Nitrogen (N) is a central nutrient in cropping systems. However, a considerable N fraction is lost through runoffs and leaching with detrimental consequences for environment and controversial effects on human health. Increasing the plant N uptake by optimizing the degree of root branching for exploring a larger soil volume in search of the mobile nitrate resource may contribute to limit soil leaching and subsequently to rely more efficiently on the soil mineralization and fertilizer inputs. Rapeseed (Brassica napus L.) is a major oil crop that highly depends on N fertilization. This doctoral thesis aims at exploring the diversity of root morphology in recently selected cultivars and in a large set of rapeseed inbred lines, and at understanding the genetic control on root morphology and how it is impacted by N nutrition.Firstly, a panel of twenty-eight European recently selected cultivars of winter oilseed rape were tested in laboratory and field conditions. Upon hydroponic culture, these hybrids showed a great diversity for biomass production and root morphological traits. Differences in root and shoot dry biomasses and lateral root length were mainly explained by the genotype, while differences in primary root length by the nutrition. The cultivars were tested in a pluriannual field trial. The observed variation for yield and seed quality traits attributed to the genotype was more important than the year or the genotype x year interaction effects. The total root length measured in laboratory could predict the proportion of nitrogen taken-up from the field and reallocated to the seeds. The genetic interrelationship between cultivars, established with polymorphic markers, indicated a very narrow genetic base. Positive correlations were found between the genetic distance measures, root morphological trait distances during nitrogen depletion conditions, and agronomic performance. Secondly, three cultivars previously selected from a root morphology screen at a young developmental stage were field tested with two nitrogen applications. The purpose was to examine the relationship between root morphology and Nitrogen Uptake Efficiency (NUpE) and to test the predictiveness of canopy optical indices for seed quality and yield. A tube-rhizotron system was used to incorporate below-ground root growth information. One-meter length clear tubes were installed in soil at an angle of 45°. The root development was followed with a camera at key growth stages in autumn (leaf development) and spring (stem elongation and flowering). Autumn was a critical time window to observe the root development and exploration in deeper horizons (36-48 cm) was faster without any fertilization treatment. Analysis of the rhizotron images was challenging and it was not possible to clearly discriminate between cultivars. Canopy reflectance and leaf optical indices were measured with proximal sensors. The Normalized Difference Vegetation Index (NDVI) was a positive indicator of biomass and seed yield while the Nitrogen Balance Index (NBI) was a positive indicator of above-ground biomass N concentration at flowering and seed N concentration at harvest.Thirdly, the natural variability offered by a diversity set of 392 inbred lines was screened to apprehend the genetic control of root morphology in rapeseed and how it is impacted by nitrogen nutrition. Seedlings grew hydroponically with low (0.2 mM) or elevated (5 mM) nitrate supplies. Low nitrate supply triggered the primary root and lateral root growth, while elevated supply promoted shoot biomass production. A considerable variation degree in the root morphological traits was observed across the diversity set, and there was no trade-off between abundant lateral root branching and shoot biomass production. Root traits were mainly dependent on the genotype and highly heritable. A genome wide association study identified some genomic regions associated with biomass production and root morphological traits. A total of fifty-nine QTLs were identified and thirty of them were integrated into seven clusters on chromosomes A01 and C07. Some candidate genes were identified with Arabidopsis orthologs related to root growth and development, nitrogen nutrition or hormone regulation.This study provides promising routes for redesigning the root system architecture by uncovering nitrogen-interactive genomic regions shaping root morphology. A perspective is to develop genetic markers associated with root morphological traits that could be used for assisted breeding. / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

Excess nitrogen (N) from terrestrial landscapes poses environmental challenges as it moves via surface runoff and groundwater flows into aquatic ecosystems. Managing and anticipating the environmental challenges associated with these altered N inputs from terrestrial to aquatic ecosystems requires a deep understanding of how N is biogeochemically transformed, retained, and/or transported in streams and rivers. Here, I used long-term data on surface stream and groundwater chemistry as well as discharge to determine the main sources of N and estimate the N mass balance of a 1.4 km boreal stream reach. The goal was to evaluate daily net uptake or production rates of different N forms (ammonium - NH4-N, nitrate NO3-N and dissolved organic N - DON) throughout the seasons, and assess physical and chemical factors that may drive changes in net processing. The mass balances analysis revealed distinct patterns in net uptake among N forms. Notably, there was clear evidence of NH4-N and DON uptake (removal) in the stream, while NO3-N processing patterns showed neither clear uptake nor production. Further, variation in net uptake for NH4-N and DON was positively related to stream DOC, DOC:DIN, and C:N ratios, indicating that carbon rich conditions promoted greater N demand in this ecosystem. By comparison, variations in net NO3-N uptake or production at the reach scale were only weakly correlated with these carbon rich conditions. Finally, I assessed these patterns within the nutrient processing domains (NPDs) framework to characterize the behavior/character of the study reach. Accordingly, during the open water season, the stream reach acted mostly as a consumer for both NH4-N and DON, while on many dates it acted as a weak enhancer for NO3-N. These findings contribute to the broader understanding of N dynamics in boreal stream ecosystems and emphasize the complex interplay among organic and inorganic N forms, carbon dynamics, and nutrient processing in these environments. This knowledge is crucial for effective environmental management and conservation efforts in the region.

Mit zunehmender Meereshöhe werden die Wachstumsbedingungen in tropischen Bergregionen im Allgemeinen ungünstiger, was sich in einer sinkenden Nährstoffverfügbarkeit, sinkenden Temperaturen und sinkendem CO2-Partialdruck zeigt. In tropischen Bergregenwäldern führen verminderte Abbauraten in größeren Höhen einerseits zu dicken organische Auflageschichten und andererseits in Kombination mit verminderten Mineralisierungs- und Nitrifizierungsraten zu Veränderungen in der Verfügbarkeit der verschiedenen Stickstoffformen, und es gibt Nachweise einer Limitierung der Produktivität dieser Wälder durch Stickstoff. Auf welche Weise sich die Photosynthesekapazität (Amax) tropischer Bäume einerseits und die Stickstoffaufnahmekapazität und Präferenz für einzelne Stickstoffformen andererseits an die veränderten Umweltbedingungen entlang von Höhengradienten adaptieren ist nicht genau bekannt. Die vorliegende Untersuchung wurde in drei tropischen Bergregenwäldern durchgeführt, die entlang eines Höhengradienten auf 1000, 2000 und 3000 m ü. NN in Südequador liegen. Das Ziel war es, (1) die Photosynthesekapazität ausgewachsener tropischer Bäume entlang eines Höhengradienten mit Hilfe von Gaswechselmessungen zu bestimmen und die Effekte von Temperatur, CO2-Partialdruck und Nährstoffverfügbarkeit auf die Photosynthese zu quantifizieren und (2) Veränderungen in der Verwendung von Nitrat, Ammonium und organischen Stickstoffquellen durch tropische Waldbäume mit der Meereshöhe mittels einer Tracer-Untersuchung mit stabilen Isotopen an Jungpflanzen zu untersuchen. Mittelwerte der lichtgesättigten Photosyntheserate (Asat) auf Bestandeseben betrugen 8.8, 11.3 und 7.2 µmol CO2 m-2 s-1, die der Dunkelatmung (RD) 0.8, 0.6 und 0.7 µmol CO2 m-2 s-1 jeweils auf 1000, 2000 and 3000 m Meereshöhe, ohne einen signifikanten Höhentrend. Die Einordnung unserer Daten in den Kontext eines pantropischen Asat-Datensatzes von tropischen Bäumen (c. 170 Arten an 18 Standorten unterschiedlicher Meereshöhe) zeigte, dass das flächenbezogene Asat in tropischen Bergen im Mittel 1.3 µmol CO2 m-2 s-1 pro km Höhenzunahme abnimmt (bzw. 0.2 µmol CO2 m-2 s-1 pro K Temperaturabnahme). Die Abnahme von Asat trat auf, obwohl die Blattmasse je Fläche mit der Höhe zunahm. Eine verminderte Photosyntheserate und eine reduzierte Bestandesblattfläche bewirken gemeinsam eine Verringerung der Kohlenstoffaufnahme des Kronenraums mit der Meereshöhe in tropischen Bergregionen. Der Phosphorgehalt pro Blattmasse war der Faktor, der Amax entlang des Höhengradienten hauptsächlich beeinflusste, während die Effekte von Blattstickstoff, Temperatur und CO2-Partialdruck nicht signifikant waren. Amax erfuhr einen teilweisen und RD einen vollständigen homöostatischen Ausgleich als Reaktion auf die Verminderung von Temperatur und CO2-Partialdruck in größeren Höhen, was hauptsächlich durch eine stark reduzierte spezifische Blattfläche (SLA) und die daraus entstehende Zunahme von Blattstickstoff und -phosphor je Blattfläche bedingt war, während keine Zunahme der Karboxylierungseffizienz festgestellt wurde. Wir schlussfolgern, dass die Verminderung von SLA und Gesamtblattfläche mit der Meereshöhe die Kohlenstoffaufnahme von tropischen Wäldern in großen Meereshöhen deutlich stärker bestimmen als adaptive physiologische Modifizierungen des Photsyntheseapparates. Jungpflanzen von sechs Baumarten unterschieden sich hinsichtlich ihrer Präferenz für verschieden Stickstoffformen, allerdings schienen weder das Amonium- und Nitratvorkommen im Boden noch die Meereshöhe die Präferenz zu beeinflussen. Zwei Arten (jeweils die, mit den höchsten Wachstumsraten) bevorzugten Amonium gegenüber Nitrat, während die restlichen vier Arten Nitrat und Amonium mit ähnlichen Raten aufnahmen, wenn beide Stickstofformen verfügbar waren. Nach der Gabe von 15N13C-Glyzin zeigte sich bei drei Arten eine signifikante Akkumulierung von 13C in der Biomasse (zwei Arten mit arbuskulären Mykorrhiza und eine Art mit Ektomykorrhiza) zusätzlich zu einer signifikanten Akkumulierung von 15N, was darauf hindeutet, dass Bäume in tropischen Bergregenwäldern organische Stickstoffverbindungen unabhängig vom Typ ihrer Mykorrhizierung aufnehmen können.

Σκοπός της παρούσας διδακτορικής διατριβής ήταν η μελέτη της δυναμικής του αζώτου σε καλλιέργεια γλυκού σόργου. Χρησιμοποιήθηκαν φυτά γλυκού σόργου [Sorghum bicolor (L) Moench] ποικιλίας Keller και πραγματοποιήθηκαν αφ’ ενός πειράματα στο πεδίο αφ’ ετέρου πειράματα σε πλαστικά δοχεία. Τα πειράματα πεδίου πραγματοποιήθηκαν σε αγρόκτημα του Πανεπιστημίου Πατρών, τις καλλιεργητικές περιόδους του 2004 και 2005, και περιλάμβαναν δύο χειρισμούς (βιολογική και συμβατική διαχείριση της γονιμότητας του εδάφους), με τρεις επαναλήψεις ο καθένας σε πλήρη τυχαιοποιημένη διάταξη. Τα αποτελέσματα των πειραμάτων πεδίου, έδειξαν ότι η βιολογική διαχείριση της γονιμότητας του εδάφους ευνόησε τη διαθεσιμότητα του εδαφικού νιτρικού αζώτου. Το 2004, μέχρι και την ολοκλήρωση της άνθησης, τα φυτά του βιολογικού χειρισμού συσσώρευσαν περισσότερο άζωτο από ό,τι τα φυτά του συμβατικού χειρισμού, αν και οι διαφορές δεν ήταν στατιστικά σημαντικές, εκτός από τη δεύτερη δειγματοληψία, όπου τα φυτά του συμβατικού χειρισμού συσσώρευσαν 2,69 N gm-2, ενώ για τα φυτά του βιολογικού χειρισμού η αντίστοιχη τιμή ήταν 5,12 N gm-2. Το 2005, η συσσώρευση αζώτου ακολούθησε παρόμοια πορεία μέχρι τα μέσα της άνθησης και οι διαφορές δεν ήταν στατιστικά σημαντικές, εκτός από τη τρίτη δειγματοληψία, όπου τα φυτά του συμβατικού χειρισμού συσσώρευσαν 3,61 N gm-2, ενώ για τα φυτά του βιολογικού χειρισμού η αντίστοιχη τιμή ήταν 4,61 N gm-2. H επίδραση εμβολίων Azospirillum brasilense, σε παραμέτρους αύξησης φυτών γλυκού σόργου και στην πρόσληψη αζώτου από τα φυτά, υπό διαφορετικά επίπεδα αζωτούχου λίπανσης μελετήθηκε σε πειράματα σε πλαστικά δοχεία. Το κάθε πείραμα περιλάμβανε πέντε χειρισμούς με τριάντα επαναλήψεις, έκαστος. Τα φυτά που εμβολιάστηκαν με Azospirillum brasilense και έλαβαν τη μισή ποσότητα αζώτου, έδωσαν 7,69 g ξηρής βιομάζας φυτό-1 στο τέλος του πρώτου πειράματος και 4,89 g ξηρής βιομάζας φυτό-1 στο τέλος του δεύτερου πειράματος, ενώ τα φυτά που δέχθηκαν πλήρη λίπανση αζώτου χωρίς εμβόλιο έδωσαν 2,39 και 2,04 g ξηρής βιομάζας φυτό-1 στο τέλος του πρώτου και δεύτερου πειράματος αντιστοίχως. Οι διαφορές των χειρισμών ανά πείραμα ήταν στατιστικά σημαντικές. Το συνολικό προσλαμβανόμενο άζωτο από τα φυτά που εμβολιάστηκαν με Azospirillum brasilense και έλαβαν τη μισή ποσότητα αζώτου ήταν 153,23 και 99,96 mg φυτό-1 στο τέλος του πρώτου και του δεύτερου πειράματος αντιστοίχως. Οι τιμές ήταν υψηλότερες σε σχέση με τις τιμές του συνολικού προσλαμβανόμενου αζώτου των φυτών των λοιπών και οι διαφορές ήταν στατιστικά σημαντικές. Τα αποτελέσματα των πειραμάτων έδειξαν υψηλή αξιοποίηση του εφαρμοζόμενου αζώτου των φυτών που εμβολιάστηκαν με Azospirillum. Τα αποτελέσματα υποδεικνύουν την βιωσιμότητα ενός βιολογικού συστήματος καλλιέργειας, όσον αφορά την κάλυψη των αναγκών των φυτών σε άζωτο. Η υψηλή αξιοποίηση του αζώτου από τα φυτά γλυκού σόργου, οδηγεί στη μείωση εφαρμογής αζωτούχων λιπασμάτων και συμβάλλει στη μείωση του κόστους καλλιέργειας, στη μείωση εκπομπών αερίων του θερμοκηπίου και στην μείωση διήθησης νιτρικών στο υπόγειο υδροφόρο ορίζοντα. / The aim of the present thesis was to study the nitrogen dynamics in sweet sorghum crop. Sweet sorghum plants [Sorghum bicolor (L) Moench] variety Keller were used, and field and experiments were conducted. Field experiments were conducted during 2004 and 2005 growing seasons at the experimental station of the University of Patras, Greece and there were two treatments (biological and conventional soil fertility treatment), in a randomized complete block experimental design with three replications. The results showed that biological soil fertility treatment favour soil nitrate nitrogen concentration. In 2004, until completion of blooming, nitrogen uptake was higher in plants cultivated on biological fertility treated soil than in them cultivated on conventional but the differences were not statistically significant, except in second sampling, which nitrogen uptake was 2,69 N gm-2 in plants cultivated on conventional fertility treated soil and it was 5,12 N gm-2 in plants cultivated on conventional fertility treated soil. In 2005, until half of blooming, nitrogen uptake was similarly ranged for both treatments but the differences were not statistically significant, except in third sampling, which nitrogen uptake was 3,61 N gm-2 in plants cultivated on conventional fertility treated soil and it was 4,61 N gm-2 in plants cultivated on conventional fertility treated soil. Τhe effect of Azospirillum brasilense inoculation on growth parameters and nitrogen uptake in sweet sorghum plants fertilized with various nitrogen levels, was studied during pot experiments. Each experiment was including five treatments and thirty replications of each. Plants inoculated with Azospirillum brasilense and receiving half amount of nitrogen fertilizer produced 7,69 g dry biomass plant-1 at the end of the first experiment and they produced 4,89 at the end of the second one, while plants receiving full amount of nitrogen fertilizer and no inoculation produced 2,39 and 2,04 g dry biomass plant-1 at the end of the first and second experiment, respectively. Differences among treatments in each experiment, were statistically significant. Total nitrogen uptake in Plants inoculated with Azospirillum brasilense and receiving half amount of nitrogen fertilizer was 153,23 and it was 99,96 mg plant-1 at the end of first and second experiment, respectively. Those plants showed higher nitrogen uptake than plants from each other treatment and the differences were statistically significant. Results showed that treatments which inoculated with Azospirillum brasilense were the most efficient in terms of nitrogen uptake. These results indicate that biological management provides an adequate nitrogen nutrition to sweet sorghum crop. High nitrogen efficiency in sweet sorghum plants leads in reduced applying nitrogen fertilization and contribute in reduced crop cost, in reduced emission of the greenhouse gas and in reduced leaching of NO3-N to ground water.

Currently looking for alternative approaches to crop production which would be in accord with sustainable development. The present thesis was aimed on testing of organic cultivation of tomato (Solanum lycopersicum L.) and leek (Allium porrum L.) by using amendment with organic maize biomass (Zea mays L.), mycorrhizal fungi and saprotrophic fungi. The effects of different combinations of microbial inoculations on nitrogen uptake, plant growth and yield were investigated in greenhouse conditions. Supplied 15 N-labelled organic matter was separated from the root system by a nylon mesh which permitted only fungal hyphae to pass through but not plant roots. In the first year experiments the treatments differed in the presence or absence of three factors: organic matter, saprotrophic fungus Agrocybe sp. and mycorrhizal fungus Glomus mosseae (Nicolaj & Gerd.) Gerd. & Trappe. Plant inoculation with Agrocybe sp. alone or together with G. mosseae increased plant growth of tomato in the presence of organic matter. Tomato yield were not increased significantly. Shoot dry weight of leek increased when plants were treated with mycorrhizal fungus G. mosseae and organic matter. Microbial inoculation did not influence nitrogen (15 N) uptake from the organic source. In following experiments, all treatments contained...

The lack of proper wastewater treatment inhibits the social and economic development in many communities. The South African town Wakkerstroom is an example where wastewater is first treated before it is released. Due to the lack of technical expertise and funding to manage the sewage disposal system, a large part of the wastewater goes directly, without any treatment, into a stream feeding the Wakkerstroom wetland. The wetland purifies the wastewater and provides clean water downstream, thus is indispensable for its detoxification capacity. One relatively cheap method to determine the absorption capacity of a wetland with respect to nitrogen loading is to investigate the nitrogen uptake by the wetland vegetation. In this study, the nitrogen uptake of the vegetation in the Wakkerstroom wetland during the growing seasons between the years 2000-2018 was investigated by using harvested biomass and its nitrogen content as a proxy. The interannual variability of Net Primary Production (NPP) was calculated using a Light Use Efficiency (LUE) model for the period 2000-2018. The NPP derived with LUE-modelling was compared to NPP based on an end-of season harvest of biomass in March 2019. The nitrogen content and carbon and nitrogen (C:N) ratio were determined in the harvested biomass by carbon and nitrogen content analysis. The annual nitrogen uptake of the growing seasons between the years 2000-2018 was subsequently determined by multiplying the calculated NPP by the fraction of nitrogen found in the harvested material. The NPPtot based on harvested biomass (NPPharvest) towards the end of the growing season 2018/2019 was estimated to be 2.01 kg‧m-2‧season-1. The NPPtot calculated from LUE modelling (NPPLUE) varied between 0.49-1.64 kg‧m-2 for the growing seasons between 2000-2018. NPPharvest was between 1.2-4 times higher compared to NPPLUE, probably due to overestimation of NPPharvest because of biomass sampling of more than one-year production, or underestimation of NPPLUE due to a low maximum radiation conversion efficiency factor, εmax. The community mean nitrogen (N) content found in the biomass harvested aboveground was 1.29 % for the Phragmites community and 1.00 % for the Typha community. The nitrogen uptake of the vegetation was estimated to vary between 6.10-20.5 g N∙m-2 per growing season between the years 2000-2018. / Bristen på adekvata reningstekniker för att behandla avloppsvatten hämmar den sociala och ekonomiska utvecklingen i många samhällen. Den sydafrikanska staden Wakkerstroom är ett exempel där avloppsvatten först renas innan det släpps ut. På grund av brisen på teknisk kompetens och finansiering att hantera reningsverket som avlägsnar avloppsvatten så läcker en stor del av det orenade avloppsvattnet ut i en våtmark i Wakkerstroom via en närliggande å. Våtmarken är av regional betydelse för sin reningskapacitet då den renar avloppsvattnet och förser användare nedströms med rent vatten. En viktig aspekt för att bestämma en våtmarks reningskapacitet med avseende på kväve (N) är att undersöka växternas kväveupptag i våtmarken. Kväveupptaget hos växterna i våtmarken i Wakkerstroom under växtsäsongerna mellan år 2000–2018 undersöktes genom att använda skördad biomassa och dess kväveinnehåll som proxy. Den årliga variabiliteten hos nettoprimärproduktionen (NPP) beräknades genom att använda en LUE (Light Use Efficiency)-modell för perioden 2000-2018. NPP framtaget med LUE-modellering jämfördes med NPP baserat på biomassa skördad i slutet av växtsäsongen i mars 2019. Kväveinnehållet och kol-kväve (C:N) kvoten bestämdes hos den skördade biomassan genom en kol- och kväveanalys. Det årliga kväveupptaget under växtsäsongerna mellan 2000–2018 togs därefter fram genom att multiplicera beräknad NPP med kvävefraktionen erhållen från den skördade biomassan. NPPtot framtaget med biomassa skördad i slutet av växtsäsongen 2018/2019 (NPPbiomassa) uppskattades vara 2,01 kg‧m-2‧säsong-1. NPPtot beräknat med LUE-modellering (NPPLUE) varierade mellan 0,49–1,64 kg‧m-2 under växtsäsongerna mellan år 2000–2018. NPPbiomassa var 1,2–4 gånger högre i jämförelse med NPPLUE, vilket troligtvis berodde på att NPPbiomassa överskattades på grund av att mer än en årsproduktion av biomassa skördades, eller för att NPPLUE underskattades på grund av ett för lågt värde på den maximala effektivitetsfaktorn εmax valdes. Medelvärdet för kväveinnehållet erhållen i biomassan skördad ovanför vattennivån var 1,29 % för Phragmites-samhället och 1,00 % för Typha-samhället. Kväveupptaget hos växterna varierade mellan 6,10–20,5 g N∙m-2 per växtsäsong mellan år 2000–2018.

Das Pflanzenwachstum fördernde Bakterien (PGPB) kommen ubiquitär sowohl an der Wurzel als auch am Spross der Pflanzen vor und sie können über direkte oder indirekte Mechanismen einen bedeutenden Beitrag zur Stickstoffernährung der Pflanzen leisten. Die vorliegende Arbeit umfasst a) die Isolierung von PGPB, welche das Wachstum verschiedener Pflanzenarten fördern und durch Fusarien verursachte Pflanzenkrankheiten bekämpfen, b) die Analyse der Möglichkeiten Probleme der Pflanzenernährung durch den Einsatz von PGPB zu lösen, c) die Entwicklung neuer molekularbiologischer Methoden zur Messung der Diversität und Aktivität der PGPB. Im Rahmen dieser Arbeit wurden Methoden zur Beschreibung der Diversität von rhizosphären PGPB entwickelt und verbessert um Verbindungen zwischen applizierten PGPB und deren Aktivitäten zu prüfen. Die sensitive quantitative real-time-PCR Methode wurde zur Quantifizierung bzw. zum Nachweis der inokulierten PGPB und zum Nachweis des nitrogenase-reduktase-Gens (nifH), des Markergens für potentiell diazotrophe Bakterien. Bakterienartspezifische Primer wurden aus dem Sequenzvergleich der 16S-23S ISR ausgewählter Bakterienstämme selektiert und Protokolle zur Quantifizierung dieser Bakterienarten erarbeitet. Die nifH Gen Quantifizierung an Pflanzen eröffnet die Möglichkeit Schlüsselorganismen in der assoziativen biologischen Luftstickstoffbindung zu identifizieren und kurzfristige Reaktionen der Bakteriengesellschaften auf Umweltveränderungen und Regulationsmechanismen in situ zu analysieren. / Plant growth promoting bacteria (PGPB) are ubiquitous in both plant root and shoot, and are important contributors to the nitrogen-input of plants exerting their positive effects on plant growth directly or indirectly through different mechanisms. The present work focuses on a) the isolation of PGPB, which promotes the growth of different plant cultures and controls plant diseases caused by Fusarium species, b) the prospects of PGPB to solve plant nutritional problems, c) developing new molecular methods for the assessment of their diversity and activity. In the frame of this thesis, the methods for the description of the diversity of root colonizing PGPB have been developed and improved to provide links between introduced PGPB abundance and activities. The approach used was based on the sensitive real – time PCR detection/quantification of introduced PGBP and the nitrogenase reductase gene (nifH), which served as a marker gene for potential diazotrophs. The amplified 16S-23S ISR sequences of studied bacteria were subjected to strain – specific primer design and a highly specific bacteria quantification protocol were developed. The bacteria quantification protocol was based on real – time PCR using strain specific primers in order to evaluate the colonization ability of studied bacteria, which were inoculated to plant roots. The results presented in this thesis have shown that monitoring of nifH amount in plant root is a suitable and promising approach to link inoculated diazotrophic bacteria abundance and its potential activity. The study of nifH gene abundance in plant offers the opportunity to identify key players in asymbiotic nitrogen fixation, to study short-term community responses in changing environments, or to analyze the effect of regulation in situ.

Cereal rye (CR), the most common and effective nitrogen (N) scavenging cover crop option in the Midwest, is often utilized in cropping systems to reduce nitrate loss for environmental benefits. To increase environmental efficiency in Midwest corn cropping systems, we must increase the overall adoption of CR. However, due to the yield reduction potential (6%) for corn planted after CR termination, CR is primarily recommended before soybean. To increase CR adoption, we must develop adaptive fertilizer management practices that achieve competitive grain yields relative to cropping systems where CR is not adopted. Therefore, the objectives of this study are to determine (1) the effect of CR and starter nitrogen rate on corn growth and nitrogen content. (2) the optimum starter nitrogen rate to achieve agronomic optimum corn yield following CR. (3) the impact of phosphorus (P) at starter on plant growth, nitrogen content, and yield with the inclusion of CR. For our study, five starter N rates were applied in a 5x5 cm band to both CR and non-CR plots, concentrations ranged from 0-84 kg N ha^-1in 28 kg N ha^-1 intervals. Total N applied was the same for each treatment, relative to its location, and was split between starter N at planting and sidedress applied at growth stage V6 relatively. Although CR termination took place at least two weeks before planting, CR decreased corn grain yield at one of three locations by an average of 8%, nitrogen recovery efficiency (NRE) by 27%, and R6 total N content by 23%, relative to the conventional control (non-CR 0N), when no starter N was applied. At one of three locations, starter N rates of 56 kg N ha^-1, 56 kg N ha^-1plus 17 kg P ha^-1, and 84 kg N ha^-1 increased corn grain yield, in CR plots, and 56 kg N ha^-1 plus 17 kg P ha^-1 increased corn grain yield in non-CR plots. Phosphorus increased corn grain N content at growth stage R6 in one of three locations and did not impact corn grain yield at all locations. We conclude that the inclusion of starter N at planting has the potential to increase agronomic productivity in CR corn cropping systems in soil environments with a high capacity to mineralize soil N. However, further research is required to refine our starter N results to find an optimum starter N rate to apply before planting corn following CR.

Nitrogen (N), an essential plant macronutrient, is among the most limiting factors of crop yield. To sustain modern agriculture, N is often amended in soil in the form of chemical N fertilizer, a major anthropogenic contributor to nutrient pollution that affects climate, biodiversity and human health. To achieve agricultural sustainability, a comprehensive understanding of the regulation of N response in plants is required, in order to engineer crops with higher N use efficiency. Recently, epigenetic mechanisms, such as histone modifications, have gained increasing importance as a new layer of regulation of biological processes. However, our understanding of how epigenetic processes regulate N uptake and assimilation is still in its infancy. To fill this knowledge gap, we first performed a meta-analysis that combined functional genomics and network inference approaches to identify a set of N-responsive epigenetic regulators and predict their effects in regulating epigenome and transcriptome during plant N response. Our analysis suggested that histone modifications could serve as a regulatory mechanism underlying the global transcriptomic reprogramming during plant N response. To test this hypothesis, I applied chromatin immunoprecipitation-sequencing (ChIP-Seq) to monitor the genome-wide changes of four histone marks (H3K27ac, H3K4me3, H3K36me3 and H3K27me3) in response to N supply in tomato plants, followed by RNA-Seq to profile the transcriptomic changes. To investigate the organ specificity of histone modifications, I assayed shoots and roots separately. My results suggest that up to two-thirds of differentially expressed genes (DEGs) are modified in at least one of the four histone marks, supporting an integral role of histone modification in regulating N response. I observed a synergistic modification of active histone marks (H3K27ac, H3K4me3 and H3K36me3) at gene loci functionally relevant to N uptake and assimilation. Surprisingly, I uncovered a non-canonical role of H3K27me3, which is conventionally associated with repressed genes, in modulating active gene expression. Interestingly, such regulatory role of H3K27me3 is specifically associated with highly expressed genes or low expressed genes, depending on the organ context. Overall, I revealed the multi-faceted role of histone marks in mediating the plant N response, which will guide breeding and engineering of better crops with higher N use efficiency