Browsing by Person "Rasche, Frank"

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Biochemical and ecophysiological characterization of BNI (Biological Nitrification Inhibition) by Brachiaria humidicola
(2021) Egenolf, Konrad; Rasche, Frank
In perennial grasslands, especially Brachiaria humidicola (syn. Urochloa humidicola) dominated swards, one hypothesized mechanism of high N efficiency is the plant exerted control of nitrification via the synthesis and release of nitrification inhibitors (NI) into the soil. This phenomenon has been conceptualized as Biological Nitrification Inhibition (BNI). This doctoral thesis was conducted with the aim of broadening our fundamental understanding on BNI ecophysiology, with a special emphasis on the edaphic parameters soil pH and soil texture as factors shaping the soil microbial community composition. The overarching objectives were to (1) screen root exudates of B. humidicola for major bioactive secondary metabolites with nitrification inhibiting activity, to (2) proof the significance of rhizosphere pH and nutritional N form for NI release and understand the underlying exudation mechanism, and to (3) elucidate the influence of soil pH and soil texture on the ammonia oxidizer community composition and BNI performance of B. humidicola. Root exudate screening via LC-MS and NMR techniques revealed several novel NI compounds with significantly higher NI activity compared to previously described brachialactone, i.e. the brachialactone isomers/derivatives 3-epi-brachialactone (ED50 ~ 20 µg ml-1, ED80 ~ 40 µg ml-1) and 3,18-epoxy-9-hydroxy-4,7-seco-brachialactone (ED50 ~ 40 µg ml-1) as well as the phenol aldehyde vanillin (ED50 ~ 12.5 µg ml-1, ED80 ~ 20 µg ml-1). In the case of the described brachialactone derivatives, internal tissue concentrations were extremely low (2-8 µg g-1 root DM), suggesting so far undiscovered cytosolic precursors. In the case of vanillin, its chemical proximity to other phenolic compounds previously described as NI, i.e. methyl-coumarate, methyl-ferulate and methyl 3-(4-hydroxyphenyl) propionate, drew the attention to phenylalanine and coumaric acid as common precursors and possible BNI breeding target. With regard to the NI exudation, the hypothesized positive effect of low rhizosphere pH and NH4+ nutrition was confirmed for both the brachialactone isomers/derivatives and vanillin. However, for 3-epi-brachialactone it was demonstrated that NH4+ did not constitute an essential prerequisite for NI synthesis and release. In contrast, NI release correlated with the transmembrane proton gradient, which in turn depends on soil pH and is favored by rhizosphere acidification occurring under cation-dominant nutrition (e.g. NH4+). These findings were considered as evidence for an active NI release via secondary transporters (possibly MATE transporters). The effects of soil pH and soil texture on the ammonia oxidizer community and BNI performance of B. humidicola were investigated through a three-factorial pot trial including liming and different soil types as experimental factors. No clear conclusion could be drawn with regard to the hypothesized effects of soil pH, soil texture and the ammonia oxidizer community composition on BNI performance of B. humidicola. In the presented pot trial, B. humidicola reduced net nitrification rates by 50-85% compared to the non-planted control, but this reduction was observable irrespective of soil pH, soil texture and the ammonia oxidizer community composition. Furthermore, the reduction of net nitrification was largely dependent on microbial N immobilization and efficient plant N (probably NO3-) uptake rather than BNI. This absence of a clear BNI effect was mainly attributed to high N inputs, which is in accordance with previous studies indicating that BNI was impaired in high nitrifying environments. The argument was underlined by theoretical enzyme-kinetic calculations, revealing a strong influence of substrate (NH4+) availability on soil nitrification dynamics, but as well BNI performance: Assuming soil NI concentrations at ED50 (~ effective dose 50% inhibition), it could be shown that – with the only exception of AOA populations suppressed by non-competitive inhibitors – the efficacy of NI is severely disrupted by increasing soil NH4+ availability. Besides contrasting AOA and AOB sensitivities towards NI, the inter-domain differences of ammonia-monooxygenase (AMO) kinetics probably delivers an additional explanation for the observation, that under field conditions BNI has mainly been confirmed for AOA, and to a lesser extent for AOB. Based on the findings of the presented doctoral thesis, it was concluded that BNI may play an important role in extensive B. humidicola pasture systems, especially on acid, coarse textured and AOA dominated soils. Intensification, especially increasing N amendments, will most likely disrupt the nitrification inhibiting effect and under these circumstances, N immobilization and efficient plant N uptake may display the dominant factors controlling net nitrification rates.
Different quality classes of decomposing plant residues influence dissolved organic matter stoichiometry which results in different soil microbial processing
(2024) Poosathit, Ratanaporn; Kunlanit, Benjapon; Rasche, Frank; Vityakon, Patma
The influence of the quantities and ratios of dissolved organic carbon (DOC) and dissolved nitrogen (DN) generated by different chemical quality classes of organic residues on soil microbial processes in the decomposition process is not well understood. If the DOC-to-DN ratio (hereafter, ratio) of the substrate is close to that of the microbial C-to-N ratio, then the DOC-and-DN stoichiometry of the substrate is balanced, resulting in enhanced microbial processing, i.e., carbon use efficiency (CUE). Uncertainty exists about the influence of DN and the DOC-to-DN ratio on CUE, particularly in high-quality class (high nitrogen) residue-treated soils. A long-term field experiment was used to explore the effect of the annual application of residues of different quality classes on decomposition processes, focusing on the effects of DOC, DN, and the ratio on the microbial metabolic quotient (qCO2), which is the inverse of CUE. DOC and DN were extracted from soils during the 13th year of the experiment. Soils treated with high-quality class groundnut residue (high-nitrogen) had higher DN (5.4 ± 2.6 mg N kg−1) and a lower ratio (6.8 ± 2.6) than those treated with medium-quality (medium-nitrogen) tamarind (3.0 ± 0.6 and 10.7 ± 2.2, respectively). The positive influence of DN on qCO2 (R2 = 0.49 *) in groundnut-treated soil suggested that the high bioavailability of DN reduced CUE due to imbalanced DOC-and-DN stoichiometry. This contradicted earlier published findings on high-nitrogen residues which had balanced DOC-and-DN stoichiometry. The positive influence of the ratio on qCO2 under the tamarind-treated soil (R2 = 0.60 *) indicated that its balanced DOC-and-DN stoichiometry enhanced CUE. High-quality class organic residues can result in either higher or lower CUE than their lower-quality class counterparts depending on whether the resulting DOC-and-DN stoichiometry is balanced or imbalanced.
Fertility and microbial functioning of soils of smallholder farming systems under contrasting tropical agro-ecologies
(2021) Balume, Isaac; Rasche, Frank
Soil fertility in tropical agroecosystems is often subjected to degradation that leads to nutrient depletion with negative effects on land productivity and food security. This challenge is aggravated by the complexity of socio-economic (market distance, farm typology) and biophysical (agro-ecology, site) conditions causing soil fertility variability. Consequently, blanket fertilizer recommendations cannot be applied in areas of high fertility variability. In this PhD study, methods were harmonized to assess drivers of soil fertility status across regions. Despite being pointed as factors contributing to soil fertility variability, market access, farm typology (resource endowment) and agro-ecology have not been subjected to soil fertility assessment. This PhD study aimed mainly at verifying that these factors have to integrated rather than considered in isolation to enable accurate assessments of soil fertility across spatial scales and socio-economic gradients. It was hypothesized that market distance and farm typology is a determinant of agricultural development in Democratic Republic of Congo (DRC). As market distance is increasing, the soil fertility status of smallholder farming systems decreases despite farmers’ wealth. In a parallel study conducted in Ethiopia, it was complementarily hypothesized that the soil fertility status is also influenced by inter-related effects of agro-ecology and farm typology. As nitrogen (N) is known to be limiting in smallholder farms, conservation and sustainable provision of this nutrient will be essential to achieve niche-based integrated soil fertility management (ISFM) strategies. Therefore, understanding of the ecological processes (proteolysis, nitrification) that control soil N availability through organic residue management in varying soil fertility variability conditions will be essential. Low concentrations of lignin (L) and polyphenols (PP) relative to N have been acknowledged to facilitate decomposition, hence, stimulate the abundance of proteolytic and nitrifying soil microbial communities. Therefore, it was hypothesized that high quality (low (L+PP)/N)) residue applied to high pH soils have a positive relationship between the functional potential of proteolytic enzymatic activities and abundance of nitrifying communities. The survey studies in DRC and Ethiopia were guided by the following objectives; 1) To determine the inter-related influence of market distance and farm typology on soil fertility status of smallholder farming systems of South-Kivu, Eastern DRC. 2) To assess the inter-related effects of agro-ecology and farm typology on soil fertility status across crop-livestock systems in Western and Central Ethiopia. Moreover, to better understand the ecological processes (proteolysis, nitrification) that control N through organic residue management in varying soil fertility variability conditions, an incubation study was performed to meet objective 3) To verify that potential proteolytic enzyme activities modulate archaeal and bacterial nitrifier abundance in soils with differing acidity and organic residue treatment. Results from the soil survey study in DRC revealed a decreasing soil fertility with increasing market distance across all farm typologies. A significant influence of farm typology was found for exchangeable calcium and magnesium, while factor site resulted in a significant difference of plant available phosphorus. Furthermore, factor “site” interacted with market distance for soil organic carbon (SOC) quality indexes. In addition, the interaction of market distance and typology became obvious in the medium wealthy and poor farms. Market distance effects were associated with walking distance, while site effects were attributed to factors such as soil type and climatic conditions. In Ethiopia, inter-related effect of agro-ecology and farm typology was found. Higher total carbon and total nitrogen was found in wealthy farmers’ field compared to poor farmers’ field in the highlands. As an indication of soil quality, lowest SOC stability indexes were revealed in soils of wealthy compared to that from poor farm typology. These differences in soil fertility were attributed to farm management practices among typology classes and agro-ecological zone distinctions. The result from the incubation study revealed a significant relationship of proteolytic enzyme activities with the abundance of ammonia oxidizing bacteria and archaea, even though the extent of this relationship was more dependent on soil pH and incubation time, but not residue quality. This suggests that the effect of soil pH is stronger than that of residue quality on enzyme activity and nitrifiers community, reflecting the importance of soil physico-chemical conditions rather than management practices. The incubation study further showed that nitrifying prokaryotes benefitted from the release of N spurred by proteolysis, and indicated a niche specialization between ammonia oxidizing bacteria and archaea depending on soil acidity and resource availability. Overall, this PhD study showed that market access, typology and agro-ecology were important drivers of soil fertility variability in the study regions of DRC and Ethiopia. However, factor site played a significant role in shaping soil fertility variability, implying that site-specific recommendations could be a way forward for designing soil fertility management in smallholder farmers. It was inferred that prospective niche-based ISFM strategies must consider such contrasting but interrelated factors including, but not limited to agro-ecology, farm typology and market access. This would reduce the effect of soil fertility variability across regions. This PhD study only considered land size (DRC, Ethiopia), livestock and mineral fertilizers (Ethiopia) as key features to define the wealth status of targeted farms; future studies should consider a wider range of socio-economic and biophysical factors including labor availability, off-farm household income and soil management history for more accuracy of soil fertility variability. This will strengthen the accuracy of prospective soil fertility assessments across socio-economic gradients and spatial scales. Finally, it is suggested to extend the results from the incubation study to field conditions considering soils with a broader soil acidity range and organic residues with more distinct biochemical quality. This will verify the given assumptions about the functional relationships between proteolytic and nitrifying soil communities. Overall, the presented PhD study has contributed to ongoing research on best-fit soil fertility recommendations and knowledge gaps about soil ecological functioning, by providing an advanced understanding of driving factors of soil fertility variability and soil microbial functioning in smallholder farms in tropical environments.
Growth of lettuce in hydroponics fed with aerobic- and anaerobic–aerobic-treated domestic wastewater
(2023) Germer, Jörn; Brandt, Christian; Rasche, Frank; Dockhorn, Thomas; Bliedung, Alexa
Reusing water and nutrients from municipal wastewater can conserve resources and reduce wastewater treatment costs. In this study, the suitability of different qualities of treated wastewater for plant production in a hydroponic flow-through system was investigated. Lettuce (Lactuca sativa L.) was grown in hydroponic lines fed with treated wastewater, i.e., conventional effluent from aerobic wastewater treatment by the activated sludge process (CE), ozonised CE (CEO), anaerobically pre-treated and nitrified wastewater (AN) and biological activated carbon filtered AN (ANC) in comparison with a modified Hoagland nutrient solution. In CEO, AN and ANC, the lettuce reached a similar weight and elemental composition as that in HS. The low N and P concentrations in CE and CEO were quickly depleted, resulting in limited plant development at the ends of these lines. The lower water content in the CE shoots was probably related to hypoxia that occurred at higher temperatures. In the CEO line, this condition did not arise due to the constant decay of O3. At lower temperatures, the CEO shoot dry weight was 90% higher than that in CE. This was possibly an effect of residual ozone and/or oxygen supersaturation. AN produced the highest yield, while carbon filtration lowered the content of cations in ANC, inducing deficiency of Fe > Mn > Cu > Zn > K. Coupling wastewater treatment with hydroponics allows for efficient nutrient recovery, and thus could reduce the energy and reactor volume needed for N and P elimination.
Impact of environmental and socio-economic factors on soil fertility variability and microbial carbon use efficiency in tropical smallholder farming systems
(2022) Agumas Endalew, Birhanu; Rasche, Frank
Die Hauptfaktoren für die Variabilität der Bodenfruchtbarkeit in Subsahara-Afrika (SAA) müssen verstanden werden, um maßgeschneiderte Strategien für ein integriertes Bodenfruchtbarkeitsmanagement (ISFM) zu entwickeln, die die agro-ökologischen Zonen, die Ressourcenausstattung der Kleinbauern und ihr indigenes Wissen über die Bodenfruchtbarkeit berücksichtigen. Darüber hinaus mangelt es den meisten Bodenfruchtbarkeitsindikatoren, einschließlich, aber nicht beschränkt auf den Gesamtgehalt an organischem Kohlenstoff (SOC) im Boden, an Empfindlichkeit und Genauigkeit. Die Unempfindlichkeit und Ungenauigkeit dieser Indikatoren erschwert ihre Anwendung für die Erfassung der Bodenfruchtbarkeit in kleinbäuerlichen Systemen auf größeren räumlichen Skalen. Daher ist die Überprüfung neuartiger Bodenfruchtbarkeitsindikatoren, wie z.B. funktionelle SOC-Gruppen und mikrobielle Kohlenstoffnutzungseffizienz (CUE), die von Umweltfaktoren (z.B. pH-Wert des Bodens, Qualität des organischen Inputs) beeinflusst werden, von größter Bedeutung, um diese Einschränkung zu überwinden. Die Umsetzung einer solchen methodischen Innovation würde helfen, das Ausmaß der regionalen Bodenfruchtbarkeitsvariabilität besser zu verstehen und anschließend nischenbasierte ISFM-Strategien für kleinbäuerliche Anbausysteme in SSA zu entwickeln. Daher war das erste Ziel dieser Studie, die wechselseitigen Auswirkungen biophysikalischer und sozioökonomischer Faktoren auf die Variabilität der Bodenfruchtbarkeit zu untersuchen, wie sie sich in den Nährstoffgehalten des Bodens sowie im SOC-Gehalt und den Qualitätsparametern (d.h. den SOC-Funktionsgruppen) widerspiegelt. Das zweite Ziel war die Bewertung des CUE als zusätzlicher Proxy zur Beurteilung der Bodenfruchtbarkeit unter Berücksichtigung des Einflusses von Umwelt- und methodischen Variationen auf die CUE-Berechnung. Die spezifischen Ziele dieser PhD-Studie waren,: - zu verifizieren, dass die Variabilität der Bodenfruchtbarkeit in zwei Modellregionen in Zentral- und West-Äthiopien mit vier unterschiedlichen agro-ökologischen Zonen durch die miteinander verbundenen Effekte der Agrarökologie und der Ressourcenausstattung der Landwirte ("reiche" versus "arme" Landwirte) bestimmt werden kann. - diesen Ansatz der lokalen Bewertung der Bodenfruchtbarkeit in Äthiopien zu bestätigen, indem die "Marktdistanz" als zusätzlicher Faktor für die Variabilität der Bodenfruchtbarkeit einbezogen wird, wie es in der Demokratischen Republik Kongo (DRC) vorgemacht wurde. - zu testen, ob das indigene Wissen der Landwirte über den Zustand der Bodenfruchtbarkeit durch interdependente Effekte der Agrarökologie, der Marktdistanz und der Betriebstypologie bestimmt wird, unter Berücksichtigung des kontinuierlichen Wissenstransfers zwischen den Landwirten innerhalb und zwischen den agro-ökologischen Zonen. - das Potenzial der funktionellen SOC-Gruppen und des mikrobiellen CUE im Boden als vielversprechende Indikatoren für den Zustand der Bodenfruchtbarkeit zu bewerten, die von den physikalisch-chemischen Bodeneigenschaften und dem Management organischer Inputs beeinflusst werden. - die bestehende Single-C-Cycling-Enzym-Stöchiometrie (SCE-STM) zu modifizieren, indem neuartige "Multi"-C-Cycling-Enzym-Stöchiometrie (MCE-STM) Methoden zur CUE-Abschätzung vorgeschlagen werden. Um die Ziele 1-3 der vorgestellten PhD-Studie anzugehen, wurden zwei lokale feldbasierte Bodenfruchtbarkeitsuntersuchungen in Äthiopien und der DRC durchgeführt. Für die Ziele 4 und 5 wurde eine laborbasierte Inkubationsstudie durchgeführt. Für die Erhebungen der Bodenfruchtbarkeit wurden die Mid-Infrarot-Spektroskopie gekoppelt mit der Partial Least Squares Regression (midDRIFTS-PLSR) und Nasslaboranalysen verwendet, um die Bodenfruchtbarkeit (d.h. pH-Wert des Bodens, Gesamtkohlenstoff (TC), Gesamtstickstoff (TN), pflanzenverfügbarer Phosphor (Pav) und Kalium (Kav), austauschbares Kalzium (Caex) und Magnesium (Mgex)) in vier agro-ökologischen Zonen in Äthiopien zu bewerten. Die MidDRIFTS-Peakflächenanalyse der Spektralfrequenzen (2930 (aliphatische C-H), 1620 (aromatische C=C), 1159 (C-O polyalkoholische und Ether-Gruppen) cm-1) wurde zur Charakterisierung der SOC-Qualität und zur Berechnung des SOC-Stabilitätsindex angewendet. In der DRC wurden beide Techniken eingesetzt, um die Bodenfruchtbarkeit über Marktentfernungen (definiert als Gehzeit) in verschiedenen Regionen zu bewerten. Für die laborbasierte Inkubationsstudie (60 Tage) wurden zwei Böden, die sich hauptsächlich im Säuregrad unterscheiden, mit zwei Proben von Pflanzenresten gemischt, die sich im Lignin- (L) und Polyphenolgehalt (PP) unterscheiden. Zur Abschätzung der mikrobiellen CUE im Boden während des Abbaus von Pflanzenresten in den verschiedenen Böden wurden die Methoden der Single-C-Cycling-Enzym-Stöchiometrie (SCE-STM) und der neu vorgeschlagenen "Multi"-C-Cycling-Enzym-Stöchiometrie (MCE-STM) gegenüber der herkömmlichen C-Bilanz-Methode validiert. Die Ergebnisse der MidDRIFTS-PLSR- und Peak-Flächen-Analyse der äthiopischen Fallstudie zeigten, dass die miteinander verbundenen Effekte der Agrarökologie und der Ressourcenausstattung der Landwirte die beobachtete Variabilität der Bodenfruchtbarkeit in vier agroökologischen Zonen bestimmten. Von der Ressourcenausstattung abhängige Optionen des Bodenfruchtbarkeitsmanagements zeigten eine höhere TZ in der hochgelegenen agroökologischen Zone, während in den niedrigeren agroökologischen Zonen auf den Feldern der wohlhabenden Landwirte eine höhere TN und Kav gefunden wurde. In ähnlicher Weise wurde eine höhere SOC-Qualität in den Böden von wohlhabenden als von armen Betrieben in den höher gelegenen Zonen gefunden. Somit trugen agro-ökologische Zonenunterschiede zu diesen Unterschieden in der Variabilität der Bodenfruchtbarkeit bei. Es wurde abgeleitet, dass dieser Unterschied im Bodenfruchtbarkeitsstatus zwischen den Feldern wohlhabender und armer Landwirte in den verschiedenen agro-ökologischen Zonen auf die hohe Variabilität in der Pro-Kopf-Größe des Landbesitzes, des Viehbestandes und der Menge des pro Flächeneinheit verwendeten Düngers zurückzuführen ist. So legen wohlhabende Landwirte im Tiefland ihr Land brach und bringen organische Reststoffe aus, während die Landwirte im Hochland den Einsatz von chemischen Düngemitteln und Hofdünger in größerem Umfang in Betracht ziehen. Ergänzend zeigten die Ergebnisse der DRC-Fallstudie, dass die "Marktdistanz" und die "Betriebstypologie" wichtige Determinanten für die Variabilität der Bodenfruchtbarkeit sind, beide mit gegensätzlichen Trends in den Untersuchungsgebieten. Ein abnehmender Bodenfruchtbarkeitsstatus wurde bei allen Betriebstypologien mit zunehmender Marktentfernung festgestellt. Ein signifikanter Einfluss der "Betriebstypologie" wurde für Caex und Mgex gefunden, während der Faktor "Standort" zu einem signifikanten Unterschied von Pav führte. Für die SOC-Qualitätsindizes (d.h. das Verhältnis 1530:2930) war der Faktor "Standort" entscheidend, was sich in seiner Interaktion mit der "Marktdistanz" widerspiegelte. Der Effekt der Marktdistanz wurde jedoch auf den Feldern der mittelreichen und armen Landwirte deutlich, wo ein steigender SOC-Qualitätsindex von 1530:2930 mit zunehmender Marktdistanz eine geringere SOC-Qualität in den abgelegenen Betrieben implizierte. Bodentiefe und Bodenfarbe waren die von den Landwirten am häufigsten verwendeten Indikatoren für die Bodenfruchtbarkeit, unabhängig von der Agrarökologie, der Marktentfernung und der Betriebstypologie. Was das indigene Wissen der Landwirte in den Untersuchungsregionen in Äthiopien und der Demokratischen Republik Kongo betrifft, wurden fruchtbare und weniger fruchtbare Felder visuell durch die Bodenfarbe unterschieden. In den meisten agro-ökologischen Zonen der äthiopischen Fallstudie wurden höhere pH-Werte und Pav-Werte in fruchtbaren (braun/schwarz) als in weniger fruchtbaren (rot) Böden gefunden. Außerdem wurden höhere Peakflächen von 1159 cm-1 und SOC-Stabilitätsindizes in weniger fruchtbaren im Vergleich zu fruchtbaren Böden in Äthiopien beobachtet. In enger Übereinstimmung mit dem einheimischen Wissen der Landwirte in der DRC-Studienregion war die Bodenfruchtbarkeit in tiefen Böden höher als in flachen Böden, was sich in höheren Nährstoffvorräten in tiefen Böden widerspiegelte, die organische Ergänzungen erhielten. Dementsprechend sind standortspezifische Bodenbewirtschaftungsstrategien mit der Integration des indigenen Wissens der Landwirte eine machbare Option, um die geringe Akzeptanz von ISFM zu überwinden. Diese PhD-Studie schlug vor, empfindlichere Indikatoren, wie z.B. den mikrobiellen CUE-Wert des Bodens, zu verwenden, um den Zustand der Bodenfruchtbarkeit genau zu beurteilen und Entscheidungen für ein nischenbasiertes Bodenfruchtbarkeitsmanagement zu treffen. Darüber hinaus zeigte die PhD-Studie, dass in fruchtbareren und weniger sauren (pH 5,1) Böden, die mit Rückständen höherer Qualität ergänzt wurden, ein höherer CUE-Wert gemessen wurde als in den anderen drei Kombinationen. Daraus wurde gefolgert, dass die Mikroorganismen mehr Energie zur Unterstützung des Wachstums in saureren (pH 4,3) Böden investierten, um die Bodensäure zu tolerieren, was wiederum die N-akquirierenden enzymatischen Aktivitäten unterdrückte und den CUE weiter reduzierte. Niedrigere CUE-Werte wurden von der Multi-C-Cycling-Enzym-Stöchiometrie-Modellierung (MCE-STM) im Vergleich zu den CUE-Werten aufgezeichnet, die von den C-Balance- und Single-C-Cycling-Enzym-Stöchiometrie-Modellierungsmethoden (SCE-STM) erhalten wurden. Die in dieser Dissertationsarbeit vorgeschlagene Modifikation der MCE-STM-Methode zur CUE-Bestimmung war in der Lage, den kombinierten Effekt von Boden-pH und Pflanzenrückstandsqualität auf die Effizienz des mikrobiellen Stoffwechsels zu quantifizieren. Dadurch verbesserte sie den ursprünglichen stöchiometrischen Modellierungsansatz (SCE-STM), der sich nur auf das Konzept der Nährstoffverfügbarkeit stützte. Zusammenfassend lässt sich sagen, dass sich die midDRIFTS-PLSR-Vorhersagen zusammen mit den midDRIFTS-Peaks, die die funktionalen SOC-Gruppen repräsentieren, für die regionale Bewertung der Bodenfruchtbarkeit als sensibler sowie effizienter und robuster Ansatz erwiesen haben, verglichen mit den bestehenden Ansätzen, die sich auf klassische Bodeneigenschaften (z. B. den SOC-Gehalt) stützen, die durch Nasslaboranalysen ermittelt werden. Basierend auf den mit midDRIFTS generierten Daten wurden die Haupttreiber für die Variabilität der Bodenfruchtbarkeit aufgedeckt, wobei insbesondere die zusammenhängenden Effekte von Agrarökologie, Ressourcenausstattung, Marktdistanz und indigenem Wissen der Landwirte berücksichtigt wurden. Darüber hinaus liefert die Integration der mikrobiellen CUE (z.B. MCE-STM) in die Bewertung der Bodenfruchtbarkeit nicht nur ein klareres Bild des Zustands der Bodenfruchtbarkeit. Sie dient auch dem besseren Verständnis ökologischer Prozesse in Böden im Allgemeinen. Damit förderte diese Doktorandenstudie das Wissen über Bodenfruchtbarkeitstreiber über räumliche Skalen hinweg und legte die wissenschaftliche Basis für die Förderung neuartiger Bodenfruchtbarkeitsindikatoren, die auf mikrobiellen CUE im Boden basieren. Dieses Ergebnis wird der Entwicklung von Nischen-basierten Bodenfruchtbarkeits-Management-Strategien zugute kommen, die von größter Bedeutung für die Sicherung der Lebensgrundlage von kleinbäuerlichen Systemen in SSA sind.
Inter-microbial competition for N and plant NO3− uptake rather than BNI determines soil net nitrification under intensively managed Brachiaria humidicola
(2021) Egenolf, Konrad; Schad, Philipp; Arevalo, Ashly; Villegas, Daniel; Arango, Jacobo; Karwat, Hannes; Cadisch, Georg; Rasche, Frank
Brachiaria humidicola (syn. Urochloa humidicola) has been acknowledged to control soil nitrification through release of nitrification inhibitors (NI), a phenomenon conceptualized as biological nitrification inhibition (BNI). Liming and N fertilization as features of agricultural intensification may suppress BNI performance, due to a decrease in NI exudation, increased NH3 availability and promotion of ammonia oxidizing bacteria (AOB) over archaea (AOA). A 2-year three-factorial pot trial was conducted to investigate the influence of soil pH and soil microbial background (ratio of archaea to bacteria) on BNI performance of B. humidicola. The study verified the capacity of B. humidicola to reduce net nitrification rates by 50 to 85% compared to the non-planted control, irrespective of soil pH and microbial background. The reduction of net nitrification, however, was largely dependent on microbial N immobilization and efficient plant N uptake. A reduction of gross nitrification could not be confirmed for the AOA dominated soil, but possibly contributed to reduced net nitrification rates in the AOB-dominated soil. However, this putative reduction of gross nitrification was attributed to plant-facilitated inter-microbial competition between bacterial heterotrophs and nitrifiers rather than BNI. It was concluded that BNI may play a dominant role in extensive B. humidicola pasture systems, while N immobilization and efficient plant N uptake may display the dominant factors controlling net nitrification rates under intensively managed B. humidicola.
Mechanistic aspects of the eco-physiology of Fusarium oxysporum f. sp. cubense TR4
(2023) Were, Evans; Rasche, Frank
Banana and plantain (Musa spp.), here termed as bananas, are a source of food security and income for more than 400 million people globally. Banana production is threatened by Fusarium wilt disease, caused by the soilborne root-infecting fungal pathogen Fusarium oxysporum f. sp. cubense (Foc). Foc Tropical Race 4 (Foc TR4) is considered the most virulent race of Foc and has gained notoriety due to its inexorable spread and devastating impact on banana cultivation. Host infection occurs when pathogen propagules, called chlamydospores, germinate and produce hyphae that penetrate host roots and subsequently invade host tissues. Infection occurs in a narrow zone of soil immediately adjacent to the roots, called rhizosphere. The rhizosphere is notable for the extensive interactions between roots, the microbiome, and soil physico-chemical factors. Banana rhizosphere interactions are poorly understood, yet profoundly influence infection and development of Fusarium wilt. It is speculated that a better understanding of banana rhizosphere interactions will improve management of Fusarium wilt through the reduction of the abundance and/or efficacy of inoculum or enhance the disease suppressiveness of soils. Hence, the overarching objective of this doctoral study was to contribute to the fundamental ecological understanding of banana rhizosphere interactions related to Foc. The first study of this thesis analysed literature from four electronic databases (AGRIS, CAB Direct, SciVerse Scopus, ProQuest) to bring together the relatively scant data available on banana rhizosphere interactions and to highlight the key knowledge gaps. Analysis of 2,281 publications revealed the complexity of banana rhizosphere interactions and the driving factors of Fusarium wilt, for which the mechanisms remain poorly understood. Data from the literature shows that management of Fusarium wilt through rhizosphere manipulation is a dominant element albeit with limited success in the field. Notably, the data from literature shows that biological control agents (bacterial and fungal strains) are highly effective in vitro and in the greenhouse with a mean efficacy of 77.1% and 73.5%, respectively, but efficacy remains below 25.0% under field conditions. The second study of this thesis provides empirical evidence for suppression of Foc TR4 by root-secreted phenolic acids of non-host plants. Hydroponic culture and targeted metabolite analysis of root exudates of two legumes, Desmodium uncinatum and Mucuna pruriens, identified phenolic compounds such as benzoic-, t-cinnamic-, and p-hydroxybenzoic acid with inhibitory potential. These phenolic compounds suppressed Foc TR4 by inhibition of chlamydospore germination, production of new spores, and hyphal growth, and specifically also the biosynthesis of fusaric acid and beauvericin toxins, which are essential in the biology of the fungus. The third study of this thesis provides empirical evidence that the process of chlamydospore germination in Foc TR4 is developmentally orchestrated and iron-dependent. Scanning electron microscopy showed that iron-starved chlamydospores are unable to form a germ tube and exhibit reduced metabolic activity. Moreover, germination exhibits plasticity regarding extracellular pH, where over 50% germination occurs between pH 3 and pH 11. This suggests that disease suppression by manipulation of soil pH may not necessarily act via alteration of iron bioavailability. The requirement for iron was further investigated by assessing the expression of two genes (rnr1 and rnr2) that encode ribonucleotide reductase (RNR), the enzyme that controls cell growth through DNA synthesis. Expression of rnr2 was significantly induced in iron-starved chlamydospores compared to the control. The fourth study assessed the production of microbial iron-sequestering metabolites (siderophores) as a potential mechanism to counteract iron starvation. Specifically, ferrichrome, a hydroxamate siderophore, was synthesized exclusively in the mycelia of iron-starved cultures, which suggests de novo biosynthesis. Moreover, amino acid precursors for siderophore biosynthesis (ornithine, arginine) were altered by iron starvation. Collectively, this doctoral thesis extends the fundamental understanding of the biology and ecology of Foc TR4 and provides a base for realizing the potential of rhizosphere manipulation for management of Fusarium wilt.
Metabolome fingerprinting reveals the presence of multiple nitrification inhibitors in biomass and root exudates of Thinopyrum intermedium
(2024) Issifu, Sulemana; Acharya, Prashamsha; Schöne, Jochen; Kaur-Bhambra, Jasmeet; Gubry-Rangin, Cecile; Rasche, Frank
Biological Nitrification Inhibition (BNI) encompasses primarily NH4 +-induced release of secondary metabolites to impede the rhizospheric nitrifying microbes from per- forming nitrification. The intermediate wheatgrass Thinopyrum intermedium (Kernza®) is known for exuding several nitrification inhibition traits, but its BNI potential has not yet been identified. We hypothesized Kernza® to evince BNI potential through the presence and release of multiple BNI metabolites. The presence of BNI metabolites in the biomass of Kernza® and annual winter wheat (Triticum aestivum) and in the root exudates of hydroponically grown Kernza®, were fingerprinted using HPLC-DAD and GC–MS/MS analyses. Growth bioassays involving ammonia-oxidizing bacteria (AOB) and archaea (AOA) strains were conducted to assess the influence of the crude root metabolome of Kernza® and selected metabolites on nitrification. In most instances, significant concentrations of various metabolites with BNI potential were observed in the leaf and root biomass of Kernza® compared to annual winter wheat. Furthermore, NH4 + nutrition triggered the exudation of various phenolic BNI metabolites. Crude root exudates of Kernza® inhibited multiple AOB strains and completely inhibited N. viennensis. Vanillic acid, caffeic acid, vanillin, and phenylalanine suppressed the growth of all AOB and AOA strains tested, and reduced soil nitrification, while syringic acid and 2,6-dihydroxybenzoic acid were ineffective. We demonstrated the considerable role of the Kernza® metabolome in suppressing nitrification through active exudation of multiple nitrification inhibitors.
Molecular perspectives on the ecologically inconsistent effectiveness of the mycoherbicide Fusarium oxysporum f. sp. strigae against Striga hermonthica
(2022) Anteyi, Williams Oyifioda; Rasche, Frank
Cereals are a major staple that is crucial for food security in sub-Saharan Africa (SSA). Sadly, the obligate hemiparasitic witchweed, Striga spp., especially Striga hermonthica (Delile) Benth., is a major biotic constraint to cereal production in SSA, causing enormous crop yield losses estimated at US$10 billion annually. Fusarium oxysporum f. sp. strigae (Fos) is the most renowned fungal biological control agent (BCA) for specifically and significantly tackling S. hermonthica under agricultural systems. Field surveys, however, have revealed the inconsistent effectiveness of Fos isolates against S. hermonthica in differing zones of SSA (i.e., West Africa, East Africa). This daunting phenomenon is a critical challenge that affects Fos reliability and deters its use for S. hermonthica management. The inconsistent effectiveness of Fos against S. hermonthica was presumably ascribed to the interactions that occur between the differing location-specific ecological factors of the pathosystem i.e., abiotic (climate, moisture, or soil physico-chemistry) or biotic (S. hermonthica, Fos isolate, or the plant microbiome). Without doubt, the diversity of a host or pathogen is a primary determinant of the innate susceptibility or virulence of the host or pathogen, respectively. In terms of S. hermonthica diversity, genomic variation of individuals, or regional genetic variation of the sampling zone, were the two major forces suspected. However, the important determiner out of the two forces was unknown. Besides, despite the suppression/death that Fos causes to S. hermonthica, the physiological damage S. hermonthica initiates to an infested cereal crop is mostly irreversible. Hence, in examining strategies for circumventing the main problem of Fos inconsistent effectiveness against S. hermonthica, and the physiological consequences of S. hermonthica on the host cereal crop, the integration of other (non-Fos inoculum) BCA were suggested as possible means for improving the efficiency of S. hermonthica biocontrol. For example, by utilizing a bioherbicide cocktail of Fos and plant growth promoting rhizobacteria (PGPR), or Striga seed germination-inhibiting fungal toxins. Apart from the popular reputation of PGPR in enhancing crop health and growth, certain PGPR strains (especially Bacillus subtilis isolate GB03) have been earlier reported for their highly-promising potential of antagonizing S. hermonthica development. Similarly, certain fungal extracellular metabolites (exometabolites), especially of Fusarium origin, were reported to completely inhibit S. hermonthica seed germination in vitro at very low concentrations (≤ 1 mM). Unfortunately, knowledge of the microbe (Fos)–microbe (PGPR) interaction, their localization and ecological niche, for enabling their expected synergistic impact of simultaneously suppressing S. hermonthica and enhancing the Striga-infected cereal crop biomass, was unknown. Also, it was unknown if highly potent/efficient Striga seed germination-inhibiting fungal exometabolites will consistently suppress S. hermonthica in planta. Thus, in the context of genetic diversity in S. hermonthica, the PhD study focused on gaining (molecular) insights into the inconsistent effectiveness of Fos against S. hermonthica; including the examination of some strategies for improving S. hermonthica biocontrol efficiency, precisely by integrating PGPR, or Striga seed germination-inhibiting Fusarium exometabolites, into a S. hermonthica biocontrol system. The first research examined the molecular genetic basis, underlying the variable susceptibility of S. hermonthica populations sampled from differing zones of SSA (West Africa, East Africa) to contrasting Fos isolates (Foxy-2, FK3). Regardless of sampling zone, the S. hermonthica populations displayed divergent susceptibility patterns to the Fos isolates i.e., a S. hermonthica class was susceptible to both Foxy-2 and FK3, while the other class was susceptible to either Foxy-2 or FK3. This manifestation correlated with nucleotide mutations at certain loci. Thus, genomic variation in S. hermonthica is a superior determinant of the inconsistent effectiveness of Fos isolates, rather than the S. hermonthica sampling zone. The second research examined the impact of coinoculating Fos and a PGPR (B. subtilis isolate GB03) into a S. hermonthica-sorghum parasitic system. Notwithstanding the colocalization of Fos and GB03 in common ecological niches of diseased S. hermonthica shoot (mainly in flavonoid-rich regions), GB03 thwarted Fos suppressive activity against S. hermonthica. Interestingly, a novel, alternative Fos entry route into S. hermonthica (through the trichome) was discovered. The coinoculation of Fos and GB03 presented no added advantage for S. hermonthica control. Finally, the third research screened a set of highly phytotoxic Fusarium exometabolites against S. hermonthica seed germination (in vitro) and incidence (in planta). This was to identify the most potent/efficient Fusarium exometabolite for S. hermonthica biocontrol. Among the tested exometabolites, diacetoxyscirpenol (DAS) was the most potent/efficient to completely suppress S. hermonthica both in vitro and in planta. Fos, however, did not produce DAS, due to underexpression of key genes necessary for Fusarium trichothecene biosynthesis. In conclusion, owing to the obligate outcrossing mating system in S. hermonthica, genomic variation is an inevitable phenomenon. This, therefore, plays a crucial role in the variable susceptibility of S. hermonthica to Fos. The newly discovered Fos (direct) entry route into S. hermonthica (trichome entry), elucidates a novel paradigm to the infection mechanism occurring under the S. hermonthica (host)–Fos (pathogen) interaction, in addition to the previously reported indirect, rhizosphere-transmission. Thus, this novel phyllosphere-transmission, paves the way for further research that exploit this alternative Fos infection route for better S. hermonthica biocontrol. Lastly, considering the potency and broadscale efficacy against diverse S. hermonthica populations, the exometabolite DAS could serve as a new agent for a more efficient S. hermonthica biocontrol. Though, further examination of its specific mode of action against the target weed (S. hermonthica), as opposed to non-target organisms, is required.
Root exudate fingerprint of Brachiaria humidicola reveals vanillin as a novel and effective nitrification inhibitor
(2023) Egenolf, Konrad; Schöne, Jochen; Conrad, Jürgen; Braunberger, Christina; Beifuß, Uwe; Arango, Jacobo; Rasche, Frank
Introduction: Biological Nitrification Inhibition (BNI) is defined as the plant-mediated control of soil nitrification via the release of nitrification inhibitors. BNI of Brachiaria humidicola (syn. Urochloa humidicola) has been mainly attributed to root-exuded fusicoccane-type diterpenes, e.g., 3-epi-brachialactone. We hypothesized, however, that BNI of B. humidicola is caused by an assemblage of bioactive secondary metabolites. Methods: B. humidicola root exudates were collected hydroponically, and metabolites were isolated by semi-preparative HPLC. Chemical structures were elucidated by HRMS as well as 1D and 2D NMR spectroscopy. Nitrification inhibiting potential of isolated metabolites was evaluated by a Nitrosomonas europaea based bioassay. Results and discussion: Besides previously described brachialactone isomers and derivatives, five phenol and cinnamic acid derivatives were identified in the root exudates of B. humidicola: 2-hydroxy-3-(hydroxymethyl)benzaldehyde, vanillin, umbelliferone and both trans- and cis-2,6-dimethoxycinnamic acid. Notably, vanillin revealed a substantially higher nitrification inhibiting activity than 3-epi-brachialactone (ED50 ∼ 12.5 μg·ml−1, ED80 ∼ 20 μg·ml−1), identifying this phenolic aldehyde as novel nitrification inhibitor (NI). Furthermore, vanillin exudation rates were in the same range as 3-epi-brachialactone (1–4 μg·h−1·g−1 root DM), suggesting a substantial contribution to the overall inhibitory activity of B. humidicola root exudates. In relation to the verification of the encountered effects within soils and considering the exclusion of any detrimental impact on the soil microbiome, the biosynthetic pathway of vanillin via the precursor phenylalanine and the intermediates p-coumaric acid/ferulic acid (precursors of further phenolic NI) might constitute a promising BNI breeding target. This applies not only to Brachiaria spp., but also to crops in general, owing to the highly conserved nature of these metabolites.