Gamma-ray spectrometry as auxiliary information for soil mapping and its application in research for development

Sustainable yield increase is desperately needed for enhancing global food security, in particular, in Sub-Saharan Africa. There population growth and resulting land degradation accompany with extreme weather events. As a consequence, famines frequently occur. For planning result-oriented agricultural research for development (R4D) like in the Trans-Sec project (www.trans-sec.org), in which this thesis was embedded, local environmental, as well as social realities must be taken into account prior to any cropping experiment. Only this way, cost-efficient and adapted solutions for local subsistence farmers, but also conclusive outcomes for researchers, can be obtained. For this purpose, methods that work quick and cost-efficient are a prerequisite. In this respect, gamma-ray spectrometry as rapid soil survey method is reviewed in the first part of this thesis. Soil or geological exploration are easily accomplishable, in either airborne (with helicopters, airplanes or drones) or proximal (stationary or on-the-go) surveys. Gamma decays of the naturally occurring isotopes 40-potassium (40K), 238-uranium (238U) and 232-thorium (232Th) that appear in sufficient amounts and decay energies for field measurements are counted per time. The counts are then transferred to the respective element contents. Water and soil organic matter attenuate gamma signals, on one hand hampering signal interpretation, on the other hand indirectly enabling soil water content and peat mappings. Gamma-ray signatures of soils depend on (1) mineral composition of the bedrock, as well as (2) weathering intensity and related soil forming processes, that, in turn, influence the environmental fate of 40K, 238U and 232Th. Hence, due to soil formation heterogeneity at the landscape scale, resulting gamma signatures are locally specific and make soils readily distinguishable. In two villages in central Tanzania, participatory soil mapping in combination with gamma-ray spectrometry served as rapid and reliable approach to map local soils for later cropping experiments. Local farmers indicated major soil types on satellite images of the village area, which were the basis for further mapping steps. Fingerprint gamma-ray signatures of reference soil profiles were collected. Subsequent gamma-ray surveys on transect walks accelerated soil unit delineation for the final soil map. Challenges were misunderstandings related to language issues, variable soil knowledge of individual farmers and erosion leading to staggered soil profiles and non-distinctive signatures in some places. The combination of indigenous knowledge and gamma-ray spectrometry, nevertheless, led to a quick overview of the study area and made laboratory soil analyses largely redundant. The gained gamma-ray signal information were further statistically evaluated. For this purpose, distinction of major local soil types via K/Th ratios were graphically and statistically tested. The results showed that gamma-ray spectrometry is a sound method to distinguish certain local clay illuviation soil types by their K/Th ratios. The last part of the thesis covers the Trans-SEC approach of testing innovations for sustainable agricultural yield increase. Pearl millet (Pennisetum glaucum (L.) R.Br.) as the typical staple food in the study region was used as example crop. The process was scientist-led but local farmers selected the innovations that they considered adequate to their needs. Tied ridging for enhancing the water storage and placed fertilizer for increasing fertilizer efficiency was offered for their choice. Transferability of results from on-station experiments and demonstration plots in the village to farmers plots and trans-disciplinary issues are discussed. The number of factors that influence the result, as well as data insecurity increased with every level of spatial aggregation (on-station, demonstration plot and on-farm plots in the village). Soil type, position of the plot in the landscape (lateral water flow, distance to homesteads and, hence, fertility status) were the major influencing factors. In particular, the data insecurity related to on-farm trials due to low control intensity suggests to only conduct such experiments if large numbers of replicates (large N-trials) are feasible in future approaches. In conlusion, the thesis shows, that local knowledge combined with modern science is beneficial for agricultural R4D projects. Shortcomings within the transdisciplinary experimental approaches are pointed out. In particular, with respect to knowledge gained from the linkage of local experience and scientific approaches, there is still high potential. For this purpose, social and applied natural sciences should both strive for more interdisciplinary collaboration.Eine nachhaltige Ertragssteigerung zur Verbesserung der globalen Ernährungssicherung ist dringend notwendig, besonders in Subsahara-Afrika. Dort gehen starkes Bevölkerungswachstum und daraus resultierende Bodendegradation mit extremen Wetterereignissen einher. Als Folge treten gehäuft Hungersnöte auf. Die Planung ergebnisorientierter landwirtschaftlicher Forschungsprojekte mit Entwicklungsansätzen wie beim Trans-SEC-Projekt (www.trans-sec.org), in das diese Arbeit eingebunden war, erfordert die Berücksichtigung lokaler Umweltbedingungen, aber auch soziokultureller Gegebenheiten vor Feldversuchen. Erst so sind kostengünstige, adaptierte Lösungen für ansässige Subsistenzbauern, aber auch aussagefähige Ergebnisse für Forscher zu erzielen. Eine Methode zur raschen Bodenkartierung, die Gammaspektrometrie, wird im ersten Teil dieser Arbeit vorgestellt. Anwendbarkeit und Grenzen für die bodenkundliche Anwendung werden diskutiert. Bodenkundliche Erkundungen sind mit dieser Methode luftgestützt (z.B. mit Helikoptern oder Drohnen) oder bodengestützt (stationär oder in Bewegung) in kurzer Zeit durchführbar. Gammazerfälle der natürlich vorkommenden Isotope 40-Kalium, 232-Thorium und 238-Uran, mit ausreichender Zerfallsenergie und Menge zur Messung im Feld, werden pro Zeiteinheit erfasst. Die spezifischen Zählraten werden dann in Elementgehalte umgerechnet. Wasser und organische Bodensubstanz schwächen das Signal, was die Signalinterpretation erschwert, aber indirekt Wassergehalts- und Torfkartierungen ermöglicht. Die Gammasignaturen von Böden hängen von (1) der mineralischen Zusammensetzung des Ausgangsgesteins, sowie (2) der Verwitterungsintensität und den damit verknüpften bodenbildenden Prozessen ab, die wiederum das Umweltverhalten der Radionuklide beeinflussen. Somit sind Gammasignaturen wegen der heterogenen Bodenbildung für lokale Umwelten spezifisch und machen Böden direkt unterscheidbar. Zur Bodenkartierung zweier Dörfer in Zentraltansania bewährte sich die Kombination aus partizipativer Bodenkartierung und Gammaspektrometrie. Ansässige Landwirte zeichneten die lokal vorkommenden Hauptbodengruppen als Basis für weitere Kartierungsschritte auf hochaufgelösten Satellitenbildern der Gegend ein. Die spezifischen Gammasignaturen von Referenzbodenprofilen wurden gemessen. Die Abgrenzung der Bodeneinheiten für die finale Bodenkarte erfolgte durch Transektkartierung unterstützt durch gammaspektrometrische Messungen. Unterschiedliche Kenntnisse der ansässigen Landwirte zu den lokalen Böden, sprachliche Unklarheiten, sowie Bodenüberlagerungen aufgrund von Erosion und resultierende schlechter unterscheidbare Bodensignaturen erschwerten den Kartierungsprozess. Der Ansatz führte dennoch zu einem raschen Überblick über das Untersuchungsgebiet und machte aufwändige Laboranalysen der Bodenproben größtenteils überflüssig. Die gammaspektrometrisch gemessenen K/Th-Verhältnisse der lokal vorkommenden Hauptbodengruppen wurden grafisch und statistisch näher untersucht. Die Ergebnisse zeigten eine gute Unterscheidbarkeit einiger lokal vorkommender Tonverlagerungsböden. Der letzte Teil der Arbeit behandelt den Trans-SEC Projektansatz zur nachhaltigen Ertragssteigerung. Perlhirse (Pennisetum glaucum (L.) R.Br.) wurde als typisches Grundnahrungsmittel im Untersuchungsgebiet für diese Untersuchungen genutzt. Wissenschaftler leiteten den Prozess, die ansässigen Landwirte wählten jedoch die zu testenden Innovationen bzgl. des Feldmanagements, angepasst an ihre Bedürfnisse aus. Als Optionen wurden tied ridging als Maßnahme zur Erhöhung der Wasserspeicherung und placed fertilizer zur Erhöhung der Düngereffizienz angeboten. Die Übertragbarkeit der Versuchsergebnisse einer Versuchsstation mit kontrollierten Bedingungen, auf Demonstrationsflächen im Dorf und Versuchsflächen on-farm unter Aufsicht der Landwirte wird diskutiert. Es zeigte sich, dass die Anzahl der Faktoren, die einen Einfluss auf das Versuchsergebnis haben und die Datenunsicherheit mit jeder räumlichen Aggregierungsebene (Versuchsstation, Demonstrationsfelder und on-farm Felder im Dorf) ansteigen. Als wichtige Faktoren wurden Bodentyp und Position des Versuchsfeldes in der Landschaft (Zuflusswasser, Distanz zu Siedlungen und damit Trophie) identifiziert. Insbesondere die Datenunsicherheit on-farm aufgrund niedriger Kontrollintensität legt nahe, solche Versuche nur durchzuführen wenn große Wiederholungsanzahlen möglich sind. Insgesamt zeigt die vorliegende Arbeit, dass die Kombination aus lokalem Wissen und moderner Forschung von Vorteil für landwirtschaftliche Entwicklungsprojekte ist. Schwächen innerhalb der transdisziplinären Versuchsansätze werden aufgezeigt. Gerade hinsichtlich des Wissensgewinns durch Verknüpfung lokalen Wissens mit wissenschaftlichen Ansätzen kann potenziell noch viel getan werden. Hierzu sollte - von beiden Seiten - mehr interdisziplinäre Zusammenarbeit der Sozial- und angewandten Naturwissenschaften angestrebt werden

Boden-Gammastrahlung und ihre Abschwächung durch Wasser, Kalk und Torf

Gammaspektrometrie wird als Möglichkeit genutzt, um nicht-invasiv über Fern- oder Naherkundung Bodendaten zu gewinnen. Sie liefert direkt bodenchemische Informationen. Da die Gammastrahlung durch Nichtstrahler (z.B. Wasser) gedämpft wird, ist es auch möglich, bodenphysikalische Daten abzuleiten. Theoretisch muss eine Kor-rektur der Messung für die Nichtstrahler vorgenommen werden. Bisher liegen aber nur wenige theoretisch abgeleitete Schwächungskoeffizienten für die Nichtstrahler vor. Deren Überprüfung fehlt. Ziel dieser Arbeit war es daher, diese theoretischen Werte anhand eines real im Gelände eingesetzten Spektrometers zu überprüfen. Es wurden die linearen Schwächungskoeffizienten von Wasser, Kalk und Torf ermittelt. Hierzu wurde die Gammastrahlung an fixen Standorten (Referenzstrahlung) mit verschiedenen Schichtdicken der Nichtstrahler über dem Boden gemessen. Die Ergebnisse zeigen deutliche Abweichungen von den theoretisch ermittelten linearen Schwächungskoeffizienten. Dies wird auf den Versuchsaufbau (gerichteter Strahler im Labor vs. Boden als „streuender" Strahler) und die theoretische Annahme eines Einphasenmodells vs. der in der Natur vorkommenden Mehrphasigkeit (Mineral, Wasser, Luft) zurückgeführt. Uranmessungen werden aufgrund zu hoher experimenteller Abweichungen nicht diskutiert. Es bedarf weiterer Labor- und Feldexperimente zur Bestimmung der linearen Schwächungskoeffizienten in Böden in Abhängigkeit von natürlichen Umweltfaktoren

Einfluss des Wassergehaltes auf das an der Bodenoberfläche messbare Gamma-Spektrum: Durchführung eines Austrocknungsversuches im Feld

Die Gammaspektrometrie ermöglicht die nicht-invasive Ermittlung verschiedener Elementgehalte im Boden auf Grundlage natürlicher Radionuklide wie 40-Kalium, 238-Uran und 232-Thorium. Da Wasser die Gammastrahlung abschwächt, können räumlich variable Bodenwassergehalte die Interpretation gammaspektrometrischer Erkundungen erschweren. Die Stärke der daraus resultierenden Ab- schwächung ist von der Bodenzusammensetzung und der Photonenenergie selbst abhängig. Das Ziel dieser Arbeit war, durch einen Austrocknungsversuch unter realen Be- dingungen im Feld, den Einfluss des Bodenwassergehaltes auf das an der Bodenoberfläche messbare Gammaspektrum zu quantifizieren. Dafür wurde ein Bodenzylinder (r = 0,9 m) angelegt und mit Folie vom umgebenden Boden separiert. Nach Aufsättigung wurde das Gammaspektrum über drei Monate während der Austrocknungsphase unter natürlichen Verdunstungsbedingungen an der Bodenoberfläche gemessen. Die Gammastrahlung nahm über den Versuchszeitraum um ca. ein Drittel zu. Regressionsanalysen lassen lineare Abhängigkeiten für Kalium und Thorium erkennen. Aussagen zu Uran und der Gesamtstrahlung ("Total Counts") sind vermutlich aufgrund eines säkularen Un- gleichgewichtes in der Uran-Zerfallsreihe (Radon-Akkumulation) nicht möglich. Die Ergebnisse bilden eine erste Grundlage für mögliche Korrekturverfahren

EIT Food - EU PRO4BAKE project: Improve artigianal bakeries performances considering both demand forecast and process optimisation: the EIT FOOD Pro4Bake approach

The bakery products subsector has the largest number of companies, value added, employees and numberof companies in Europe (Food and Drinks, 2011). Over-consumption of energy in bakeries due to inefficientscheduling and production planning together with high shares of unsold bread waste (5-10% in Europe) is abig issue. Not only avoidable CO2 emissions affecting climate change and society, but also excessive costsfor SME bakeries are severe consequences. Recently, the EU has identified the bakery sector as one of thetarget sectors to apply best environmental practices. The aim of the envisaged project is in line with thegoals of the EU (Regulation (EC) No 1221/2009, 2017/1508 of 28 August 2017 EU): minimising food wasteand reducing energy consumption.The Pro4Bake project aims to provide tools that could improve the bakery situation. A prospectiveproduction-planning tool for bakeries is being developed in this trans- and interdisciplinary project. Presentmachinery in bakeries is used to optimise the production process. The reduction of make span and idle timeof machines, but also combinations thereof will lead to a higher economic and ecologic efficiency, thus,lower production costs for bakeries and lower climate change impact for society. The tool is developedusing a flow-shop model, optimised by evolutionary algorithms, digital twins and artificial intelligenceprocedures. Adaptation to consumers’ preferences will minimise food waste; hence, ecological footprint inbakeries, and lead to further optimisation of the baking process, product range and amount. Consumers’demands and expectations related to e.g. weather or holidays, and their acceptance of changes in productavailability will play a significant role in the analysis. In the end, a computational application will help SMEbakeries as users to adapt their production planning and processes to best practice. Subsequently, itspotential in practical application will be examined and its impact broadened to the rest of Europe andbeyond. Dissemination through technology transfer to users by involving professionals, students andlearning videos will be performed. The product will be commercialised in the end to make it possible forbakeries to adapt to the truly needed amount and product range with optimised baking schedules toreduce energy consumption. The multidisciplinary approach, combining research optimisation methods anddemand forecast approach used could be easily transferred to other agri-food sectors

Genetic diversity in the parthenogenetic reproducing tardigrade <i>Echiniscus testudo</i> (Heterotardigrada: Echiniscoidea)

Little is known about the genetic structure of microscopic animals from mosses and lichens. A few studies have investigated the geographic variation in tardigrades from mosses, but so far no study has investigated the intra-population or local clonal lineage variation. Echiniscus testudo (Echiniscoidea: Echiniscidae) belongs to a large cosmopolitan genus of terrestrial tardigrades comprising more than 150 species. It is a common tardigrade in mosses in the temperate part of the Northern hemisphere, and is highly tolerant of desiccation and freezing. In a previous study, we reported a maximum of 1.28% sequence variation (uncorrected p-distance) in cytochrome c oxidase subunit I (COI) haplotypes between clonal lineages covering a large geographical area. However, in this previous study we used pooled specimens to constitute a sample, and the genetic diversity from single specimens within a locality therefore remains unknown. Accordingly, the present study investigates the COI sequence variation and haplotype diversity between single specimens of E. testudo collected at three Danish localities, separated by 80 m and 186 km. A total of 10 COI haplotypes were found in the present study (Et2, Et3, Et9, Et12-Et18); only three of these were previously reported (Et2, Et3 and Et9). The uncorrected COI sequence diversity ranged between 0-2.07%, with haplotype Et18 having the highest genetic difference. The second most variable haplotypes (Et14, Et15, and Et17) all showed a maximum diversity of 1.19% compared to the other haplotypes. No general pattern of haplotype distribution was evident. Our data suggest that E. testudo has dispersed across the Baltic sea as haplotypes Et3, Et13 and Et14 are present at all three localities. The most likely dispersal mode is passive wind dispersal in the cryptobiotic tun stage. The current study emphasises that numerous sequences from single specimens are needed to describe the genetic diversity within single moss cushions

High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates

Campylobacter jejuni is currently the leading cause of bacterial gastroenteritis in humans. Comparison of multiple Campylobacter strains revealed a high genetic and phenotypic diversity. However, little is known about differences in transcriptome organization, gene expression, and small RNA (sRNA) repertoires. Here we present the first comparative primary transcriptome analysis based on the differential RNA–seq (dRNA–seq) of four C. jejuni isolates. Our approach includes a novel, generic method for the automated annotation of transcriptional start sites (TSS), which allowed us to provide genome-wide promoter maps in the analyzed strains. These global TSS maps are refined through the integration of a SuperGenome approach that allows for a comparative TSS annotation by mapping RNA–seq data of multiple strains into a common coordinate system derived from a whole-genome alignment. Considering the steadily increasing amount of RNA–seq studies, our automated TSS annotation will not only facilitate transcriptome annotation for a wider range of pro- and eukaryotes but can also be adapted for the analysis among different growth or stress conditions. Our comparative dRNA–seq analysis revealed conservation of most TSS, but also single-nucleotide-polymorphisms (SNP) in promoter regions, which lead to strain-specific transcriptional output. Furthermore, we identified strain-specific sRNA repertoires that could contribute to differential gene regulation among strains. In addition, we identified a novel minimal CRISPR-system in Campylobacter of the type-II CRISPR subtype, which relies on the host factor RNase III and a trans-encoded sRNA for maturation of crRNAs. This minimal system of Campylobacter, which seems active in only some strains, employs a unique maturation pathway, since the crRNAs are transcribed from individual promoters in the upstream repeats and thereby minimize the requirements for the maturation machinery. Overall, our study provides new insights into strain-specific transcriptome organization and sRNAs, and reveals genes that could modulate phenotypic variation among strains despite high conservation at the DNA level

Comparative myoanatomy of Tardigrada:new insights from the heterotardigrades <i>Actinarctus doryphorus</i> (Tanarctidae) and <i>Echiniscoides sigismundi</i> (Echiniscoididae)

Abstract Background Tardigrada is a group of microscopic invertebrates distributed worldwide in permanent and temporal aquatic habitats. Famous for their extreme stress tolerance, tardigrades are also of interest due to their close relationship with Arthropoda and Cycloneuralia. Despite recent efforts in analyzing the musculature of a number of tardigrade species, data on the class Heterotardigrada remain scarce. Aiming to expand the current morphological framework, and to promote the use of muscular body plans in elucidating tardigrade phylogeny, the myoanatomy of two heterotardigrades, Actinarctus doryphorus and Echiniscoides sigismundi, was analyzed by cytochemistry, scanning electron and confocal laser scanning microscopy and 3D imaging. We discuss our findings with reference to other tardigrades and internal phylogenetic relationships of the phylum. Results We focus our analyses on the somatic musculature, which in tardigrades includes muscle groups spanning dorsal, ventral, and lateral body regions, with the legs being musculated by fibers belonging to all three groups. A pronounced reduction of the trunk musculature is seen in the dorsoventrally compressed A. doryphorus, a species that generally has fewer cuticle attachment sites as compared to E. sigismundi and members of the class Eutardigrada. Interestingly, F-actin positive signals were found in the head appendages of A. doryphorus. Our analyses further indicate that cross-striation is a feature common to the somatic muscles of heterotardigrades and that E. sigismundi—as previously proposed for other echiniscoidean heterotardigrades—has relatively thick somatic muscle fibers. Conclusions We provide new insights into the myoanatomical differences that characterize distinct evolutionary lineages within Tardigrada, highlighting characters that potentially can be informative in future phylogenetic analyses. We focus our current analyses on the ventral trunk musculature. Our observations suggest that seven paired ventromedian attachment sites anchoring a large number of muscles can be regarded as part of the ground pattern of Tardigrada and that fusion and reduction of cuticular attachment sites is a derived condition. Specifically, the pattern of these sites differs in particular details between tardigrade taxa. In the future, a deeper understanding of the tardigrade myoanatomical ground pattern will require more investigations in order to include all major tardigrade lineages

VAPYRIN Marks an endosomal trafficking compartment involved in arbuscular mycorrhizal symbiosis

Arbuscular mycorrhiza (AM) is a symbiosis between plants and AM fungi that requires the intracellular accommodation of the fungal partner in the host. For reciprocal nutrient exchange, AM fungi form intracellular arbuscules that are surrounded by the peri-arbuscular membrane. This membrane, together with the fungal plasma membrane, and the space in between, constitute the symbiotic interface, over which nutrients are exchanged. Intracellular establishment of AM fungi requires the VAPYRIN protein which is induced in colonized cells, and which localizes to numerous small mobile structures of unknown identity (Vapyrin-bodies). In order to characterize the identity and function of the Vapyrin-bodies we pursued a dual strategy. First, we co-expressed fluorescently tagged VAPYRIN with a range of subcellular marker proteins, and secondly, we employed biochemical tools to identify interacting partner proteins of VAPYRIN. As an important tool for the quantitative analysis of confocal microscopic data sets from co-expression of fluorescent proteins, we developed a semi-automated image analysis pipeline that allows for precise spatio-temporal quantification of protein co-localization and of the dynamics of organelle association from movies. Taken together, these experiments revealed that Vapyrin-bodies have an endosomal identity with trans-Golgi features, and that VAPYRIN interacts with a symbiotic R-SNARE of the VAMP721 family, that localizes to the same compartment