Bacteria with ACC deaminase can promote plant growth and help to feed the world

The root exudate composition reflects the contradictory-concomitantly attractive and repulsive-behaviour of plants towards soil microorganisms. Plants produce antimicrobial, insecticide and nematicide compounds to repel pathogens and invaders. They also produce border cells that detach from roots and play an important role as biological and physical barrier against aggressors. Plants produce also metabolites used as carbon source resulting in the attraction of phytobeneficial soil microorganisms that help plants in controlling diseases directly via the production of antimicrobial compounds or indirectly via the induction of plant systemic resistance. The root exudates may have a direct impact on carbon and nitrogen cycling, as they exhibit a rhizosphere priming effect towards soil organic matter degraders, and may inhibit nitrification process by soil nitrifying microorganisms. They also contain signalling molecules required for the establishment of ‘plant-microorganisms’ interactions. The composition of root exudates is therefore broad ranging, consisting of feeding, antimicrobial and signalling molecules. We thus focused this review on current research concerning the role of the root exudate composition in ‘plant-microorganisms’ interactions and functioning of the rhizosphere.

Root exudates mediated interactions belowground

Nitrogen (N) is the main mineral element in plant tissues and almost all of this nutrient is acquired from the soil by the roots. Nitrogen is available in many different forms in the soil, but the three most abundant forms are nitrate, ammonium and amino acids. The relative importance of these different soil N pools to a plant is difficult to measure and depends on many different environmental factors. Changes in the available amounts and imbalance in the supply of some N forms can even be toxic to plants and in extreme cases can lead to changes in the vegetation. However, the importance of this element for agriculture is reflected in the amounts of N-fertiliser applied to crops and this is a major cost (economic and environmental) for world agriculture. This review covers the molecular mechanisms that the plant uses for accessing these soil N pools and briefly includes consideration of the root N assimilatory pathways that exist in the plant. The soil forms of N that are used by plants depend on many factors, but a series of different transporter and assimilatory genes that can provide access to these pools have been identified. This information can now provide the molecular tools to identify the N sources accessed by a plant and the relative importance of these different pools.

Root Nitrogen Acquisition and Assimilation

The concentration of carbon dioxide in Earth's atmosphere may double by the end of the 21st century. The response of higher plants to a carbon dioxide doubling often includes a decline in their nitrogen status, but the reasons for this decline have been uncertain. We used five independent methods with wheat and Arabidopsis to show that atmospheric carbon dioxide enrichment inhibited the assimilation of nitrate into organic nitrogen compounds. This inhibition may be largely responsible for carbon dioxide acclimation, the decrease in photosynthesis and growth of plants conducting C(3) carbon fixation after long exposures (days to years) to carbon dioxide enrichment. These results suggest that the relative availability of soil ammonium and nitrate to most plants will become increasingly important in determining their productivity as well as their quality as food.

https://science.sciencemag.org/content/sci/328/5980/899.full.pdf

Carbon Dioxide Enrichment Inhibits Nitrate Assimilation in Wheat and Arabidopsis

Faba bean in cropping systems

In many legumes, the nitrogen fixing root nodules produce H2 gas that diffuses into soil. It has been demonstrated that such exposure of soil to H2 can promote plant growth. To assess whether this may be due to H2-oxidizing microorganisms, bacteria were isolated from soil treated with H2 under laboratory conditions and from soils collected adjacent to H2 producing soybean nodules. Nineteen isolates of H2-oxidizing bacteria were obtained and all exhibited a half-saturation coefficient (Ks) for H2 of about 1 ml l(-1). The isolates were identified as Variovorax paradoxus, Flavobacterium johnsoniae and Burkholderia spp. using conventional microbiological tests and 16S rRNA gene sequence analysis. Seventeen of the isolates enhanced (57-254%) root elongation of spring wheat seedlings. Using an Arabidopsis thaliana bioassay, plant biomass was increased by 11-27% when inoculated by one of four isolates of V. paradoxus or one isolate of Burkholderia that were selected for evaluation. The isolates of V. paradoxus found in both H2-treated soil and in soil adjacent to soybean nodules had the greatest impact on plant growth. The results are consistent with the hypothesis that H2-oxidizing bacteria in soils have plant growth promoting properties.

Isolation and characterization of hydrogen-oxidizing bacteria induced following exposure of soil to hydrogen gas and their impact on plant growth

Simultaneous measurements of CO 2 (CER) and O 2 (OER) exchange in roots and shoots of vegetative white lupin ( Lupinus albus ) were used to calculate the flow of reducing power to the synthesis of biomass that was more reduced per unit of carbon than carbohydrate. On a whole-plant basis, the diverted reductant utilization rate (DRUR which is: 4 × [CER + OER]) of shoot tissue was consistently higher than that of roots, and values obtained in the light were greater than those in the dark. An analysis of the biomass being synthesized over a 24-h period provided an estimate of whole-plant DRUR (3.5 mmol e − plant −1 d −1 ), which was similar to that measured by gas exchange (3.2 mmol e − plant −1 d −1 ). Given that nitrate reduction to ammonia makes up about 74% of whole-plant DRUR, root nitrate reduction in white lupin was estimated to account for less than 43% of whole-plant nitrate reduction. The approach developed here should offer a powerful tool for the noninvasive study of metabolic regulation in intact plants or plant organs.

/pdf/whole-plant-gas-exchange-and-reductive-biosynthesis-in-white-23ctlbdnwt.pdf

Whole-plant gas exchange and reductive biosynthesis in white lupin.

A gas analysis system was built to study the relationship between the reductant cost of NO(3)(-) assimilation and the measured rate of CO(2) and O(2) exchange in roots, leaves, and stems+ petioles of soybean (Glycine max L. Merr. cv Maple glen) plants. The measurements were used to calculate the diverted reductant utilization rate (DRUR = 4*[measured rate of CO(2) + measured rate of O(2)], in moles of high-energy electron [e(-)] per gram per hour) in plants in the presence (N+) and absence (N-) of NO(3)(-). The differences in DRUR between the N+ and N- treatments provided a measure of the NO(3)(-)-coupled DRUR of 25-d-old plants, whereas a (15)NO(3)(-)-enriched nutrient solution was used to obtain an independent measure of the rate of NO(3)(-) assimilation. The measured reductant cost for the whole plant was 9.6 e(-) per N assimilated, a value within the theoretical range of four to 10 e(-) per N assimilated. The results predicted that shoots accounted for about 55% of the whole-plant NO(3)(-) assimilation over the entire day, with shoots dominating in the light, and roots in the dark. The gas analysis approach described here holds promise as a powerful, noninvasive tool to study the regulation of NO(3)(-) assimilation in plant tissue.

In Vivo Gas Exchange Measurement of the Site and Dynamics of Nitrate Reduction in Soybean

Air temperature freeze–thaw cycles often occur during the early spring period directly after snowmelt and before budbreak in low arctic tundra. This early spring period may be associated with nitrogen (N) and carbon (C) loss from soils as leachate or as trace gases, due to the detrimental impact of soil freeze–thaw cycles and a developing active layer on soil microorganisms. We measured soil and microbial pools of C and N in early spring during a period of fluctuating air temperature (ranging from −4 to +10°C) and in midsummer, in low arctic birch hummock tundra. In addition we measured N2O, CH4 and CO2 production in the early spring. All of these biogeochemical variables were also measured in long-term snowfence (deepened snow) and N-addition plots to characterize climate-change related controls on these variables. Microbial and soil solution pools of C and N, and trace gas production varied among the five early spring sample dates, but only marginally and no more than among sample dates in midsummer. N-addition greatly elevated N2O fluxes, indicating that although denitrifiers were present their activity during early spring was strongly limited by N-availability, but otherwise trace gas production was very low in early spring. The later thaw, warmer winter and colder spring soil temperatures resulting from deepened snow did not significantly alter N pools or rates in early spring. Together, our results indicate strong stability in microbial and soil solution C and N pool sizes in the early spring period just after snowmelt when soil temperatures are close to 0°C (−1.5 to +5°C). A review of annual temperature records from this and other sites suggests that soil freeze–thaw cycles are probably infrequent in mesic tundra in early spring. We suggest that future studies concerned with temperature controls on soil and microbial biogeochemistry should focus not on soil freeze–thaw cycles per se, but on the rapid and often stepped increases in soil temperature that occur under the thawing snowpack.

Soil biogeochemistry during the early spring in low arctic mesic tundra and the impacts of deepened snow and enhanced nitrogen availability

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Isolation and characterization of hydrogen-oxidizing bacteria induced following exposure of soil to hydrogen gas and their impact on plant growth

Whole-plant gas exchange and reductive biosynthesis in white lupin.

In Vivo Gas Exchange Measurement of the Site and Dynamics of Nitrate Reduction in Soybean

Soil biogeochemistry during the early spring in low arctic mesic tundra and the impacts of deepened snow and enhanced nitrogen availability