-enriched environment) were characterised through metabarcoding. Among trees naturally growing on the landfill, Betula pendula is the only tree species in the centre of the area, whereas companion tree species such as Populus nigra, P. tremula and Salix purpurea were present on the edges. The bacterial community was dominated by Proteobacteria (38%), Actinobacteria (35%) and Bacteroidetes (20%) and the most abundant bacterial OTU belonged to the family Streptomycetaceae. The fungal community was dominated by Ascomycota (60%) and Basidiomycota (30%) and the most abundant family was Pyronemataceae. Analysis of similarities, heatmap and hierarchical cluster analysis showed that B. pendula grown in the centre of the landfill harboured a specific microbial community, which was unique and different, not only from other tree species (Populus or Salix spp.), but also from other B. pendula growing at the edges. Our findings on relevant indicator OTUs associated to the birches located in the centre of the landfill (such as Otu00716 Catellatospora sp. (family Micromonosporaceae, phylum Actinobacteria) or Otu4_35502 Russula sp. (family Russulaceae, phylum Basidiomycota)) may have important implications for the successful revegetation of these harsh environments using microbial-based phytostabilisation approaches.

Targeting Acr3 from Ensifer medicae to the plasma membrane or to the tonoplast of tobacco hairy roots allows arsenic extrusion or improved accumulation. Effect of acr3 expression on the root transcriptome

Transgenic tobacco hairy roots expressing the bacterial arsenite efflux pump Acr3 from Ensifer medicae were generated. The gene product was targeted either to the plasma membrane (ACR3 lines) or to the tonoplast by fusing the ACR3 protein to the tonoplast integral protein TIP1.1 (TIP-ACR3 lines). Roots expressing Acr3 at the tonoplast showed greater biomass than those expressing Acr3 at the plasma membrane. Furthermore, higher contents of malondialdehyde (MDA) and RNA degradation in ACR3 lines were indicative of higher oxidative stress. The determination of ROS-scavenging enzymes depicted the transient role of peroxidases in ROS detoxification, followed by the action of superoxide dismutase during both short- and medium-term exposure periods. Regarding As accumulation, ACR3 lines accumulated up to 20-30% less As, whereas TIP-ACR3 achieved a 2-fold increase in As accumulation in comparison to control hairy roots. Strategies that presumably induce As uptake, such as phosphate deprivation or dehydration followed by rehydration in the presence of As, fostered As accumulation up to 10 800 μg g-1. Finally, the effects of the heterologous expression of acr3 on the root transcriptome were assessed. Expression at the plasma membrane induced drastic changes in gene expression, with outstanding overexpression of genes related to electron transport, ATP synthesis and ATPases, suggesting that As efflux is the main detoxification mechanism in these lines. In addition, genes encoding heat shock proteins and those related to proline synthesis and drought tolerance were activated. On the other hand, TIP-ACR3 lines showed a similar gene expression profile to that of control roots, with overexpression of the glutathione and phytochelatin synthesis pathways, together with secondary metabolism pathways as the most important resistance mechanisms in TIP-ACR3, for which As allocation into the vacuole allowed better growth and stress management. Our results suggest that modulation of As accumulation can be achieved by subcellular targeting of Acr3: expression at the tonoplast enhances As accumulation in roots, whereas expression at the plasma membrane could promote As efflux. Thus, both approaches open the possibilities for developing safer crops when grown on As-polluted paddy soils, but expression at the tonoplast leads to better growth and less stressed roots, since the high energy cost of As efflux likely compromises growth in ACR3 lines.

Safe Cultivation of Medicago sativa in Metal-Polluted Soils from Semi-Arid Regions Assisted by Heat- and Metallo-Resistant PGPR

Soil contamination with heavy metals is a constraint for plant establishment and development for which phytoremediation may be a solution, since rhizobacteria may alleviate plant stress under these conditions. A greenhouse experiment was conducted to elucidate the effect of toxic metals on growth, the activities of ROS (reactive oxygen species)-scavenging enzymes, and gene expression of Medicago sativa grown under different metal and/or inoculation treatments. The results showed that, besides reducing biomass, heavy metals negatively affected physiological parameters such as chlorophyll fluorescence and gas exchange, while increasing ROS-scavenging enzyme activities. Inoculation of M. sativa with a bacterial consortium of heat- and metallo-resistant bacteria alleviated metal stress, as deduced from the improvement of growth, lower levels of antioxidant enzymes, and increased physiological parameters. The bacteria were able to effectively colonize and form biofilms onto the roots of plants cultivated in the presence of metals, as observed by scanning electron microscopy. Results also evidenced the important role of glutathione reductase (GR), phytochelatin synthase (PCS), and metal transporter NRAMP1 genes as pathways for metal stress management, whereas the gene coding for cytochrome P450 (CP450) seemed to be regulated by the presence of the bacteria. These outcomes showed that the interaction of metal-resistant rhizobacteria/legumes can be used as an instrument to remediate metal-contaminated soils, while cultivation of inoculated legumes on these soils is still safe for animal grazing, since inoculation with bacteria diminished the concentrations of heavy metals accumulated in the aboveground parts of the plants to below toxic levels.

Impact of double inoculation with Bradyrhizobium japonicum E109 and Azospirillum brasilense Az39 on soybean plants grown under arsenic stress

Inoculation practice with plant growth-promoting bacteria (PGPB) has been proposed as a good biotechnological tool to enhance plant performance and alleviate heavy metal/metalloid stress. Soybean is often cultivated in soil with high arsenic (As) content or irrigated with As-contaminated groundwater, which causes deleterious effects on its growth and yield, even when it was inoculated with rhizobium. Thus, the effect of double inoculation with known PGPB strains, Bradyrhizobium japonicum E109 and Azospirillum brasilense Az39 was evaluated in plants grown in pots under controlled conditions and treated with As. First, the viability of these co-cultivated bacteria was assayed using a flow cytometry analysis using SYTO9 and propidium iodide (PI) dyes. This was performed in vitro to evaluate the bacterial population dynamic under 25 μM AsV and AsIII treatment. A synergistic effect was observed when bacteria were co-cultured, since mortality diminished, compared to each growing alone. Indole acetic acid (IAA) produced by A. brasilense Az39 would be one of the main components involved in B. japonicum E109 mortality reduction, mainly under AsIII treatment. Regarding in vivo assays, under As stress, plant growth improvement, nodule number and N content increase were observed in double inoculated plants. Furthermore, double inoculation strategy reduced As translocation to aerial parts thus improving As phytostabilization potential of soybean plants. These results suggest that double inoculation with B. japonicum E109 and A. brasilense Az39 could be a safe and advantageous practice to improve growth and yield of soybean exposed to As, accompanied by an important metalloid phytostabilization.

Phenotypic and Molecular-Phylogenetic Analysis Provide Novel Insights into the Diversity of Curtobacterium flaccumfaciens

A multiphasic approach was used to decipher the phenotypic features, genetic diversity, and phylogenetic position of 46 Curtobacterium spp. strains isolated from dry beans and other annual crops in Iran and Spain. Pathogenicity tests, resistance to arsenic compounds, plasmid profiling and BOX-PCR were performed on the strains. Multilocus sequence analysis (MLSA) was also performed on five housekeeping genes (i.e., atpD, gyrB, ppk, recA, and rpoB) of all the strains, as well as five pathotype strains of the species. Pathogenicity test showed that six out of 42 strains isolated in Iran were nonpathogenic on common bean. Despite no differences found between pathogenic and nonpathogenic strains in their plasmid profiling, the former were resistant to different concentrations of arsenic, while the latter were sensitive to the same concentrations. Strains pathogenic on common bean were polyphyletic with at least two evolutionary lineages (i.e., yellow-pigmented strains versus red/orange-pigmented strains). Nonpathogenic strains isolated from solanaceous vegetables were clustered within either the strains of C. flaccumfaciens pv. flaccumfaciens or different pathovars of the species. The results of MLSA and BOX-PCR analysis were similar to each other and both methods were able to discriminate the yellow-pigmented strains from the red/orange-pigmented strains. A comprehensive study of a worldwide collection representing all five pathovars as well as nonpathogenic strains of C. flaccumfaciens is warranted for a better understanding of the diversity within this phytopathogenic bacterium.

Metal(loid)-resistant bacteria reduce wheat Cd and As uptake in metal(loid)-contaminated soil

This study characterized the effect of the metal(loid)-resistant bacteria Ralstonia eutropha Q2-8 and Exiguobacterium aurantiacum Q3-11 on Cd and As accumulation in wheat grown in Cd- and As-polluted soils (1 mg kg^-1 of Cd + 40 mg kg^-1 of As and 2 mg kg^-1 of Cd + 60 mg kg^-1 of As). The influence of strains Q2-8 and Q3-11 on water-soluble Cd and As and NH₄⁺concentration and pH in the soil filtrate were also analyzed. Inoculation with these strains significantly reduced wheat plant Cd (12-32%) and As (9-29%) uptake and available Cd (15-28%) and As (22-38%) contents in rhizosphere soils compared to the controls. Furthermore, these strains significantly increased the relative abundances of the arsM bacterial As metabolism gene and of Fe- and Mn-oxidizing Leptothrix species in rhizosphere soils. Notably, these strains significantly reduced water-soluble Cd and As concentrations and increased pH and NH₄⁺ concentration in the soil filtrate. These results suggest that these strains increased soil pH and the abundance of genes possibly involved in metal(loid) unavailability, resulting in reduced wheat Cd and As accumulation and highlight the possibility of using bacteria for in situ remediation and safe production of wheat or other food crops in metal(loid)-polluted soils.

Metal resistant rhizobia and ultrastructure of Anthyllis vulneraria nodules from zinc and lead contaminated tailing in Poland

This present paper studies the response of Anthyllis vulneraria-Rhizobium symbiosis to heavy metal stress. The symbiotic rhizobium bacteria isolated from root nodules of A. vulneraria from zinc and lead wastes were examined in this project. Light microscopy (LM) and transmission electron microscopy (TEM) were used to analyze the nodule anatomy and ultrastructure and conduct a comparison with nonmetal-treated nodules. 16S ribosomal DNA sequence analysis of bacteria isolated from metal-treated nodules revealed the presence of Rhizobium metallidurans and Bradyrhizobium sp. In regard to heavy metal resistance/tolerance, a similar tolerance to Pb was shown by both strains, and a high tolerance to Zn and a lower tolerance to Cd and Cu by R. metallidurans, whereas a high tolerance to Cd and Cu and a lower tolerance to Zn by Bradyrhizobium were found. The nodules of Anthyllis from metal-polluted tailing sites were identified as the typical determinate type of nodules. Observed under TEM microscopy changes in nodules ultrastructure like: (1) wall thickening; (2) infection thread reduction; (3) vacuole shrinkage; (4) synthesis of phenolics in vacuoles; (5) various differentiation of bacteroids and (6) simultaneous symbiosis with arbuscular mycorrhiza fungi could be considered as a form of the A.vulneraria-Rhizobium symbiosis adaptation to metal stress.

Remediation of arsenic in mung bean (Vigna radiata) with growth enhancement by unique arsenic-resistant bacterium Acinetobacter lwoffii

Arsenic, a carcinogenic and toxic contaminant of soil and water, affects human health adversely. During last few decades, it has been an important global environmental issue. Among several arsenic detoxification methods remediation using arsenic resistant microbes is proved to be environment-friendly and cost-effective. This study aimed to test the effects of arsenic utilizing bacterial strain Acinetobacter lwoffii (RJB-2) on arsenic uptake and growth of mung bean plants (Vigna radiata). RJB-2 exhibited tolerance up to 125mM of arsenic (V) and 50mM of arsenic (III). RJB-2 produced plant growth promoting substances e.g. indole acetic acid (IAA), siderophores, exopolysaccharide (EPS) and phosphate solubilization in the absence and in presence of arsenic. Pot experiments were used to scrutinize the role of RJB-2 on arsenic uptake and growth of mung bean plants grown in soil amended with 22.5mgkg^-1 of sodium arsenate (Na₂HAsO₄·7H₂O). RJB-2 could arrest arsenic uptake in just 7days and increase plant growth, number of plants per pot, chlorophyll and carotenoid content of the mung bean plants. RJB-2 formed biofilm and its root-association helped to abate arsenic uptake in mung bean. Confocal and light microscopic studies also revealed the abatement of arsenic uptake and increase in chlorophyll content in mung bean plants in presence of RJB-2. RJB-2 was also responsible for less production of reactive oxygen species (ROS) in mung bean plants reducing the oxidative damage caused by arsenic. The lower percentage of electrolytic leakage (EL) in RJB-2 inoculated mung bean plants proved arsenic abatement. The study also reported the distribution of arsenic in various parts of mung bean plant. RJB-2 owing to its intrinsic abilities of plant growth promotion even in presence of high concentrations of arsenic could inhibit arsenic uptake completely and therefore it could be used in large-scale cultivation for phytostabilization of plants.

Investigating the mechanisms underlying phytoprotection by plant growth-promoting rhizobacteria in Spartina densiflora under metal stress

Pollution of coasts by toxic metals and metalloids is a worldwide problem for which phytoremediation using halophytes and associated microbiomes is becoming relevant. Metal(loid) excess is a constraint for plant establishment and development, and plant growth promoting rhizobacteria (PGPR) mitigate plant stress under these conditions. However, mechanisms underlying this effect remain elusive. The effect of toxic metal(loid)s on activity and gene expression of ROS-scavenging enzymes in roots of the halophyte Spartina densiflora grown on real polluted sediments in a greenhouse experiment was investigated. Sediments of the metal-polluted joint estuary of Tinto and Odiel rivers and control, unpollutred samples from the Piedras estuary were collected and submitted to ICP-OES. Seeds of S. densiflora were collected from the polluted Odiel marshes and grown in polluted and unpolluted sediments. Rhizophere biofilm-forming bacteria were selected based on metal tolerance and inoculated to S. densiflora and grown for 4 months. Fresh or frozen harvested plants were used for enzyme assays and gene expression studies, respectively. Metal excess induced SOD (five-fold increase), whereas CAT and ascorbate peroxidase displayed minor induction (twofold). A twofold increase of TBARs indicated membrane damage. Our results showed that metal-resistant PGPR (P. agglomerans RSO6 and RSO7 and B. aryabhattai RSO25) contributed to alleviate metal stress, as deduced from lower levels of all antioxidant enzymes to levels below those of non-exposed plants. The oxidative stress index (OSI) decreased between 50 and 75% upon inoculation. The results also evidenced the important role of PAL, involved in secondary metabolism and/or lignin synthesis, as a pathway for metal stress management in this halophyte upon inoculation with appropriate PGPR, since the different inoculation treatments enhanced PAL expression between 3.75- and five-fold. Our data confirm, at the molecular level, the role of PGPR in alleviating metal stress in S. densiflora and evidence the difficulty of working with halophytes for which little genetic information is available.

Effective rhizoinoculation and biofilm formation by arsenic immobilizing halophilic plant growth promoting bacteria (PGPB) isolated from mangrove rhizosphere: A step towards arsenic rhizoremediation

Arsenic (As) uptake by plants is largely influenced by the presence of microbial consortia and their interactions with As. In the coastal region of Bengal deltaic plain of Eastern India, the As-contaminated groundwater is frequently used for irrigation purposes resulting in an elevated level of soil As in agricultural lands. The health hazards associated with As necessitates development of cost-effective remediation strategies to reclaim contaminated agricultural lands. Among the available technologies developed in recent times, bioremediation using bacteria has been found to be the most propitious. In this study, two As-resistant halophilic bacterial strains Kocuria flava AB402 and Bacillus vietnamensis AB403 were isolated, identified and characterized from mangrove rhizosphere of Sundarban. The isolates, AB402 and AB403, could tolerate 35mM and 20mM of arsenite, respectively. The effect of As on the exopolysaccharide (EPS) synthesis, biofilm formation, and root association was evaluated for both the bacterial strains. Arsenic adsorption on the cell surfaces and intracellular accumulation in both the bacterial strains were promising under culture conditions. Moreover, both the strains when used as inoculum, not only promoted the growth of rice seedlings but also decreased As uptake and accumulation in plants.

Bacterial community dynamic associated with autochthonous bioaugmentation for enhanced Cu phytoremediation of salt-marsh sediments

Autochthonous bioaugmentation for metal phytoremediation is still little explored, particularly its application to estuarine salt marshes, but results obtained so far are promising. Nevertheless, understanding the behaviour of the microbial communities in the process of bioaugmentation and their role in improving metal phytoremediation is very important to fully validate the application of this biological technology. This study aimed to characterize the bacterial community dynamic associated with the application of autochthonous bioaugmentation in an experimentation which showed that Phragmites australis rhizosphere microorganisms could increase this salt marsh plant potential to phytoremediate Cu contaminated sediments. Bacterial communities present in the autochthonous microbial consortium resistant to Cu added to the medium and in the sediment at the beginning and at the end of the experiment were characterized by ARISA. Complementarily, the consortium and the sediment used for its production were characterized by next generation sequencing using the pyrosequencing platform 454. The microbial consortium resistant to Cu obtained from non-vegetated sediment was dominated by the genus Lactococcus (46%), Raoultella (25%), Bacillus (12%) and Acinetobacter (11%), whereas the one obtained form rhizosediment was dominated by the genus Gluconacetobacter (77%), Bacillus (17%) and Dyella (3%). Results clearly showed that, after two months of experiment, Cu caused a shift in the bacterial community structure of sediments, an effect that was observed either with or without addition of the metal resistant microbial consortium. Therefore, bioaugmentation application improved the process of phytoremediation (metal translocation by the plant was increased) without inducing long term changes in the bacterial community structure of the sediments. So, phytoremediation combined with autochthonous bioaugmentation can be a suitable technology for the recovery of estuarine areas, contributing for an efficient risk management strategy of these coastal zones.

Linking Genes to Microbial Biogeochemical Cycling: Lessons from Arsenic

The biotransformation of arsenic is highly relevant to the arsenic biogeochemical cycle. Identification of the molecular details of microbial pathways of arsenic biotransformation coupled with analyses of microbial communities by meta-omics can provide insights into detailed aspects of the complexities of this biocycle. Arsenic transformations couple to other biogeochemical cycles, and to the fate of both nutrients and other toxic environmental contaminants. Microbial redox metabolism of iron, carbon, sulfur, and nitrogen affects the redox and bioavailability of arsenic species. In this critical review we illustrate the biogeochemical processes and genes involved in arsenic biotransformations. We discuss how current and future metagenomic-, metatranscriptomic-, metaproteomic-, and metabolomic-based methods will help to decipher individual microbial arsenic transformation processes, and their connections to other biogeochemical cycle. These insights will allow future use of microbial metabolic capabilities for new biotechnological solutions to environmental problems. To understand the complex nature of inorganic and organic arsenic species and the fate of environmental arsenic will require integrating systematic approaches with biogeochemical modeling. Finally, from the lessons learned from these studies of arsenic biogeochemistry, we will be able to predict how the environment changes arsenic, and, in response, how arsenic biotransformations change the environment.

Natural rhizobial diversity helps to reveal genes and QTLs associated with biological nitrogen fixation in common bean

Common bean is one of the most important crops for human feed, and the most important legume for direct consumption by millions of people, especially in developing countries. It is a promiscuous host legume in terms of nodulation, able to associate with a broad and diverse range of rhizobia, although the competitiveness for nodulation and the nitrogen fixation capacity of most of these strains is generally low. As a result, common bean is very inefficient for symbiotic nitrogen fixation, and nitrogen has to be supplied with chemical fertilizers. In the last years, symbiotic nitrogen fixation has received increasing attention as a sustainable alternative to nitrogen fertilizers, and also as a more economic and available one in poor countries. Therefore, optimization of nitrogen fixation of bean-rhizobia symbioses and selection of efficient rhizobial strains should be a priority, which begins with the study of the natural diversity of the symbioses and the rhizobial populations associated. Natural rhizobia biodiversity that nodulates common bean may be a source of adaptive alleles acting through phenotypic plasticity. Crosses between accessions differing for nitrogen fixation may combine alleles that never meet in nature. Another way to discover adaptive genes is to use association genetics to identify loci that common bean plants use for enhanced biological nitrogen fixation and, in consequence, for marker assisted selection for genetic improvement of symbiotic nitrogen fixation. In this review, rhizobial biodiversity resources will be discussed, together with what is known about the loci that underlie such genetic variation, and the potential candidate genes that may influence the symbiosis' fitness benefits, thus achieving an optimal nitrogen fixation capacity in order to help reduce reliance on nitrogen fertilizers in common bean.

Use of Endophytic and Rhizosphere Bacteria To Improve Phytoremediation of Arsenic-Contaminated Industrial Soils by Autochthonous Betula celtiberica

The aim of this study was to investigate the potential of indigenous arsenic-tolerant bacteria to enhance arsenic phytoremediation by the autochthonous pseudometallophyte Betula celtiberica The first goal was to perform an initial analysis of the entire rhizosphere and endophytic bacterial communities of the above-named accumulator plant, including the cultivable bacterial species. B. celtiberica's microbiome was dominated by taxa related to Flavobacteriales, Burkholderiales, and Pseudomonadales, especially the Pseudomonas and Flavobacterium genera. A total of 54 cultivable rhizobacteria and 41 root endophytes, mainly affiliated with the phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria, were isolated and characterized with respect to several potentially useful features for metal plant accumulation, such as the ability to promote plant growth, metal chelation, and/or mitigation of heavy-metal stress. Seven bacterial isolates were further selected and tested for in vitro accumulation of arsenic in plants; four of them were finally assayed in field-scale bioaugmentation experiments. The exposure to arsenic in vitro caused an increase in the total nonprotein thiol compound content in roots, suggesting a detoxification mechanism through phytochelatin complexation. In the contaminated field, the siderophore and indole-3-acetic acid producers of the endophytic bacterial consortium enhanced arsenic accumulation in the leaves and roots of Betula celtiberica, whereas the rhizosphere isolate Ensifer adhaerens strain 91R mainly promoted plant growth. Field experimentation showed that additional factors, such as soil arsenic content and pH, influenced arsenic uptake in the plant, attesting to the relevance of field conditions in the success of phytoextraction strategies.IMPORTANCE Microorganisms and plants have developed several ways of dealing with arsenic, allowing them to resist and metabolize this metalloid. These properties form the basis of phytoremediation treatments and the understanding that the interactions of plants with soil bacteria are crucial for the optimization of arsenic uptake. To address this in our work, we initially performed a microbiome analysis of the autochthonous Betula celtiberica plants growing in arsenic-contaminated soils, including endosphere and rhizosphere bacterial communities. We then proceeded to isolate and characterize the cultivable bacteria that were potentially better suited to enhance phytoextraction efficiency. Eventually, we went to the field application stage. Our results corroborated the idea that recovery of pseudometallophyte-associated bacteria adapted to a large historically contaminated site and their use in bioaugmentation technologies are affordable experimental approaches and potentially very useful for implementing effective phytoremediation strategies with plants and their indigenous bacteria.

Transcriptomic Analysis Reveals Adaptive Responses of an Enterobacteriaceae Strain LSJC7 to Arsenic Exposure

Arsenic (As) resistance determinant ars operon is present in many bacteria and has been demonstrated to enhance As(V) resistance of bacteria. However, whole molecular mechanism adaptations of bacteria in response to As(V) stress remain largely unknown. In this study, transcriptional profiles of Enterobacteriaceae strain LSJC7 responding to As(V) stress were analyzed using RNA-seq and qRT-PCR. As expected, genes involved in As(V) uptake were down-regulated, those involved in As(V) reduction and As(III) efflux were up-regulated, which avoided cellular As accumulation. Reactive oxygen species and nitric oxide (NO) were induced, which caused cellular damages including DNA, protein, and Fe–S cluster damage in LSJC7. The expression of specific genes encoding transcriptional regulators, such as nsrR and soxRS were also induced. NsrR and SoxRS modulated many critical metabolic activities in As(V) stressed LSJC7 cells, including reactive species scavenging and repairing damaged DNA, proteins, and Fe–S clusters. Therefore, besides As uptake, reduction, and efflux; oxidative stress defense and damage repair were the main cellular adaptive responses of LSJC7 to As(V) stress.

Microcystin-tolerant Rhizobium protects plants and improves nitrogen assimilation in Vicia faba irrigated with microcystin-containing waters

Irrigation of crops with microcystins (MCs)-containing waters-due to cyanobacterial blooms-affects plant productivity and could be a way for these potent toxins entering the food chain. This study was performed to establish whether MC-tolerant rhizobia could benefit growth, nodulation, and nitrogen metabolism of faba bean plants irrigated with MC-containing waters. For that, three different rhizobial strains-with different sensitivity toward MCs-were used: RhOF96 (most MC-sensitive strain), RhOF125 (most MC-tolerant strain), or Vicz1.1 (reference strain). As a control, plants grown without rhizobia and fertilized by NH4NO3 were included in the study. MC exposure decreased roots (30-37 %) and shoots (up to 15 %) dry weights in un-inoculated plants, whereas inoculation with rhizobia protects plants toward the toxic effects of MCs. Nodulation and nitrogen content were significantly impaired by MCs, with the exception of plants inoculated with the most tolerant strain RhOF125. In order to deep into the effect of inoculation on nitrogen metabolism, the nitrogen assimilatory enzymes (glutamine synthetase (GS) and glutamate synthase (GOGAT)) were investigated: Fertilized plants showed decreased levels (15-30 %) of these enzymes, both in shoots and roots. By contrast, inoculated plants retained the levels of these enzymes in shoots and roots, as well as the levels of NADH-GOGAT activity in nodules. We conclude that the microcystin-tolerant Rhizobium protects faba bean plants and improves nitrogen assimilation when grown in the presence of MCs.

Mechanisms of Soybean Roots' Tolerances to Salinity Revealed by Proteomic and Phosphoproteomic Comparisons Between Two Cultivars

Understanding molecular mechanisms underlying plant salinity tolerance provides valuable knowledgebase for effective crop improvement through genetic engineering. Current proteomic technologies, which support reliable and high-throughput analyses, have been broadly used for exploring sophisticated molecular networks in plants. In the current study, we compared phosphoproteomic and proteomic changes in roots of different soybean seedlings of a salt-tolerant cultivar (Wenfeng07) and a salt-sensitive cultivar (Union85140) induced by salt stress. The root samples of Wenfeng07 and Union85140 at three-trifoliate stage were collected at 0 h, 0.5 h, 1 h, 4 h, 12 h, 24 h, and 48 h after been treated with 150 mm NaCl. LC-MS/MS based phosphoproteomic analysis of these samples identified a total of 2692 phosphoproteins and 5509 phosphorylation sites. Of these, 2344 phosphoproteins containing 3744 phosphorylation sites were quantitatively analyzed. Our results showed that 1163 phosphorylation sites were differentially phosphorylated in the two compared cultivars. Among them, 10 MYB/MYB transcription factor like proteins were identified with fluctuating phosphorylation modifications at different time points, indicating that their crucial roles in regulating flavonol accumulation might be mediated by phosphorylated modifications. In addition, the protein expression profiles of these two cultivars were compared using LC MS/MS based shotgun proteomic analysis, and expression pattern of all the 89 differentially expressed proteins were independently confirmed by qRT-PCR. Interestingly, the enzymes involved in chalcone metabolic pathway exhibited positive correlations with salt tolerance. We confirmed the functional relevance of chalcone synthase, chalcone isomerase, and cytochrome P450 monooxygenase genes using soybean composites and Arabidopsis thaliana mutants, and found that their salt tolerance were positively regulated by chalcone synthase, but was negatively regulated by chalcone isomerase and cytochrome P450 monooxygenase. A novel salt tolerance pathway involving chalcone metabolism, mostly mediated by phosphorylated MYB transcription factors, was proposed based on our findings. (The mass spectrometry raw data are available via ProteomeXchange with identifier PXD002856).