Fakultät Agrarwissenschaften

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Die Fakultät entwickelt in Lehre und Forschung nachhaltige Produktionstechniken der Agrar- und Ernährungswirtschaft. Sie erarbeitet Beiträge für den ländlichen Raum und zum Verbraucher-, Tier- und Umweltschutz.

Homepage: https://agrar.uni-hohenheim.de/

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A low-tech approach to mobilize nutrients from organic residues to produce bioponic stock solutions
(2024) Heintze, Sebastian; Beckett, Marc; Kriem, Lukas Simon; Germer, Jörn; Asch, Folkard; Liu, Guodong
Organic residues, as a nutrient source suitable of producing solutions for hydroponic crop production, have the potential to reduce the dependence on mineral fertilizers. Especially in remote and resource-constrained regions, organic residues might be the only option to produce hydroponic nutrient solutions. However, nutrient solutions made from organic residues, called bioponic solutions, are usually unbalanced in their nutrient composition, which leads to deficiencies and poor plant growth. This study aimed to experimentally develop a low-tech approach to produce bioponic stock solutions rich in NO3−, P, and K, to create a balanced bioponic solution. The mixed bioponic solution contained 58 mg L−1 NH4+-N, 43 mg L−1 NO3−-N, 50 mg L−1 PO43−-P, and 246 mg L−1 K+. This approach resulted in satisfactory levels of P, K and micronutrients. The solution was tested pure and spiked with Ca(NO3)2 on lettuce in comparison with a mineral Hoagland nutrient solution. Neither the bioponic nor the spiked bioponic solution achieved comparable lettuce yields to the Hoagland solution. The poor growth of the plants in the bioponic solution was attributed to an unfavorable NH4+:NO3− ratio, high microorganism load, and elevated pH levels. However, the approach of preparing bioponic stock solutions could be promising for future research into the production of balanced bioponic nutrient solutions from organic residues.
Challenges of green production of 2,5‐furandicarboxylic acid from bio‐derived 5‐hydroxymethylfurfural: Overcoming deactivation by concomitant amino acids
(2022) Neukum, Dominik; Baumgarten, Lorena; Wüst, Dominik; Sarma, Bidyut Bikash; Saraçi, Erisa; Kruse, Andrea; Grunwaldt, Jan‐Dierk
The oxidation of 5‐hydroxymethylfurfural (HMF) to 2,5‐furandicarboxylic acid (FDCA) is highly attractive as FDCA is considered as substitute for the petrochemically derived terephthalic acid. There are only few reports on the direct use of unrefined HMF solutions from biomass resources and the influence of remaining constituents on the catalytic processes. In this work, the oxidation of HMF in a solution as obtained from hydrolysis and dehydration of saccharides in chicory roots was investigated without intermediate purification steps. The amount of base added to the solution was critical to increase the FDCA yield. Catalyst deactivation occurred and was attributed to poisoning by amino acids from the bio‐source. A strong influence of amino acids on the catalytic activity was found for all supported Au, Pt, Pd, and Ru catalysts. A supported AuPd(2 : 1)/C alloy catalyst exhibited both superior catalytic activity and higher stability against deactivation by the critical amino acids.
Computational sizing of solar powered peanut oil extraction in Senegal using a synthetic load profile
(2024) Bonzi, Joévin Wiomou; Romuli, Sebastian; Diouf, Djicknoum; Piriou, Bruno; Meissner, Klaus; Müller, Joachim
This paper presents an approach for sizing a hybrid photovoltaic system for a small-scale peanut oil processing company (Yaye Aissatou, Passy) in rural Senegal using a synthetic load profile. In this study, a predictive model of the electrical load of a service-based plant oil processing company was developed through a diagnosis, to evaluate the extraction process. The mass and energy balance were measured, and the process was implemented into MATLAB Simulink. The simulated load profile was implemented in HOMER Pro and the characteristics of the most profitable hybrid systems were identified. The results showed that the lowest net present cost over 25 years was found with a PV/battery/grid-system with 18.6 kWp solar panels, 16 kWh of storage, and an initial investment of 20,019 €. Compared to a grid-only scenario, this solution reduces the net present cost from an initial 72,163 € to 31,603 €, the operating cost from 3675 € per year to 590 € per year, and the cost of energy from 0.29 to 0.13 €/kWh. The renewable fraction of the proposed system is 90.0 % while the expected payback period is 6.2 years. The study demonstrates the economic feasibility of using solar energy for plant oil processing.
Computing optimal allocation of trials to subregions in crop‐variety testing in case of correlated genotype effects
(2025) Prus, Maryna
The subject of this work is the allocation of trials to subregions in crop variety testing in the case of correlated genotype effects. A solution for computation of optimal allocations using the OptimalDesign package in R is proposed. The obtained optimal designs minimize linear criteria based on the mean squared error matrix of the best linear unbiased prediction of the genotype effects. The proposed computational approach allows for any kind of additional linear constraint on the designs. The results are illustrated by a real data example.
DeepCob: precise and high-throughput analysis of maize cob geometry using deep learning with an application in genebank phenomics
(2021) Kienbaum, Lydia; Correa Abondano, Miguel; Blas, Raul; Schmid, Karl
Background: Maize cobs are an important component of crop yield that exhibit a high diversity in size, shape and color in native landraces and modern varieties. Various phenotyping approaches were developed to measure maize cob parameters in a high throughput fashion. More recently, deep learning methods like convolutional neural networks (CNNs) became available and were shown to be highly useful for high-throughput plant phenotyping. We aimed at comparing classical image segmentation with deep learning methods for maize cob image segmentation and phenotyping using a large image dataset of native maize landrace diversity from Peru. Results: Comparison of three image analysis methods showed that a Mask R-CNN trained on a diverse set of maize cob images was highly superior to classical image analysis using the Felzenszwalb-Huttenlocher algorithm and a Window-based CNN due to its robustness to image quality and object segmentation accuracy (r = 0.99). We integrated Mask R-CNN into a high-throughput pipeline to segment both maize cobs and rulers in images and perform an automated quantitative analysis of eight phenotypic traits, including diameter, length, ellipticity, asymmetry, aspect ratio and average values of red, green and blue color channels for cob color. Statistical analysis identified key training parameters for efficient iterative model updating. We also show that a small number of 10–20 images is sufficient to update the initial Mask R-CNN model to process new types of cob images. To demonstrate an application of the pipeline we analyzed phenotypic variation in 19,867 maize cobs extracted from 3449 images of 2484 accessions from the maize genebank of Peru to identify phenotypically homogeneous and heterogeneous genebank accessions using multivariate clustering. Conclusions: Single Mask R-CNN model and associated analysis pipeline are widely applicable tools for maize cob phenotyping in contexts like genebank phenomics or plant breeding.
Digital agriculture: socio-technical-physical interactions and the transformation of the rural world(s)
(2024) Hidalgo Jaramillo, Francisco Javier; Regina, Birner
The social and environmental challenges that humanity faces today to produce food, fuel, and fibers in a sustainable and fair way call for a transformation. Digital agriculture has been embraced with much enthusiasm by many as the contour of such transformation. Proponents of these technologies, including international organizations as well as numerous researchers focused on innovations, describe this innovation as a paradigm shift. Associated with increased efficiencies and enhanced communication, digital agriculture is commonly depicted by these groups as the advent of a more sustainable and ‘smart’ future. Other groups, including grassroots organizations, socio-environmental activists, and critical scholars, on the other hand, see digital agriculture with skepticism and concern. They refer to the entrenchment of digital agriculture in productivist, capitalist, and extractivist forms of production, and a linkage with the consolidation of corporate power and state surveillance. Using a critical and systems approach, this thesis scrutinizes these arguments, examining the socio-technical transitions that emerge from agricultural digitalization, and discerns their societal and environmental consequences. This examination is relevant given that despite digital agriculture can transform the face of agricultural systems, it is not yet clear in what way. The emergent condition of digitalization requires this analysis to inform responsible governance of this innovation. Critical studies have made important contributions to this understanding. However, the complexity of digital agriculture calls for additional conceptual frameworks to be incorporated. The coffee production system has been selected as a case study in this thesis. This selection responds to the global scope of this system and the relevance that it represents for rural development. To set the picture: coffee is one of the most traded agricultural products in the world. Yet, more than 70% of it is produced by smallholder farmers who receive less than 10% of its final value. Meanwhile, coffee farmers experience manifold social and environmental challenges that threaten their livelihoods and the sustainability of the whole system. Poverty, power and information asymmetries, and climate change are among them. Against this background, this thesis takes the perspective of coffee as a crop, a cultural system, and a value chain. Following a qualitative research approach, the analysis is informed by a theoretical literature review and data from semi-structured interviews with developers and users of digital technologies. The thesis is divided into three studies (chapters 2, 3, and 4) which together present a critical analysis applied at three scales: 1) global, 2) value chain, and 3) local. Across these studies, three main socio-technical aspects of digital agriculture are addressed. First, global governance of digital agriculture and its consequences for farmers’ rights and capabilities. Second, the consequences of different technical assemblages for the sustainability of agricultural systems. Third, local forms of interaction with digital technologies. After presenting and introduction in Chapter 1, Chapter 2 presents a literature review on the political dynamics of digital agriculture. Drawing upon an emancipatory conceptualization of agency and sovereignty, this chapter is focused on describing two main forms of governance: governance through and governance of digital technologies in the context of agriculture. This description is followed by an analysis of the multiple effects of these two forms of governance on farmer’s sovereignty and agency. The analysis revealed that the governance of digital agriculture is an assemblage of multiple agencies of human and cyber agents (smart devices, automated machines, algorithms). Socio-technical interactions in this assemblage result simultaneously in sovereignty and agency gains and losses for farmers - a complex set of power transactions in which farmers participate many times inadvertently. Together with oppressive forms of governance associated with corporate technological lock-in, data extractivism, and a surveilling state, there is evidence also of a democratic facet of digitalization. This facet is integrated by open-collaborative networks, data cooperatives, cyberactivism, and open-source software. With this analysis, the study aimed to understand how the political position of farmers is affected by digitalization, understanding that this process is occurring in a context of structural power imbalance. A socio-technical perspective is applied in Chapter 3 to explore 20 digital tools designed for the coffee value chain, examining the pathways toward sustainability (environmental, social, and economic) promoted by these tools. The socio-technical perspective mainly proposes that social and technical systems shape each other in reciprocal interactions. Building on this idea, the chapter examines the technical attributes of these tools (functionality, technologies included, operation rules, information flow). Subsequently, it analyzes the consequences of these attributes in terms of three broad social dynamics: 1) knowledge and value systems represented, 2) power structures, and 3) possibilities for using these tools effectively. The forms in which these social dynamics are shaped by these tools, in turn, yield specific sustainability outcomes. These include the kind of production systems that are endorsed - and not endorsed -, the access to these technologies and their benefits, and the way in which social inequalities and power asymmetries are addressed - or not addressed -. The data for this analysis comes from interviews with 15 developers of these tools and secondary information. The analysis shows that technical attributes play a fundamental role in directing the kinds of pathways toward sustainability that are made available for agricultural systems. Additionally, it shows that in some cases, rather than a revolution, digital agriculture can look like business as usual but tweaked. Chapter 4 presents a local perspective on digitalization. Using data from interviews with 73 households in two selected coffee growing communities in Colombia, this chapter explores how they engage with digital technologies. The study parts from the idea that important reality-design gaps in digital agriculture result from a lack of understanding and inclusion of local worldviews around digital technologies and farming. Amartya Sen’s capabilities approach was adopted as the conceptual framework for the analysis. This framework posits that resources only become assets when they can be used by individuals to accomplish the life they value. For that reason, the analysis in this chapter was focused on first, understanding the elements that configure a valuable life for these communities, and next, understanding how they use digital technologies to support the accomplishment of this life. The underlying values of this local process of technological appropriation were compared with the values represented by broader narratives of digital agriculture. This offered a picture of the negotiations and tensions that occur when contrasting visions of farming, digitalization, and a desirable future, interface. Drawing upon a relational perspective, the local appropriation process is characterized by multiple negotiations between farmers’ personal and collective goals, situated knowledge, institutional programs, and the agency of non-humans (e.g. land, plants, animals, machines). From these interactions emerge distinctive forms of digitalization and non-digitalization. This process of local appropriation revealed the critical view of farmers and agency, for example, by following a digitalization pathway that profoundly diverges from dominant imaginaries and discourses around digital agriculture. By applying a systems approach and by integrating three frameworks into critical scholarship - (1) emancipatory conceptualization of agency and sovereignty, (2) Sen´s capabilities approach, and (3) a relational approach - this thesis presents evidence of the complexity of socio-technical-physical interactions that lead to certain broad-mainstream and local-everyday digitalization pathways. These pathways, in turn, present particular societal consequences, such as the kind of agricultural worlds that are made possible, the interests that are represented in them, and the possibilities of participation for different social groups. More than a single trajectory, digital agriculture is a space of multiplicity and permanent emergence, also for reproducing current – not necessarily sustainable - models. For this reason, this thesis calls for abandoning notions of immutability, universality, and uniformity in development discourses, perspectives of rurality, and the generation of new technologies. Instead, it proposes to integrate a critical and systems-relational perspective into inclusionary innovation research and practice.
Effects of different ground segmentation methods on the accuracy of UAV-based canopy volume measurements
(2024) Han, Leng; Wang, Zhichong; He, Miao; He, Xiongkui
The nonuniform distribution of fruit tree canopies in space poses a challenge for precision management. In recent years, with the development of Structure from Motion (SFM) technology, unmanned aerial vehicle (UAV) remote sensing has been widely used to measure canopy features in orchards to balance efficiency and accuracy. A pipeline of canopy volume measurement based on UAV remote sensing was developed, in which RGB and digital surface model (DSM) orthophotos were constructed from captured RGB images, and then the canopy was segmented using U-Net, OTSU, and RANSAC methods, and the volume was calculated. The accuracy of the segmentation and the canopy volume measurement were compared. The results show that the U-Net trained with RGB and DSM achieves the best accuracy in the segmentation task, with mean intersection of concatenation (MIoU) of 84.75% and mean pixel accuracy (MPA) of 92.58%. However, in the canopy volume estimation task, the U-Net trained with DSM only achieved the best accuracy with Root mean square error (RMSE) of 0.410 m 3 , relative root mean square error (rRMSE) of 6.40%, and mean absolute percentage error (MAPE) of 4.74%. The deep learning-based segmentation method achieved higher accuracy in both the segmentation task and the canopy volume measurement task. For canopy volumes up to 7.50 m 3 , OTSU and RANSAC achieve an RMSE of 0.521 m 3 and 0.580 m 3 , respectively. Therefore, in the case of manually labeled datasets, the use of U-Net to segment the canopy region can achieve higher accuracy of canopy volume measurement. If it is difficult to cover the cost of data labeling, ground segmentation using partitioned OTSU can yield more accurate canopy volumes than RANSAC.
Etablierung und Vernetzung digital-gestützter Systeme auf Pferdebetrieben unter Berücksichtigung der betriebswirtschaftlichen Optimierung
(2024) Speidel, Linda Thurid; Dickhöfer, Uta
Das Management eines pferdehaltenden Betriebs umfasst eine Vielzahl arbeitswirtschaftlicher Herausforderungen. Dazu zählen unter anderem die zeitintensiven Arbeitsabläufe, das notwendige Kundenmanagement in Pensions- und Schulpferdebetrieben sowie die begrenzte Verfügbarkeit von Fachkräften. Auf Ackerbau- und Veredelungsbetrieben wird der Nutzen der Digitalisierung bereits wahrgenommen, da deren Einsatz unter anderem Potenzial zur Zeitersparnis und Arbeitserleichterung bietet. Obgleich des genannten Potenzials sind Pferdebetriebe bisher wenig digitalisiert und technisiert, die Grundversorgung erfolgt meist manuell. Im Rahmen dieser, im Projekt „Digitale Wertschöpfungsketten für eine nachhaltige kleinstrukturiert Landwirtschaft“ (DiWenkLa) angefertigten, Forschungsarbeit wurde daher untersucht, welche Möglichkeiten der Digitalisierung bisher genutzt werden und unter welchen Voraussetzungen die einzelnen Systeme in Pferdebetrieben etabliert werden können. Des Weiteren wurde analysiert, welche Auswirkungen der Einsatz dieser Systeme auf den Arbeitszeitbedarf im Pferdebetrieb hat und welche Informationen über Schnittstellen zwischen den Systemen ausgetauscht werden können. Dafür wurden von März 2020 bis Oktober 2023 Experteninterviews, (Arbeitszeit-)Beobachtungen und Online-Befragungen durchgeführt. Zunächst wurden die vorhandenen Möglichkeiten der digitalen Technisierung auf Pferdebetrieben in der Fütterung von Rau- und Krippenfutter, der Entmistung und Einstreu, der Gesundheits- und Sicherheitsüberwachung sowie der Kommunikation und dem Betriebsmanagement untersucht. Der Schwerpunkt lag auf den Voraussetzungen, die erfüllt sein müssen, um ausgewählte digital-technische Systeme auf den Betrieben zu etablieren. Zu diesem Zweck wurden Beobachtungen und Befragungen bei pferdehaltenden Betrieben (N=1235) und den Kooperationspartnern aus der Industrie des Projekts DiWenkLa durchgeführt. Die Ergebnisse zeigen, dass die Einbindung digital-technischer Systeme von der Investitionsbereitschaft der Betriebsleitenden, der stabilen Internetverbindung, einer verfügbaren Stromversorgung in den Stallgebäuden (Steckdosen) und dem vorhandenen Haltungssystem (z. B. Einzel- oder Gruppenhaltung sowie Gliederung der Haltung in Funktionsbereiche) abhängt. Auf den an einer Online-Befragung teilnehmenden Pferdebetrieben (N=451) wurden Kameras zur Sicherheits- (30,8 %) und Gesundheitsüberwachung (22,6 %) sowie Software für die Kundenkommunikation (24,8 %) und das Betriebsmanagement (13,7 %) eingesetzt. Die automatisierte Fütterung von Krippenfutter (9,3 %) und Raufutter (7,3 %) war selten vorhanden. Eine Gliederung der Haltung in Funktionsbereiche führte zu einem vermehrten Einsatz digital-technischer Systeme. Als Gründe gegen den Einsatz neuer digital-technischer Systeme wurden von den 207 teilnehmenden Betriebsleitenden die fehlenden Finanzmittel, der unbekannte wirtschaftliche Nutzen sowie der Kontaktverlust zu den Tieren genannt. In Anlehnung an die vorliegenden Ergebnisse erscheint eine erneute Erhebung der vorhandenen Systeme auf Pferdebetrieben sinnvoll, um etwaige Veränderungen im Verlauf der Zeit abzubilden und die Gründe für die Investition in neue digital-technische Systeme zu ermitteln. Des Weiteren sollte untersucht werden, ob Einsteller bei einem höheren Digitalisierungsgrad im Pferdebetrieb bereit sind, einen höheren Pensionspreis zu bezahlen. Zu diesem Zweck könnte die Zahlungsbereitschaft beim Einsatz von z. B. Futterautomation und intelligenten Kameras zur Gesundheitsüberwachung abgefragt werden. Des Weiteren wurde analysiert, welche betriebswirtschaftlichen Vorteile die auf den Pferdebetrieben etablierten, digital gesteuerten Systeme mit sich bringen können. Dazu wurden die möglichen Auswirkungen der Digitalisierung auf den Arbeitszeitbedarf für verschiedene Arbeitsabläufe wie die Fütterung, Entmistung und Hütesicherheit untersucht. Dies wurde durch Zeiterfassungen mit und ohne den Einsatz der Systeme sowie mit Hilfe von Online-Befragungen (N=1014) und Experteninterviews (N=16) realisiert. Die Ergebnisse der Untersuchungen zeigen bei der Einzelhaltung von Pferden eine potenzielle Arbeitszeitersparnis in der Fütterung und Entmistung von bis zu 65 % durch eine automatisierte Fütterung von Rau- und Krippenfutter und den Einsatz von mobiler Technik, wie beispielsweise einem Hoflader. Zudem kann der Einsatz dieser Systeme auch dazu führen, dass die benötigte Arbeitszeit in anderen Arbeitsabläufen sinkt. Ein Beispiel hierfür ist der Einsatz einer automatisierten Fütterung, welcher zu einer geringeren Arbeitszeit in der Kundenkommunikation führte. Dies wurde in den durchgeführten Datenerhebungen dadurch begründet, dass gewünschte Änderungen in der Rationsgestaltung automatisiert erfolgen und somit nicht persönlich kommuniziert werden müssen. Darüber hinaus lassen sich durch eine digitale Absprache und die Dokumentation wesentlicher Arbeitsschritte und Änderungen in den Abläufen sowie Kundenwünschen Fehler reduzieren und Missverständnisse vermeiden. Auf Basis der Ergebnisse sollten die Abfragen der Arbeitszeitbedarfe der Arbeitsabläufe mit exakten und vorgegebenen Werten wiederholt und teilweise ergänzt werden. Dies betrifft z. B. den Zeitbedarf für das Betriebsmanagement, die Tierkontrolle und den Weidegang. Dadurch können die vorhandenen Kalkulationsgrundlagen aktualisiert und das Bewusstsein der Betriebsleitenden für teils unbeachteten Arbeitszeitaufwand geschärft werden. Dieser kann wiederum durch den Einsatz von digital-technischen Systemen reduziert werden. Darüber hinaus wurde ein Konzept für eine Schnittstelle für digitale Systeme für Pferdebetriebe entwickelt, um den Datenaustausch zwischen Systemen zu vereinfachen und somit die Übersichtlichkeit der verschiedenen Informationen aus den eingesetzten Technologien zu optimieren sowie zusätzliche Zeitersparnis zu gewährleisten. Dazu wurden mittels Experteninterviews (N=20 Experten) die auszutauschenden Informationen zwischen Systemen für die Fütterung, die Entmistung und Einstreu, die Gesundheits- und Sicherheitsüberwachung sowie das Betriebsmanagement und die Kommunikation identifiziert, um eine verbesserte Übersicht für die Betriebsleitenden zu gewährleisten. In diesem Kontext wurde der Datenaustausch zwischen Futterautomationen und Kommunikationssoftware als besonders relevant hervorgehoben. Je nach Bedarf können die Informationen aus dem Datenaustausch transparent an die Kunden (z. B. Einsteller) weitergegeben werden. Eine Online-Befragung ergab, dass die Mehrheit (57,2 %) aller Teilnehmenden (N=451) Interesse an einer Vernetzung der Systeme zeigt. In zukünftigen Untersuchungen könnten zum einen die Gründe für das Interesse an einer Vernetzung analysiert werden, da bisher lediglich die Gegenposition untersucht wurde (d.h. Gründe gegen das Interesse an der Vernetzung). Zum anderen könnte die Einbindung weiterer Systeme neben den genannten geprüft werden, insbesondere die Anbindung der vorhandenen Hardware (z. B. Solarien, Aquatrainer) an das Internet und die (standardisierte) Programmierung der Schnittstelle, um z. B. eine unkomplizierte und transparente Abrechnung der Nutzung zu ermöglichen. Die Etablierung und Vernetzung digital-technischer Systeme in Pferdebetrieben ist bei erfüllbaren Voraussetzungen als sinnvoll anzusehen, da sie eine Arbeitszeiteinsparung generieren, eine Entlastung der Arbeitskräfte ermöglichen, die Kommunikation verbessern und das Betriebsmanagement sowie die Sicherheits- und Gesundheitskontrolle der Tiere vereinfachen. Diese Faktoren sind neben der Beachtung und Verbesserung des Tierwohls für eine nachhaltige, zukunftsfähige Pferdehaltung unabdingbar.
Fed-batch bioreactor cultivation of Bacillus subtilis using vegetable juice as an alternative carbon source for lipopeptides production: a shift towards a circular bioeconomy
(2024) Gugel, Irene; Vahidinasab, Maliheh; Benatto Perino, Elvio Henrique; Hiller, Eric; Marchetti, Filippo; Costa, Stefania; Pfannstiel, Jens; Konnerth, Philipp; Vertuani, Silvia; Manfredini, Stefano; Hausmann, Rudolf; Gudiña, Eduardo
In a scenario of increasing alarm about food waste due to rapid urbanization, population growth and lifestyle changes, this study aims to explore the valorization of waste from the retail sector as potential substrates for the biotechnological production of biosurfactants. With a perspective of increasingly contributing to the realization of the circular bioeconomy, a vegetable juice, derived from unsold fruits and vegetables, as a carbon source was used to produce lipopeptides such as surfactin and fengycin. The results from the shake flask cultivations revealed that different concentrations of vegetable juice could effectively serve as carbon sources and that the fed-batch bioreactor cultivation strategy allowed the yields of lipopeptides to be significantly increased. In particular, the product/substrate yield of 0.09 g/g for surfactin and 0.85 mg/g for fengycin was obtained with maximum concentrations of 2.77 g/L and 27.53 mg/L after 16 h, respectively. To conclude, this study provides the successful fed-batch cultivation of B. subtilis using waste product as the carbon source to produce secondary metabolites. Therefore, the consumption of agricultural product wastes might be a promising source for producing valuable metabolites which have promising application potential to be used in several fields of biological controls of fungal diseases.
Food informatics - Review of the current state-of-the-art, revised definition, and classification into the research landscape
(2021) Krupitzer, Christian; Stein, Anthony
Background: The increasing population of humans, changing food consumption behavior, as well as the recent developments in the awareness for food sustainability, lead to new challenges for the production of food. Advances in the Internet of Things (IoT) and Artificial Intelligence (AI) technology, including Machine Learning and data analytics, might help to account for these challenges. Scope and Approach: Several research perspectives, among them Precision Agriculture, Industrial IoT, Internet of Food, or Smart Health, already provide new opportunities through digitalization. In this paper, we review the current state-of-the-art of the mentioned concepts. An additional concept is Food Informatics, which so far is mostly recognized as a mainly data-driven approach to support the production of food. In this review paper, we propose and discuss a new perspective for the concept of Food Informatics as a supportive discipline that subsumes the incorporation of information technology, mainly IoT and AI, in order to support the variety of aspects tangent to the food production process and delineate it from other, existing research streams in the domain. Key Findings and Conclusions: Many different concepts related to the digitalization in food science overlap. Further, Food Informatics is vaguely defined. In this paper, we provide a clear definition of Food Informatics and delineate it from related concepts. We corroborate our new perspective on Food Informatics by presenting several case studies about how it can support the food production as well as the intermediate steps until its consumption, and further describe its integration with related concepts.
Functionality of the Na+-translocating NADH:quinone oxidoreductase and quinol:fumarate reductase from Prevotella bryantii inferred from homology modeling
(2024) Hau, Jann-Louis; Schleicher, Lena; Herdan, Sebastian; Simon, Jörg; Seifert, Jana; Fritz, Günter; Steuber, Julia
Members of the family Prevotellaceae are Gram-negative, obligate anaerobic bacteria found in animal and human microbiota. In Prevotella bryantii , the Na + -translocating NADH:quinone oxidoreductase (NQR) and quinol:fumarate reductase (QFR) interact using menaquinone as electron carrier, catalyzing NADH:fumarate oxidoreduction. P. bryantii NQR establishes a sodium-motive force, whereas P. bryantii QFR does not contribute to membrane energization. To elucidate the possible mode of function, we present 3D structural models of NQR and QFR from P. bryantii to predict cofactor-binding sites, electron transfer routes and interaction with substrates. Molecular docking reveals the proposed mode of menaquinone binding to the quinone site of subunit NqrB of P. bryantii NQR. A comparison of the 3D model of P. bryantii QFR with experimentally determined structures suggests alternative pathways for transmembrane proton transport in this type of QFR . Our findings are relevant for NADH-dependent succinate formation in anaerobic bacteria which operate both NQR and QFR.
Genetic architecture underlying the expression of eight α-amylase trypsin inhibitors
(2021) El Hassouni, Khaoula; Sielaff, Malte; Curella, Valentina; Neerukonda, Manjusha; Leiser, Willmar; Würschum, Tobias; Schuppan, Detlef; Tenzer, Stefan; Longin, C. Friedrich H.
Amylase trypsin inhibitors (ATIs) are important allergens in baker’s asthma and suspected triggers of non-celiac wheat sensitivity (NCWS) inducing intestinal and extra-intestinal inflammation. As studies on the expression and genetic architecture of ATI proteins in wheat are lacking, we evaluated 149 European old and modern bread wheat cultivars grown at three different field locations for their content of eight ATI proteins. Large differences in the content and composition of ATIs in the different cultivars were identified ranging from 3.76 pmol for ATI CM2 to 80.4 pmol for ATI 0.19, with up to 2.5-fold variation in CM-type and up to sixfold variation in mono/dimeric ATIs. Generally, heritability estimates were low except for ATI 0.28 and ATI CM2. ATI protein content showed a low correlation with quality traits commonly analyzed in wheat breeding. Similarly, no trends were found regarding ATI content in wheat cultivars originating from numerous countries and decades of breeding history. Genome-wide association mapping revealed a complex genetic architecture built of many small, few medium and two major quantitative trait loci (QTL). The major QTL were located on chromosomes 3B for ATI 0.19-like and 6B for ATI 0.28, explaining 70.6 and 68.7% of the genotypic variance, respectively. Within close physical proximity to the medium and major QTL, we identified eight potential candidate genes on the wheat reference genome encoding structurally related lipid transfer proteins. Consequently, selection and breeding of wheat cultivars with low ATI protein amounts appear difficult requiring other strategies to reduce ATI content in wheat products.
Governance of land rehabilitation and remediation: case studies of Ghana’s small-scale mining sector
(2024) Adu-Baffour, Ferdinand Ababio; Birner, Regina
The artisanal and small-scale mining (ASM) sector is a complex and evolving industry that presents unique challenges within the global resource landscape. Despite its traditional labeling as artisanal, ASM operations are increasingly becoming mechanized, utilizing heavy machinery and hazardous chemicals such as mercury and cyanide for mineral extraction. Concurrently, the informal nature of most ASM operations limits effective top-down regulatory enforcements due to governance challenges. These developments have led to wide spreads of degraded, contaminated and abandoned rural community lands which also serve as valuable agricultural and forest lands for inhabitants of affected mining communities. While the existing literature has extensively analyzed the impacts of these developments on local, national, and global economies, ecologies, health, and welfare, there remains a notable gap in understanding the governance of rehabilitating and remediating affected environments post-mineral extraction. Furthermore, phytoremediation – a biological innovation which can help remediate contaminated sites and address the problem of soil degradation and erosion, with reported economic and environmental benefits – has only seen very limited global commercial adoption. In regions where traditional remediation approaches are financially untenable, like in the Global South, however, phytoremediation is argued to be a suitable and viable solution towards a greener future for remediation and environmental restoration. This thesis aims to address the knowledge gaps pertaining to the governance of rehabilitating and remediating affected environments affected by mineral extraction in the artisanal and small-scale mining (ASM) sector. Specifically, it focuses on systematically investigating the governance challenges in ASM, exploring community-based solutions for sustainable land restoration, and proposing a framework for the broader-based application of phytoremediation to address land contamination in the small-scale gold mining sector in Ghana. These research objectives are structured around three chapters, with the first two focusing on empirical case studies and the last chapter serving as a review of scientific and grey literature, as well as project reports on land rehabilitation and phytoremediation. Chapter 2, which addresses the first objective, delves into the obstacles hindering the implementation of the legal framework for artisanal small-scale mining (ASM) in Ghana. The first part conducts an institutional analysis of the legal and political framework governing Ghana’s small scale mining sector, with a particular focus on its implications for post-mined land rehabilitation efforts. This is followed by an assessment of the practical application of the legal framework in the context of small-scale gold mining (ASGM) value chain, using the Process Net-Mapping tool along with stakeholder interviews. The study reveals outdated legislation, formal licensing bureaucracies, land tenure issues, and ineffective collaboration among stakeholders as major bottlenecks. Drawing on these insights, the chapter discusses the broader implications of the findings for the effective running of the ASGM value chain and recommends, among other things, the adoption of collaborative governance systems, like co-management, to ensure sustainability. Chapter 3, which addresses the second objective, examines community-based solutions for sustainable mined land restoration through a case study of an NGO-initiated project in five active mining communities in Ghana's Amansie West district. The chapter utilizes a combination of qualitative methods including the participatory Net-Mapping tool to explore conditions under which local communities would engage in restoration efforts without financial incentives, revealing community support, using communal labor, dependent on factors like land tenure arrangements and local leadership influence. The study underscores the potential of community-led efforts for land rehabilitation, emphasizing the role of social networks, norms, and land tenure structures. Chapter 4, which addresses the third objective, introduces a conceptual framework for the effective and sustainable application of phytoremediation to clean contaminated lands resulting from mining activities. This is the result of insights drawn from existing phytoremediation literature, including case studies where the field application or/and commercialization of phytoremediation has been successful, and lessons gleaned from other real-world applications of the technology. The framework encompasses technical considerations across the phytoremediation process and identifies the socio-cultural, economic, political, and institutional conditions necessary for successful large-scale implementation. The paper provides valuable guidance for regions seeking to leverage phytoremediation to benefit society and the environment. In conclusion, this thesis contributes to understanding the challenges facing the ASM sector and proposes innovative solutions to address governance issues, promote community-based land restoration, and facilitate the scaling of phytoremediation initiatives for sustainable development in the mining sector, particularly in developing regions. The holistic approach advocated in this thesis underscores the importance of legal reforms tailored to the constantly evolving ASM sector, stakeholder collaboration, adaptive governance systems, and community engagement to effectively navigate the intricate ASM landscape and maximize its beneficial effects on local livelihoods and development worldwide.
Haemotrophic mycoplasmas infecting pigs: a review of the current knowledge
(2024) Ade, Julia; Eddicks, Matthias; Ritzmann, Mathias; Hoelzle, Katharina; Hoelzle, Ludwig E.; Stadler, Julia; Highland, Margaret A.
Haemotrophic mycoplasmas (haemoplasmas) are a group of highly specific and adapted bacteria. Three different haemoplasma species in pigs are known to date: Mycoplasma ( M .) suis , M. parvum and ‘ Candidatus ( Ca .) M. haemosuis’. Even though these bacteria have been known in pig farming for a long time, it is difficult to draw general conclusions about the relevance of their infections in pigs. This review summarizes the current knowledge on the three porcine haemoplasma species with regards to clinical and pathological descriptions, pathobiology, epidemiology and diagnostics as well as prevention and therapy. Overall, it is clear that considerably more data are available for M. suis than for the other two species, but generally, porcine haemoplasmas were found to be highly prevalent all over the world. Mycoplasma suis is the most virulent species, causing acute infectious anaemia in pigs (IAP), whereas M. parvum usually results in chronic and subclinical infections associated with performance losses. Little is known about the clinical significance of the recently discovered third porcine species ‘ Ca . M. haemosuis’. So far, the described pathogenic mechanisms mainly include direct destruction of erythrocytes via adhesion, invasion, eryptosis and nutrient scavenging, indirect erythrocyte lysis due to immune-mediated events and immune dysregulation processes. A review of published diagnostic data confirms PCR assays as the current standard method, with various cross-species and species-specific protocols. Overall, there is a need for further examination to obtain valuable insights for practical application, specifically regarding the importance of subclinical infections in naturally infected animals. An essential requirement for this will be to gain a more comprehensive understanding of the mechanisms operating between the host and the pathogen.
Hemotrophic mycoplasmas - vector transmission in livestock
(2024) Arendt, Mareike; Stadler, Julia; Ritzmann, Mathias; Ade, Julia; Hoelzle, Katharina; Hoelzle, Ludwig E.; Dozois, Charles M.
Hemotrophic mycoplasmas (HMs) are highly host-adapted and specialized pathogens infecting a wide range of mammals including farm animals, i.e., pigs, cattle, sheep, and goats. Although HMs have been known for over 90 years, we still do not know much about the natural transmission routes within herds. Recently, it has been repeatedly discussed in publications that arthropod vectors may play a role in the transmission of HMs from animal to animal. This is mainly since several HM species could be detected in different potential arthropod vectors by PCR. This review summarizes the available literature about the transmission of bovine, porcine, ovine, and caprine HM species by different hematophagous arthropod vectors. Since most studies are only based on the detection of HMs in potential vectors, there are rare data about the actual vector competence of arthropods. Furthermore, there is a need for additional studies to investigate, whether there are biological vectors in which HMs can multiply and be delivered to new hosts.
How many checks are needed per cycle in a plant breeding or variety testing programme?
(2025) Piepho, Hans‐Peter; Laidig, Friedrich
Check varieties are used in plant breeding and variety testing for a number of reasons. One important use of checks is to provide connectivity between years, which facilitates comparison among genotypes of interest that are tested in different years. When long‐term data are available, such comparisons allow an assessment of realized genetic gain (RGG). Here, we consider the question of how many check varieties are needed per cycle for a reliable assessment of RGG. We propose an approach that makes use of variance component estimates for relevant random effects in a linear mixed model and plugs them into an analysis of dummy datasets set up to represent the design options being considered. Our results show that it is useful to employ a larger number of checks and to keep the replacement rate low. Furthermore, there is intercycle information to be recovered, especially when there are few checks and replacement rates are high, so modelling the cycle main effect as random pays off.
Hybrid transcriptome sequencing approach improved assembly and gene annotation in Cynara cardunculus (L.)
(2020) Puglia, Giuseppe D.; Prjibelski, Andrey D.; Vitale, Domenico; Bushmanova, Elena; Schmid, Karl J.; Raccuia, Salvatore A.
Background: The investigation of transcriptome profiles using short reads in non-model organisms, which lack of well-annotated genomes, is limited by partial gene reconstruction and isoform detection. In contrast, long-reads sequencing techniques revealed their potential to generate complete transcript assemblies even when a reference genome is lacking. Cynara cardunculus var. altilis (DC) (cultivated cardoon) is a perennial hardy crop adapted to dry environments with many industrial and nutraceutical applications due to the richness of secondary metabolites mostly produced in flower heads. The investigation of this species benefited from the recent release of a draft genome, but the transcriptome profile during the capitula formation still remains unexplored. In the present study we show a transcriptome analysis of vegetative and inflorescence organs of cultivated cardoon through a novel hybrid RNA-seq assembly approach utilizing both long and short RNA-seq reads. Results: The inclusion of a single Nanopore flow-cell output in a hybrid sequencing approach determined an increase of 15% complete assembled genes and 18% transcript isoforms respect to short reads alone. Among 25,463 assembled unigenes, we identified 578 new genes and updated 13,039 gene models, 11,169 of which were alternatively spliced isoforms. During capitulum development, 3424 genes were differentially expressed and approximately two-thirds were identified as transcription factors including bHLH, MYB, NAC, C2H2 and MADS-box which were highly expressed especially after capitulum opening. We also show the expression dynamics of key genes involved in the production of valuable secondary metabolites of which capitulum is rich such as phenylpropanoids, flavonoids and sesquiterpene lactones. Most of their biosynthetic genes were strongly transcribed in the flower heads with alternative isoforms exhibiting differentially expression levels across the tissues. Conclusions: This novel hybrid sequencing approach allowed to improve the transcriptome assembly, to update more than half of annotated genes and to identify many novel genes and different alternatively spliced isoforms. This study provides new insights on the flowering cycle in an Asteraceae plant, a valuable resource for plant biology and breeding in Cynara and an effective method for improving gene annotation.
Impacts of different light spectra on CBD, CBDA and terpene concentrations in relation to the flower positions of different cannabis Sativa L. strains
(2022) Reichel, Philipp; Munz, Sebastian; Hartung, Jens; Kotiranta, Stiina; Graeff-Hönninger, Simone
Cannabis is one of the oldest cultivated plants, but plant breeding and cultivation are restricted by country-specific regulations. The plant has gained interest due to its medically important secondary metabolites, cannabinoids and terpenes. Besides biotic and abiotic stress factors, secondary metabolism can be manipulated by changing light quality and intensity. In this study, three morphologically different cannabis strains were grown in a greenhouse experiment under three different light spectra with three real light repetitions. The chosen light sources were as follows: a CHD Agro 400 ceramic metal-halide lamp with a sun-like broad spectrum and an R:FR ratio of 2.8, and two LED lamps, a Solray (SOL) and an AP67, with R:FR ratios of 13.49 and 4, respectively. The results of the study indicated that the considered light spectra significantly influenced CBDA and terpene concentrations in the plants. In addition to the different light spectra, the distributions of secondary metabolites were influenced by flower positions. The distributions varied between strains and indicated interactions between morphology and the chosen light spectra. Thus, the results demonstrate that secondary metabolism can be artificially manipulated by the choice of light spectrum, illuminant and intensity. Furthermore, the data imply that, besides the cannabis strain selected, flower position can have an impact on the medicinal potencies and concentrations of secondary metabolites.
New insights into the phylogeny of the A.Br.161 (“A.Br.Heroin”) clade of Bacillus anthracis
(2024) Antwerpen, Markus; Beyer, Wolfgang; Grass, Gregor; Anderson, Deborah
Bacillus anthracis is a rare but highly dangerous zoonotic bacterial pathogen. At the beginning of this century, a new manifestation of the disease, injectional anthrax, emerged as a result of recreational heroin consumption involving contaminated drugs. The organisms associated with this 13-year-lasting outbreak event in European drug consumers were all grouped into the canonical single-nucleotide polymorphism (canSNP) clade A-branch (A.Br.) 161 of B. anthracis . Related clade A.Br.161 strains of B. anthracis not associated with heroin consumption have also been identified from different countries, mostly in Asia. Because of inadvertent spread by anthropogenic activities, other strains of this A.Br.161 lineage were, however, isolated from several countries. Thus, without additional isolates from this clade, its origin of evolution or its autochthonous region remains obscure. Here, we genomically characterized six new A.Br.161 group isolates, some of which were from Iran, with others likely historically introduced into Germany. All the chromosomes of these isolates could be grouped into a distinct sub-clade within the A.Br.161 clade. This sub-clade is separated from the main A.Br.161 lineage by a single SNP. We have developed this SNP into a PCR assay facilitating the future attribution of strains to this group.
Optimum breeding strategies using genomic and phenotypic selection for the simultaneous improvement of two traits
(2021) Marulanda, Jose J.; Mi, Xuefei; Utz, H. Friedrich; Melchinger, Albrecht E.; Würschum, Tobias; Longin, C. Friedrich H.
Selection indices using genomic information have been proposed in crop-specific scenarios. Routine use of genomic selection (GS) for simultaneous improvement of multiple traits requires information about the impact of the available economic and logistic resources and genetic properties (variances, trait correlations, and prediction accuracies) of the breeding population on the expected selection gain. We extended the R package “selectiongain” from single trait to index selection to optimize and compare breeding strategies for simultaneous improvement of two traits. We focused on the expected annual selection gain (ΔGa) for traits differing in their genetic correlation, economic weights, variance components, and prediction accuracies of GS. For all scenarios considered, breeding strategy GSrapid (one-stage GS followed by one-stage phenotypic selection) achieved higher ΔGa than classical two-stage phenotypic selection, regardless of the index chosen to combine the two traits and the prediction accuracy of GS. The Smith–Hazel or base index delivered higher ΔGa for net merit and individual traits compared to selection by independent culling levels, whereas the restricted index led to lower ΔGa in net merit and divergent results for selection gain of individual traits. The differences among the indices depended strongly on the correlation of traits, their variance components, and economic weights, underpinning the importance of choosing the selection indices according to the goal of the breeding program. We demonstrate our theoretical derivations and extensions of the R package “selectiongain” with an example from hybrid wheat by designing indices to simultaneously improve grain yield and grain protein content or sedimentation volume.

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