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Nitrogen (N) is one of the essential elements for life on Earth and is mainly distributed in an inert form in the atmosphere, so it cannot be used by plants. Therefore, the N found in the atmosphere must undergo several transformations to be fixed in the soil and then used by plants. With the presence of N in several organic molecules, the acquisition of this element by plants has an impact on the growth and development of several agricultural crops. Understanding the metabolic mechanisms related to N and the methods of uptake, transport and use of this nutrient by plants have always been a topic of interest in several types of research. N also influences the soil microbiota, because microorganisms participate in the N cycle, especially in relation to the process of biological application of N. Thus, with the discovery of N-fixing microorganisms, it was possible to explore the impact that the microbiota would have on the plant’s N metabolism. In this context, we have gathered in this chapter, information about the ecophysiology of N in plants and how some fungi and bacteria are able to influence the metabolism of this element. We also explain a little how the association between plants and endophytic bacteria occurs, since this symbiotic relationship is very important to make N available to the plants.

Main conclusion: Higher vacuolar proton pump activity may increase plant energy and nutrient use efficiency and provide the nexus between plant inoculation with Herbaspirillum seropedicae and growth promotion. Abstract: Global change and growing human population are exhausting arable land and resources, including water and fertilizers. We present inoculation with the endophytic plant-growth promoting bacterium (PGPB) Herbaspirillum seropedicae as a strategy for promoting growth, nutrient uptake and photosynthetic efficiency in rice (Oryza sativa L.). Because plant nutrient acquisition is coordinated with photosynthesis and the plant carbon status, we hypothesize that inoculation with H. seropedicae will stimulate proton (H+) pumps, increasing plant growth nutrient uptake and photosynthetic efficiency at low nutrient levels. Plants were inoculated and grown in pots with sterile soil for 90 days. Herbaspirillum seropedicae endophytic colonization was successful and, as hypothesized, inoculation (1) stimulated root vacuolar H+ pumps (vacuolar H+-ATPase and vacuolar H+-PPase), and (2) increased plant growth, nutrient contents and photosynthetic efficiency. The results showed that inoculation with the endophytic bacterium H. seropedicae can promote plant growth, nutrient uptake and photosynthetic efficiency, which will likely result in a more efficient use of resources (nutrients and water) and higher production of nutrient-rich food at reduced economic and environmental costs.

Serendipita indica (former Piriformospora indica) is a non-obligate endophytic fungus and generally a plant growth and defence promoter with high potential to be used in agriculture. However, S. indica may switch from biotrophy to saprotrophy losing its plant growth promoting traits. Our aim was to understand if the free-living stage growth conditions (namely C availability) regulate S. indica’s phenotype, and its potential as plant-growth-promoting-microbe (PGPM). We grew S. indica in its free-living stage under increasing C availabilities (2–20 g L–1 of glucose or sucrose). We first characterised the effect of C availability during free-living stage growth on fungal phenotype: colonies growth and physiology (plasma membrane proton pumps, stable isotopic signatures, and potential extracellular decomposing enzymes). The effect of the C availability during the free-living stage of the PGPM was evaluated on wheat. We observed that C availability during the free-living stage regulated S. indica’s growth, ultrastructure and physiology, resulting in two distinct colony phenotypes: compact and explorer. The compact phenotype developed at low C, used peptone as the major C and N source, and displayed higher decomposing potential for C providing substrates; while the explorer phenotype developed at high C, used glucose and sucrose as major C sources and casein and yeast extract as major N sources, and displayed higher decomposing potential for N and P providing substrates. The C availability, or the C/N ratio, during the free-living stage left a legacy to the symbiosis stage, regulating S. indica’s potential to promote plant growth: wheat growth promotion by the explorer phenotype was ± 40% higher than that by the compact phenotype. Our study highlights the importance of considering microbial ecology in designing PGPM/biofertilizers. Further studies are needed to test the phenotypes under more extreme conditions, and to understand if the in vitro acquired characteristics persist under field conditions.

Achieving food security in a context of environmental sustainability is one of the main challenges of the XXI century. Two competing strategies to achieve this goal are the use of genetically modified plants and the use of plant growth promoting microorganisms (PGPMs). However, few studies assess the response of genetically modified plants to PGPMs. The aim of this study was to compare the response of over-expressing the vacuolar H+-PPase (AVP) and wild-type rice types to the endophytic fungus; Piriformospora indica. Oryza sativa plants (WT and AVP) were inoculated with P. indica and 30 days later, morphological, ecophysiological and bioenergetic parameters, and nutrient content were assessed. AVP and WT plant heights were strongly influenced by inoculation with P. indica, which also promoted increases in fresh and dry matter of shoot in both genotypes. This may be related with the stimulatory effect of P. indica on ecophysiological parameters, especially photosynthetic rate, stomatal conductance, intrinsic water use efficiency and carboxylation efficiency. However, there were differences between the genotypes concerning the physiological mechanisms leading to biomass increment. In WT plants, inoculation with P. indica stimulated all H+ pumps. However, in inoculated AVP plants, H+-PPase was stimulated, but P- and V-ATPases were inhibited. Fungal inoculation enhanced nutrient uptake in both shoots and roots of WT and AVP plants, compared to uninoculated plants; but among inoculated genotypes, the nutrient uptake was lower in AVP than in WT plants. These results clearly demonstrate that the symbiosis between P. indica and AVP plants did not benefit those plants, which may be related to the inefficient colonization of this fungus on the transgenic plants, demonstrating an incompatibility of this symbiosis, which needs to be further studied.

Soils with low fertility due to low availability of nutrients limit agricultural productivity, once crops will not possess the ideal conditions for development. Plants depend on their root systems to acquire the water and nutrients necessary for their survival in nature and for their yield and nutritional quality in agriculture. Thus, the use of plant growth-promoting microorganisms that form symbiosis with plant roots is an essential strategy to promote more efficient use of mineral resources in agriculture. Mycorrhizae are symbiotic associations between soil fungi and roots of vascular plants, which provide several benefits to the plant, like absorption and translocation of nutrients, mainly nitrogen and phosphate. The benefits of mycorrhizal symbiosis depend on the interaction between plant fungus and the environmental characteristics, such as availability of phosphorus and carbon supply to the symbiont. Mycorrhizal fungi can also protect plants from several biotic and abiotic stresses such as heavy metal contamination, salt and water stress, and pathogens, and they can influence soil properties like increase soil aggregation and stability. But, to assure the efficiency of these benefits, an adequate management of native fungi is necessary, which can be assured through the adoption of conservation practices related to soil preparation and management and which has been associated to the increased diversity of native mycorrhizal fungi. In these conditions, mycorrhizal fungi can represent an important technology to make agricultural production sustainable, both ecologically and economically, decreasing the costs with mineral fertilizers, irrigation, and pesticides.

Several pollutants interfere with plant metabolism and heavy metals (HMs) are one of the most common. The HM toxicity can cause plant growth retardation, inhibition of photosynthesis, induction and inhibition of enzymes, DNA damage, and the generation of oxidative stress. To avoid toxicity from HMs, plants developed a range of different response mechanisms acting in additive and/or synergistic ways. The plant protection against metal toxicity occurs through control of root uptake of metal and metal transport within the plant. Proteins such as ferritin, metallothioneins, and glutathione-derived peptides (phytochelatins) and organic molecules such as organic acids and phytate play an important role in plant storage and detoxification process in metal homeostasis; when these systems are overloaded, oxidative stress defense mechanisms are activated. Understanding the functioning of these mechanisms in climate change is of utmost importance to understanding the process of adaptation of plants to environmental changes and their use in bioremediation process. This chapter chapter briefly summarizes some recent aspects of biological, molecular, and proteomic mechanisms concerning the responses of plants to HMs.

Crop management systems influence plant productivity and nutrient use efficiency, as well as plant growth-promoting rhizobacteria (PGPR), which are known to influence the growth of plants via phytohormone production, phosphate solubilization, nitrogen (N) fixation and antimicrobial activity. The objective of this study was to compare the influence of two crop management system on microbial PGPR features. PGPR isolated from the rhizospheres of Carica papaya L. grown under two distinct management systems (conventional and organic) were identified and characterized. The 12 strains most efficient in solubilizing inorganic phosphate belonged to the genera Burkholderia, Klebsiella, and Leclercia. N fixation was observed in the strains B. vietnamiensis from the conventional farming system and B. vietnamiensis, B. cepacia and Leclercia sp. from the organic farming system. The B. vietnamiensis, B. cepacia, Klebsiella sp. and Klebsiella sp. isolates showed antifungal activity, while Leclercia sp. did not. The strains B. vietnamiensis and Enterobcter sp. (isolated from the conventional farming system) and Klebsiella sp. (isolated from the organic farming system) were efficient at solubilizing phosphate, producing phytohormones and siderophores, and inhibiting the mycelial growth of various phytopathogenic fungi (Botrytis cinerea, Pestalotia sp., Alternaria sp., Phoma sp., Fusarium culmorum, Geotrichum candidum). Physiological differences between the isolates from the two crop management regimes were distinguishable after 10 years of distinct management.