Phylogenetic assignment and mechanism of action of a crop growth promoting Rhizobium radiobacter strain used as a biofertiliser on graminaceous crops in Russia

The use of phosphate rock and plant growth promoting microorganisms for the management of Urochloa decumbens (Stapf.) R.D. Webster in acidic soils

Background

Forage production in tropical soils is primarily limited by nutrient deficiencies, especially nitrogen (N) and phosphorus (P). The use of phosphate rock by plants is limited by its low and slow P availability and microbial phosphate solubilization is the main mechanism for P bioavailability in the soil-root system. The objectives of this study were (i) select a nitrogen-fixing bacteria which could be used as a co-inoculant with the Penicillium rugulosum IR94MF1 phosphate-solubilizing fungus and (ii) evaluate under field conditions the effect of inoculation combined with phosphate rock (PR) application on yield and nutrient absorption of a Urochloa decumbens pasture which was previously established in a low-fertility, acidic soil.

Methods

Various laboratory and greenhouse tests allowed for the selection of Enterobacter cloacae C17 as the co-inoculant bacteria with the IR94MF1 fungus. Later, under field conditions, a factorial, completely randomized block design was used to evaluate the inoculation with the IR94MF1 fungus, the IR94MF1+C17 co-inoculation, and a non-inoculated control. Two levels of fertilization with PR treatment (0 kg/ha and 200 kg/ha P2O5) were applied to each.

Results

During five consecutive harvests it was observed that the addition of biofertilizers significantly increased (p < 0.05) the herbage mass and N and P assimilation compared to the non-inoculated control. However, no statistically significant differences were observed for the PR application as P source.

Conclusion

P. rugulosum IR94MF1 is capable of solubilizing and accumulating P from the phosphate rock, making it available for plants growing in acid soils with low N content. These inoculants represent a good option as biofertilizers for tropical grasses already established in acidic soils with low N content.

Lead toxicity induced phytotoxic impacts on rapeseed and clover can be lowered by biofilm forming lead tolerant bacteria

Lead (Pb⁺²) is a heavy metal and one of the main environmental pollutant, toxic to plants, animals and humans. Present study was conducted to evaluate ten plant growth promoting bacteria strains (B1-10) for biofilm production and their effect on growth indices, physiology, yield, antioxidant profile and lead uptake in rapeseed (Brassica napus) and clover (Trifolium repens) in lead polluted soil under nutrient broth medium and pot condition. Three pre-characterized biofilm forming lead tolerant growth promoting strains (B3: Pseudomonas fluorescens), B6: Pseudomonas putida and (B8: Bacillus safensis) were used to inoculate rapeseed and clover growing in the soil polluted with different levels (400, 800 and 1200 mg kg^-1) of Pb arranged in completely randomized design with factorial arrangement. Results from screening experiment exhibited that more biofilm was produced by B3, B6 and B8 under highest level of lead contamination (1200 mg kg^-1). Further, lead contamination decreased rapeseed and clover growth, physiology and yield at all levels of lead stress. But biofilm forming lead tolerant growth promoting bacteria application in lead contaminated soil enhanced rapeseed and clover growth, physiology, yield, antioxidant profile, proline and decreased malanodialdehyde content (which was decreased by different strains application under lead stress) of rapeseed and clover over no inoculation. Inoculation with all strains also increased the lead uptake in roots, shoots and decreased lead uptake in seeds of rapeseed and clover than plants in lead stress without inoculation.

Mycorrhizae and Rhizobacteria on Precambrian Rocky Gold Mine Tailings: I. Mine-Adapted Symbionts Promote White Spruce Health and Growth

White spruce [Picea glauca (Moench) Voss] is a commercially valuable boreal tree that has been known for its ability to colonize deglaciated rock tailings. Over the last decade, there has been an increasing interest in using this species for the revegetation and successful restoration of abandoned mine spoils. Herein, we conducted a glasshouse experiment to screen mycorrhizal fungi and rhizobacteria capable of improving the health and growth of white spruce seedlings growing directly on waste rocks (WRs) or fine tailings (FTs) from the Sigma-Lamaque gold mine located in the Canadian Abitibi region. After 32 weeks, measurements of health, growth, and mycorrhizal colonization variables of seedlings were performed. Overall, symbionts isolated from roots of healthy white spruce seedlings growing on the mining site, especially Cadophora finlandia Cad. fin. MBN0213 GenBank No. KC840625 and Pseudomonas putida MBN0213 GenBank No. AY391278, were more efficient in enhancing seedling health and growth than allochthonous species and constitute promising microbial symbionts. In general, mycorrhizae promoted plant health and belowground development, while rhizobacteria enhanced aboveground plant biomass. The observed beneficial effects were substrate-, strain-, and/or strains combination-specific. Therefore, preliminary experiments in control conditions such as the one described here can be part of an efficient and integrated strategy to select ecologically well-adapted symbiotic microorganisms, critical for the success of a long-term revegetation program.

Mycorrhizae and Rhizobacteria on Precambrian Rocky Gold Mine Tailings: II. Mine-Adapted Symbionts Alleviate Soil Element Imbalance for a Better Nutritional Status of White Spruce Seedlings

In the context of a phytorestoration project, the purpose of this study was to assess the respective contribution to the nutritional status of Picea glauca seedlings of ectomycorrhizae and rhizobacteria native or not to the Sigma-Lamaque gold mine wastes in northern Quebec, Canada. In a glasshouse experiment, inoculated plants were grown for 32 weeks on coarse waste rocks or fine tailings obtained from the mining site. The survival, health, growth, and nutritional status of plants were better on coarse waste rocks than on fine tailings. Fe and Ca were especially found at high levels in plant tissues but at much lower concentrations on waste rocks. Interestingly, inoculation of microsymbionts had only minimal effects on N, P, K, and Mg plant status that were indeed close or within the concentration range encountered in healthy seedlings. However, both fungal and bacterial treatments improved Fe and Ca concentrations in plant tissues. Fe concentration in the foliage of plants inoculated with the fungi Tricholoma scalpturatum Tri. scalp. MBN0213 GenBank #KC840613 and Cadophora finlandia Cad. fin. MBN0213 GenBank #KC840625 was reduced by >50%. Both fungi were isolated from the mining site. The rhizobacteria, Azotobacter chroococcum, also improved plant Fe level in some cases. Regarding Ca nutritional status, the native bacterial strain Pseudomonas putida MBN0213 GenBank #AY391278 was the only symbiont that reduced foliar content by up to 23%. Ca concentration was negatively correlated with the fungal mycorrhization rate of seedling roots. This relation was especially strong (r = -0.66, p-value ≤ 0.0001) in the case of C. finlandia. Also, a similar relationship existed with root Fe concentration (r = -0.44, p-value ≤ 0.0001). In fact, results showed that seedling performance was more correlated with elevated Ca and Fe concentration in planta than with nutrient deficiency. Also, native microsymbionts were capable of regulating seedling nutrition in the poor substrate of the Sigma-Lamaque gold mine tailings.

Distinct Communities of Poplar Endophytes on an Unpolluted and a Risk Element-Polluted Site and Their Plant Growth-Promoting Potential In Vitro

Numerous studies demonstrated that endophytic microbes can promote plant growth and increase plant stress resistance. We aimed at isolating poplar endophytes able to increase their hosts' fitness both in nutrient-limited and polluted environments. To achieve this goal, endophytic bacteria and fungi were isolated from roots and leaves of hybrid poplars (Populus nigra × P. maximowiczii clone Max-4) on an unpolluted and a risk element-polluted site in the Czech Republic and subsequently screened by a number of in vitro tests. Bacterial communities at the unpolluted site were dominated by Gammaproteobacteria with Pseudomonas sp. as the prominent member of the class, followed by Bacilli with prevailing Bacillus sp., whereas Alphaproteobacteria, mostly Rhizobium sp., prevailed at the polluted site. The fungal endophytic community was dominated by Ascomycetes and highly distinct on both sites. Dothideomycetes, mostly Cladosporium, prevailed at the non-polluted site while unclassified Sordariomycetous fungi dominated at the polluted site. Species diversity of endophytes was higher at the unpolluted site. Many tested endophytic strains solubilized phosphate and produced siderophores, phytohormones, and antioxidants. Some strains also exhibited ACC-deaminase activity. Selected bacteria showed high tolerance and the ability to accumulate risk elements, making them promising candidates for use in inocula promoting biomass production and phytoremediation. Graphical Abstract ᅟ.

Impact of lead tolerant plant growth promoting rhizobacteria on growth, physiology, antioxidant activities, yield and lead content in sunflower in lead contaminated soil

Present study was conducted to evaluate the effect of lead tolerant plant growth promoting rhizobacteria (LTPGPR) on growth, physiology, yield, antioxidant activities and lead uptake in sunflower in soil contaminated with lead under pot conditions. Three pre-characterized LTPGP strains (S2 (Pseudomonas gessardii strain BLP141), S5 (Pseudomonas fluorescens A506) and S10 (Pseudomonas fluorescens strain LMG 2189)) were used to inoculate sunflower growing in soil contaminated with different levels (300, 600 and 900 mg kg^-1) of lead by using lead nitrate salt as source of lead. Treatments were arranged according to completely randomized design with factorial arrangements. At harvesting, data regarding growth attributes (root shoot length, root shoot fresh and dry weights), yield per plant, physiological attributes (Chlorophyll 'a', 'b' and carotenoids content), antioxidant activities (Ascorbate peroxidase, catalase, superoxide dismutase and glutathione reductase), proline and malanodialdehyde content, and lead content in root, shoot and achenes of sunflower were recorded. Data were analysed by standard statistical procedures. Results showed that lead contamination reduced the plants growth, physiology and yield at all levels of lead stress. But application of LTPGPR in soil contaminated with lead improved plant growth, physiology, yield, and antioxidant activities, proline, and reduced the malanodialdehyde content (that is reduced by the application of different strains in lead contamination) of sunflower as compared to plants grown in soil without inoculation. Inoculation also promoted the uptake of lead in root, shoots and reduced the uptake of lead in achenes of plants as compared to plants in lead contamination without inoculation.

Insight into litter decomposition driven by nutrient demands of symbiosis system through the hypha bridge of arbuscular mycorrhizal fungi

Arbuscular mycorrhizal fungi (AMF) play an important role in litter decomposition. This study investigated how soil nutrient level affected the process. Results showed that AMF colonization had no significant effect on litter decomposition under normal soil nutrient conditions. However, litter decomposition was accelerated significantly under lower nutrient conditions. Soil microbial biomass in decomposition system was significantly increased. Especially, in moderate lower nutrient treatment (condition of half-normal soil nutrient), litters exhibited the highest decomposition rate, AMF hypha revealed the greatest density, and enzymes (especially nitrate reductase) showed the highest activities as well. Meanwhile, the immobilization of nitrogen (N) in the decomposing litter remarkably decreased. Our results suggested that the roles AMF played in ecosystem were largely affected by soil nutrient levels. At normal soil nutrient level, AMF exhibited limited effects in promoting decomposition. When soil nutrient level decreased, the promoting effect of AMF on litter decomposition began to appear, especially on N mobilization. However, under extremely low nutrient conditions, AMF showed less influence on decomposition and may even compete with decomposer microorganisms for nutrients.

Biodegradation of the cross-linked copolymer of acrylamide and potassium acrylate by soil bacteria

Chemical cross-linking and the high molecular weight of superabsorbent copolymers (SAPs) are the two main causes of their resistance to biodegradation. However, SAP particles are colonized by microorganisms. For the purposes of this study, the dry technical copolymer of acrylamide and potassium acrylate containing 5.28 % of unpolymerized monomers was wrapped in a geotextile and incubated in unsterile Haplic Luvisol soil as a water absorbing geocomposite. The highest number of soil bacteria that colonized the hydrated SAP and utilized it as the sole carbon and energy source was found after the first month of incubation in soil. It was equal to 7.21-7.49 log10 cfu g(-1) of water absorbed by the SAP and decreased by 1.35-1.61 log10 units within the next 8 months. During this time, the initial SAP water holding capacity of 1665.8 g has decreased by 24.40 %. Moreover, the 5 g of SAP dry mass has declined by 31.70 %. Two bacteria, Rhizobium radiobacter 28SG and Bacillus aryabhattai 31SG isolated from the watered SAP were found to be able to biodegrade this SAP in pure cultures. They destroyed 25.07 and 41.85 mg of 300 mg of the technical SAP during the 60-day growth in mineral Burk's salt medium, and biodegradation activity was equal to 2.95 and 6.72 μg of SAP μg(-1) of protein, respectively. B. aryabhattai 31SG and R. radiobacter 28SG were also able to degrade 9.99 and 29.70 mg of 82 mg of the ultra-pure SAP in synthetic root exudate medium during the 30-day growth, respectively.

Biochar Treatment Resulted in a Combined Effect on Soybean Growth Promotion and a Shift in Plant Growth Promoting Rhizobacteria

The application of biochar to soil is considered to have the potential for long-term soil carbon sequestration, as well as for improving plant growth and suppressing soil pathogens. In our study we evaluated the effect of biochar on the plant growth of soybeans, as well as on the community composition of root-associated bacteria with plant growth promoting traits. Two types of biochar, namely, maize biochar (MBC), wood biochar (WBC), and hydrochar (HTC) were used for pot experiments to monitor plant growth. Soybean plants grown in soil amended with HTC char (2%) showed the best performance and were collected for isolation and further characterization of root-associated bacteria for multiple plant growth promoting traits. Only HTC char amendment resulted in a statistically significant increase in the root and shoot dry weight of soybeans. Interestingly, rhizosphere isolates from HTC char amended soil showed higher diversity than the rhizosphere isolates from the control soil. In addition, a higher proportion of isolates from HTC char amended soil compared with control soil was found to express plant growth promoting properties and showed antagonistic activity against one or more phytopathogenic fungi. Our study provided evidence that improved plant growth by biochar incorporation into soil results from the combination of a direct effect that is dependent on the type of char and a microbiome shift in root-associated beneficial bacteria.

The response of maize (Zea mays L.) plant assisted with bacterial consortium and fertilizer under oily sludge

The objective of this study was to evaluate the role of PGPR consortium and fertilizer alone and in combination on the physiology of maize grown under oily sludge stress environment as well on the soil nutrient status. Consortium was prepared from Bacillus cereus (Acc KR232400), Bacillus altitudinis (Acc KF859970), Comamonas (Delftia) belonging to family Comamonadacea (Acc KF859971) and Stenotrophomonasmaltophilia (Acc KF859973). The experiment was conducted in pots with complete randomized design with four replicates and kept in field. Oily sludge was mixed in ml and Ammonium nitrate and Diammonium phosphate (DAP) were added at 70 ug/g and 7 ug/g at sowing. The plant was harvested at 21 d for estimation of protein, proline and antioxidant enzymes superoxide dismutase (SOD) and peroxidase (POD). To study the degradation, total petroleum hydrocarbon was extracted by soxhelt extraction and extract was analyzed by GC-FID at different period after incubation. Combined application of consortium and fertilizer enhanced the germination %, protein and, proline content by 90,130 and 99% higher than untreated maize plants. Bioavailability of macro and micro nutrient was also enhanced with consortium and fertilizer in oily sludge. The consortium and fertilizer in combined treatment decreased the superoxide dismutase (SOD), peroxidase dismutase (POD) of the maize leaves grown in oily sludge. Degradation of total petroleum hydrocarbon (TPHs) was 59% higher in combined application of consortium and fertilizer than untreated maize at 3 d. The bacterial consortium can enhanced the maize tolerance to oily sludge and enhanced degradation of total petroleum hydrocarbon (TPHs). The maize can be considered as tolerant plant species to remediate oily sludge contaminated soils.

Piriformospora indica-a mutualistic basidiomycete with an exceptionally large plant host range

Piriformospora indica is a basidiomycete of the order Sebacinales, representing a model for the study of mutualistic symbiosis and, beyond that, the plant immune system. The fungus colonizes the roots of a wide range of vascular plants, increasing their growth, seed yield and adaptation to abiotic and biotic stresses. The fungal colonization of roots begins with a biotrophic growth phase, in which living cells are colonized, and continues with a cell death-dependent phase, in which root cells are actively killed by the fungus. The complexity of sebacinalean symbiosis is further enhanced by the presence of endocellular bacteria which may represent significant determinants for a successful outcome of the symbioses. Molecular ecological analyses have revealed an exceptional relevance of sebacinoid fungi in natural ecosystems worldwide. This natural competence could be rooted in their phenotypic adaptability, which, for instance, allows P. indica to grow readily on various synthetic media and to colonize distinct hosts. In molecular and genetic studies, P. indica's mutualistic colonization strategy has been partly unravelled, showing that the jasmonate pathway is exploited for immune suppression and successful development in roots. Research on P. indica supports efforts to make the bioprotective potential of the fungus accessible for agricultural plant production. The decoding of P. indica's genome has revealed its potential for application as bioagent and for targeted improvement of crop plants in biotechnology-based approaches.

Nodulation of Sesbania species by Rhizobium (Agrobacterium) strain IRBG74 and other rhizobia

Concatenated sequence analysis with 16S rRNA, rpoB and fusA genes identified a bacterial strain (IRBG74) isolated from root nodules of the aquatic legume Sesbania cannabina as a close relative of the plant pathogen Rhizobium radiobacter (syn. Agrobacterium tumefaciens). However, DNA:DNA hybridization with R. radiobacter, R. rubi, R. vitis and R. huautlense gave only 44%, 5%, 8% and 8% similarity respectively, suggesting that IRBG74 is potentially a new species. Additionally, it contained no vir genes and lacked tumour‐forming ability, but harboured a sym‐plasmid containing nifH and nodA genes similar to those in other Sesbania symbionts. Indeed, IRBG74 effectively nodulated S. cannabina and seven other Sesbania spp. that nodulate with Ensifer (Sinorhizobium)/Rhizobium strains with similar nodA genes to IRBG74, but not species that nodulate with Azorhizobium or Mesorhizobium. Light and electron microscopy revealed that IRBG74 infected Sesbania spp. via lateral root junctions under flooded conditions, but via root hairs under non‐flooded conditions. Thus, IRBG74 is the first confirmed legume‐nodulating symbiont from the Rhizobium (Agrobacterium) clade. Cross‐inoculation studies with various Sesbania symbionts showed that S. cannabina could form fully effective symbioses with strains in the genera Rhizobium and Ensifer, only ineffective ones with Azorhizobium strains, and either partially effective (Mesorhizobium huakii) or ineffective (Mesorhizobium plurifarium) symbioses with Mesorhizobium. These data are discussed in terms of the molecular phylogeny of Sesbania and its symbionts.

Detection and identification of bacteria intimately associated with fungi of the order Sebacinales

Because of their beneficial impact on plants, the highly diverse mycorrhizal fungi grouped in the order Sebacinales lay claim to high ecological and agricultural significance. Here, we describe for the first time associations of Sebacinoid members with bacteria. Using quantitative PCR, denaturating gradient gel electrophoresis and fluorescence in situ hybridization, we detected an intimate association between Piriformospora indica and Rhizobium radiobacter, an alpha-Proteobacterium. The stability of the association, vertical transmission of the bacteria during asexual fungal reproduction and fungal plant colonization was monitored using R. radiobacter-specific primers. Treatment of mycelium or fungal protoplasts with antibiotics highly efficient against the free bacteria failed to cure the fungus. Barley seedlings dip-inoculated with R. radiobacter showed growth promotion and systemic resistance to the powdery mildew fungus Blumeria graminis comparable to P. indica inoculation. By screening additional isolates of the Sebacina vermifera complex, three species-specific associations with bacteria from the genera Paenibacillus, Acinetobacter and Rhodococcus were found. These findings suggest that Sebacinales species regularly undergo complex interactions involving host plants and bacteria reminiscent of other ectomycorrhizal and endomycorrhizal associations.