Newest publications
From glands to ground plans: Evolutionary morphology in Hymenoptera through space and time
(2023) Ulmer, Jonah Michael; Krogmann, Lars
Hymenoptera is one of the most species-rich and diverse groups of life, with over 153000 extant species described and another 2000 extinct. The evolutionary history of the group spans from the Triassic, around 250 million years ago, to the present day. In that time the order has spread and adapted to nearly every corner of the earth and nearly every conceivable ecological niche. That adaptation and time has led to innumerable forms and morphologies which have come and gone. Understanding the underlying patterns and impacts of these forms is perhaps the most fundamental and significant endeavor within systematics.
In the first chapter, the earliest lineage of the megadiverse Chalcidoidea, Protoididae, is described from fourteen pieces of amber from the Lower Cretaceous, approximately 130 million years ago. Two genera and ten new species are described along with a key to the new family. This newly discovered stem-group chalcid provides unique insights into the early ground-plan of the superfamily which is investigated relative to other fossil and early crown-group lineages. From a thorough morphological investigation of the group, we evaluate the earliest forms of known plesiomorphies and hypothesize the transitionary forms of stem-group to crown-group chalcids. Due to its age, Protoitidae also allows us to examine the early transition of chalcids and their ground-plan relative to other early Proctotrupomorpha. Based on this study we provide palaeontological and morphological evidence for a late Cretaceous radiation in the superfamily and a modified hypothesis for the biogeographic origins of chalcid wasps. Based on the diversity of paleotaxa from the Cretaceous, an early, unsuccessful diversification event in the Cretaceous is hypothesized prior to the mega-radiation of the early Eocene. The presence of a “gap” in the paleocene record is also discussed and the utility of morphological data from the fossil record clarifies uncertainty in the parallelism versus secondary reversal in some characters in early crown-group lineages. Several ground-plan characters are confirmed from within the family, such as tarsal and antennomere counts, along with a putative plesiomorphy within Proctotrupomorpha of a strongly, proximally curving basal vein.
In the second chapter, a metapleural gland is described from the parasitoid wasp Pelecinus polyturator. The unique gland is previously known only from Formicidae where it is hypothesized to be a key innovation in eusociality and an autapomorphy for the family. The gland is investigated both morphologically, behaviorally and chemically relative to the metapleural gland of ants. Hypotheses as to why the evolution of the gland was so impactful for ant diversification and less so for Pelecinidae are presented. The gland is shown to be the product of deep convergence within Hymenoptera due to a lack of transitional forms between the distantly related groups. Using this research as a basis, the “homology problem” of exocrine glands in insects is explored and formalized due to the presence of disparate evolutionary pathways occurring in a single organ system, the biosynthetic and morphological. Exaptation rather than adaptation is hypothesized to be the primary driver of glandular diversity in Hymenoptera. Within Pelecinidae, the gland ultrastructure and gross morphology is similar to that of the primitive ant lineages, suggesting a base form of the gland within Hymenoptera is present. The subsequent diversification and exaptation of the metapleural gland in Formicidae is hypothesized to be driven by eusociality, which is lacking in the asocial, parthenogenic pelecinids. A novel evolutionary model for examining exocrine glands is proposed with respect to underlying gene regulatory networks which signal the formation of exocrine glands in “hotspot” regions of the body while the biosynthetic pathways are highly homoplastic.
Collectively, this work aims to elucidate the potential causes and effects of morphological “innovation” which leads to diversification in taxa. The examination of the earliest taxa of a hyper-diverse lineage provides insight into the ancestral states and morphology prior to radiation, and provides additional evidence for ground-plan characters. In lineages which have a dense radiation event such as Chalcidoidea, the transitionary forms of characters can be easily lost or obscured within a sparse fossil record, or overwhelmed by convergence and reversals across multiple lineages through time. Homoplasy can also be a boon for examining the impact of morphological innovation on diversification in a lineage relative to a convergent structure in a different group which is less successful.
Bioprocess strategies for efficient microbial conversion of acetate as alternative biotechnological carbon source derived from lignocellulose streams
(2024) Kiefer, Dirk; Hausmann, Rudolf
In near future, humanity will be faced with the global challenges from climate change, fossil fuel depletion to food shortage. Our current economic system will thus need to make a transition into a sustainable bioeconomy which uses key technologies like biotechnology for conversion of renewable feedstocks. The majority of all biotechnological carbon sources is generated from food plants. In context to the global population growth coming along with food insecurity, competing use of these food plants for human and animal nutrition creates a substrate dilemma for future biotechnology. Future biorefineries will thus need to realize a paradigm shift to carbon sources generated from non-competing or waste resources. As such, especially lignocellulosic biomass is regarded as the central feedstock for a bio-based industry.
Among the different substrate streams obtained by lignocellulose refining strategies, the C2 carboxylic acid acetic acid (from now on referred to as acetate) is one of the most common occurring components. In contrast to its high economic role as building block in the chemical industry, acetate shows low relevance as biotechnological carbon source yet. This is mainly related to its inhibitory characteristic, the reason for why acetate has been used in food preservation for thousands of years. However, most industrial platform organisms are also capable to grow on acetate as sole carbon source. It also shows several attractive characteristics for bioprocessing which is why research studies on microbial acetate conversion have significantly increased in the past years. Together with the potential routes to generate non-fossil bio-acetate in large quantities from non-food competing resources like lignocellulose and biomass-derived/waste C1 gas streams, acetate might become a next-generation platform substrate for a future bio-industry. In order to make acetate-based bioprocesses competitive to those using conventional sugar-based carbon sources, adapted process strategies for efficient acetate conversion need to be established.
The present thesis is aimed to address efficient bioprocess strategies for biotechnological conversion of lignocellulosic acetate into microbial biomass and growth-coupled products under fed-batch culture conditions. The experimental studies presented in this work were divided into two parts:
In Part I, the potential of acetate as carbon source for high cell density cultivation of industrial platform bacterium Corynebacterium glutamicum was evaluated. Preliminary growth studies with different initial acetate concentrations revealed a high natural acetate tolerance for wild-type ATCC 13032 with growth at high acetate levels up to 60 g/L. In addition, it was shown that maximum growth rates (μmax) of 0.47 h-1 for acetate concentrations below 10 g/L are competitive to that on D-glucose as common carbon source. By implementation of an online feeding control which enables automated supply of pure acetic acid (HAc) via pH control, high cell density cultivation on lignocellulosic acetate was demonstrated for the first time in a 42 L stirred-tank bioreactor. Optimization of the molar carbon-to-nitrogen feeding ratio resulted in a highly efficient bioprocess yielding cell densities up to 80.2 g/L CDW after 28.9 h with biomass yields (YXIS) of 0.35 g/g and space-time yields (STY) of 66.6 g/L·d.
Part II focused on the potential of acetate as carbon source for integrated protein production in C. glutamicum. Batch cultures of genome-reduced strains MB001/MB001(DE3) demonstrated that acetate clearly shows no inhibitory effect on protein production of eYFP as model protein using C. glutamicum as production host. Interestingly, comparative expression studies with C. glutamicum T7 expression system indicated an up to 83 % higher biomass-specific production on acetate compared to D-glucose as carbon source. By transferring the implemented pH-coupled online feeding control for high cell density cultivation of strain MB001(DE3) pMKEX2-eyfp in a 42 L stirred-tank bioreactor, this study showed efficient protein accumulation on lignocellulosic acetate yielding final protein titers of 2.7 g/L after 27 h with product yields (YPIX) of 40 mg/g and volumetric productivities (PV) of 0.10 g/L·h.
In conclusion, the presented results demonstrate the high biotechnological potential of acetate as alternative carbon source. In contrast to most other studies before, it is shown that a suitable process strategy based on pH-coupled online feeding control allows efficient microbial acetate conversion under industry-relevant fed-batch culture conditions. This work provides exemplary proof-of-concept bioprocesses for high cell density cultivation on lignocellulosic acetate and its growth-coupled conversion into protein using industrial platform organism C. glutamicum. Therefore, the presented thesis contributes to the development of efficient concepts for microbial conversion of next-generation platform substrates like lignocellulosic acetate.
Increasing soil phosphate availability and phosphate fertilizer efficiency
(2023) Wanke, Daniel; Müller, Torsten
Phosphate is an important nutrient for agricultural animal and plant production. However, phosphate resources are limited, and unevenly distributed worldwide. Furthermore, accessing phosphate in the soil solution is complicated by the fact that soil phosphate solution concentrations generally remain low because the majority of soil phosphate is adsorbed to soil particles. Therefore, to efficiently utilize P, it is important to have an optimal fertilizer strategy where plants receive only the amount of phosphate needed to be adequately fertilized while minimizing soil phosphate accumulation. To determine precise fertilizer recommendations, phosphate extraction and detection methods are needed which indicate a high correlation between extracted soil phosphate and phosphate plant uptake. During the last decades, inductively coupled plasma optical emission spectroscopy (ICP OES) began to be used for phosphate detection more frequently in labs and, to some extent, replaced colorimetric phosphate detection. As a consequence, the question then arose whether ICP-OES and colorimetry can be used interchangeably for fertilizer recommendations. To answer this question, the Mehlich 3 extraction method was used to investigate differences between the colorimetric phosphate detection (Col-P) and phosphate detection with ICP-OES (ICP-P). It was found that the differences were great enough to state that Col-P and ICP-OES cannot be used interchangeably in Mehlich 3 extracts. Since Germany primarily uses the CAL extraction method, and not Mehlich 3, we chose to investigate whether there would be differences in results when using CAL extracts. The main objective of the first paper in this thesis was to investigate potential differences between Col-P and ICP-P for CAL extracts and compare the results to widely used phosphate extraction methods. Activated charcoal (AC) was used to explore whether the resulting differences could be reduced between both detection methods by the potential removal of organic phosphate from the solutions. The results of this experiment showed that among all tested extraction methods (CAL, Water, Olsen and Mehlich 3), CAL detected a low concentration of soil molybdate unreactive phosphate (MURP), and, simultaneously, a very strong correlation between ICP-P and Col-P with and without AC (-AC: RS = 0.990 and +AC: RS = 0.996). The regression line was nearly parallel to the 1:1 line, thus, making a conversion factor calculation for a broad spectrum of soils feasible. Although the correlation was less strong (-AC: RS = 0.85) between Col-P and ICP-P in Olsen extracts without an AC treatment, the addition of AC increased the correlation (+AC: RS = 0.99). Therefore, adding AC may be obligatory if a conversion factor needs to be calculated for Olsen extracts. Liquid 31P-NMR is predominantly used to differentiate between different organic phosphate (Porg) species. In addition, we used Raman spectroscopy to test if it can be used for the detection of Pi species in different soil matrices. For this purpose, Ca(H2PO4)2⋅H2O, CaHPO4 and β Ca3(PO4)2 were added to Luvos® healing earth, loess (C-horizon) and Filder loam (Ap horizon). All Pi species were detected using Raman spectroscopy which demonstrated its feasibility as an instrument to investigate different Pi species in soil, and which is expected to be useful in gaining further knowledge about the soil phosphate cycle. In the next experiment, we investigated whether the CAL extraction method is also reliable to characterize plant phosphate availability in organic agriculture. Organic farmers have frequently reported sufficient yield levels despite low or even very low soil CAL-P concentrations and, as a result, questioned the applicability of the acidic CAL method as a method for fertilizer recommendations for organic agriculture. This raised the question whether an alkaline extraction method such as Olsen would show more reliable results due to the extraction of labile Porg species. Therefore, phosphate of 22 soil samples of organic farms were extracted with different extractants (Water, CAL, Olsen, Mehlich 3, Bray P1, Bray P2, NaOH + EDTA) and phosphate was detected with ICP-OES and colorimetry. Using Olsen extracts, showed a correlation between plant offtake and Olsen-P that was very strong (RS = 0.94) compared to the very acidic extractants. Nevertheless, the correlation between plant offtake and CAL-P was also strong (RS = 0.91) despite the low extraction of Porg. Therefore, it was concluded that CAL can be used in organic agriculture for fertilizer recommendations. Furthermore, the comparison of CAL-P extracted and determined at the University of Hohenheim compared to CAL-P provided by farmers showed large discrepancies at times. Those differences may be explained by soil heterogeneity or the use of different phosphate detection methods; therefore, we recommended that soil samples be taken on a regular basis to increase the precision of the fertilizer strategy. Soil Porg may be an important phosphate source for plants. Therefore, in the fourth paper 31P NMR was used to gain an insight into how long-term compost application influence Porg in soil. Additionally, we measured phosphate turnover indicators such as phosphatase activity and microbial biomass P. Especially high compost application (treatment 400) increased the soil phosphatase activity and the inorganic phosphate (Pi) (CAL-P and Olsen P) in comparison to the control. Furthermore, 31P-NMR analysis showed that phospholipid-P and DNA-P in the treatment 400 increased due to compost application while all phosphomonoesters decreased compared to the control. These results suggest that organic fertilization in the form of compost increases mineralization processes which, in turn, reduces the phosphomonoesters.
Characterization of aroma and sensorial variation of basil and ginger during short-time drying process
(2024) Liang Jiaqi; Zhang, Yanyan
Industries are increasingly interested in aromatic herbs and spices, such as basil and ginger, which play a crucial role in daily life as flavoring agents in foods, beverages, and pharmaceuticals. Basil, an annual herb from the mint family (Lamiaceae), is renowned for its wonderful “royal” fragrance and numerous health benefits. Ginger, one of the most widely consumed dietary spices worldwide, has seen a surge in interest due to its significant healthpromoting properties. In 2023, global market sales for basil leaves and ginger reached 50 million euros and 4.2 billion euros, respectively. As may other herbs and spices, basil and ginger are typically used in dried form to extend shelf life and facilitate transportation. However, the drying process significantly alter the aroma from fresh samples, reduce the quality of the final products and generate numerous by-products. This study aims to identify the off-odor compound(s) produced during basil drying process using molecular sensory techniques and to develop effective strategies to inhibit their formation. Additionally, ginger peel and ginger fiber by-products generated during the industrial and domestic use, as well as the spray drying process, were investigated and reintroduced into the procedure to preserve the aroma compounds of ginger and promote environmental sustainability.
In the first part of the study, a method using stir bar sorptive extraction combined with gas chromatography-mass spectrometry-olfactory (SBSE-GC-MS-O) was established to analyse the aroma changes of basil and ginger during short-term spray drying. This approach was designed to maximize desorption efficiency for various odorants with diverse physicochemical properties under different desorption conditions through four types of mathematical modelling. Among these models, the Random Forest model demonstrated the highest performance and minimal errors, with an R value of 0.910 after validation using a dataset of six new compounds. In addition, the model determined that cryo-focusing temperature was the most important factor, followed by molecular weight, log P, boiling point, desorption temperature, desorption time, and helium flow. This algorithm can be further utilized to predict the optimal parameters for maximizing desorption efficiency in aroma analysis of basil and ginger by SBSE-GC-MS-O.
Subsequently, to investigate the formation of the hay-like off-odor that lowers consumer acceptability in dried basil products, the responsible compound was identified in thawed, airdried, and spray-dried basil samples using a trained human panel (n = 10) and gas chromatography–mass spectrometry–olfactometry. 3-Methylnonane-2,4-dione (3-MND) was found to be the odorant contributing to the hay-like off-odor in all basil samples. In order to reduce this odorant, the effects of light, oxygen, and temperature on the formation of 3-MND during the processes of thawing, spray drying, and air drying were studied based on a potential pathway involving 3-MND precursors. The results revealed that controlling light exposure, employing nitrogen protective environment, and maintaining low temperatures are critical processing parameters for minimizing the generation of the hay-like compound 3-MND, thereby meeting consumer demands for high-quality dried basil products.
Regarding the processing of ginger, the drying process generates a significant amount of ginger peel as an industrial by-product. To facilitate environmental sustainability and establish a reference for its potential applications, the effect of ginger peel on aroma, sensory profiles, and nutrition-related physicochemical properties was investigated. The total concentration of aroma compounds in unpeeled ginger was 1.3 times higher than that in peeled ginger, according to SBSE-GC-MS-O analysis. Sensory evaluation data indicated that unpeeled ginger had significantly enhanced citrus-like and fresh impressions compared to peeled ginger, which is associated with the higher odor activity values of odorants such as β-myrcene (pungent, citruslike),
geranial (citrus-like), citronellal (citrus-like, sourish), and linalool (floral, fresh). Additionally, the total polyphenol content in unpeeled ginger was 7.96 mg/100 g higher than that in peeled ginger. Unpeeled ginger not only demonstrates more intense aromatic and sensory qualities but also offers superior nutritional and environmental benefits, making it a promising option for future global spice use and reducing ginger side streams.
In the spray drying process of ginger, ginger fibre is also typically regarded as industrial byproduct, as ginger juice is often used as a feed material. To achieve sustainable development and produce a clean-labeled product, a split-stream spray-drying process was developed to address sugar-rich feed solutions by reintroducing ginger fiber in their natural composition as a carrier material, rather than treating them as a by-product. The characterizations of both feed materials were then compared. The method was optimized for aroma retention by adjusting the inlet and outlet temperatures to 220 ℃ and 80 ℃, respectively. Aroma decoding results using SBSE-GC-MS-O demonstrated that reintegrating ginger fiber significantly increased the concentration of eight key odorants, including hexanal, linalool, neral, borneol, geranial, citronellol, nonanoic acid, and α-bisabolol, in comparison to the concentration observed in
ginger juice. This presents a promising solution for maximizing the utilization of ginger in spray drying, enhancing the aroma profiles of feed material, and addressing sustainability considerations in the food industry.
Overall, the presented work comprehensively explores the challenges and potential solutions associated with the drying process of basil and ginger, highlighting the impact of various processing conditions on aroma and sensory properties. By identifying key off-odor compounds and optimizing techniques to reduce their formation, as well as investigating aroma profiles and sustainable approaches for utilizing by-products such as ginger peel and ginger fiber, this research offers valuable insights into improving both the aromatic quality and environmental sustainability of dried herb and spice products.
Unveiling the interplay between gut microbiota and protein for sustainable pig production
(2024) Sarpong, Naomi; Camarinha-Silva, Amélia
Recent forecasts predict a rise in global pork consumption due to increased incomes and population growth. Intensive pig production is frequently linked with environmental pollution, wherein nitrogen (N) emissions are a significant contributor. A growing pig retains only around 30% of the ingested N, while the remainder is excreted via urine and feces. nitrogen utilization efficiency (NUE) indicates the percentage of ingested N retained by the pig, and its maximization is crucial for sustainable pig production. This work investigates the gut microbiome’s role in protein utilization in fattening pigs with defined family structure.
In the initial phase, 508 pigs were kept under standardized conditions and fed in a two-phase feeding regime with marginal lysine supply (90% of supply recommendation). In each phase, a sample period (SP) was conducted (body weight (BW): SP 1 = 40.5 kg, SP 2 = 60.3 kg), where a fecal sample was collected from each pig. These samples underwent 16S rRNA gene sequencing and volatile fatty acid (VFA) determination. Results showed the influence of sire, SP and sex on fecal microbiota composition. In each SP, samples were divided into two groups based on <25%- and >75%-quantile of NUE, and in SP 1, differences in the microbial composition were observed between pigs with high and low predisposition for NUE. LinDA model identified Streptococcus as a potential biomarker for NUE in SP 1. The offspring of some sires were either entirely absent or unevenly represented in the groups, highlighting a genetic predisposition to NUE. All samples (n = 892) were grouped into two enterotype-like clusters named by the highest taxon weights in cluster Lactobacillus and cluster Clostridium sensu stricto. Pigs' affiliation with enterotype-like clusters altered over time and might be sex-dependent. No differences were observed for the BW and gain to feed ratio between the subgroups of enterotype-like clusters. Pigs in the stable cluster Clostridium sensu stricto, characterized by higher NUE but lower dry matter intake, align with goals for sustainable pig production. This cluster also showed the highest VFA concentrations, suggesting enterotype-specific metabolic efficiencies.
The second part of the study focused on the intestinal microbiome, analyzing digesta and mucosa samples from 48 euthanized pigs. This study provides a comprehensive characterization of the entire gastrointestinal tract (GIT) microbiome of pigs, including mucosa and digesta samples, investigated using 16S rRNA gene sequencing and whole-genome shotgun (WGS) metagenomic sequencing. Several differences regarding microbial diversity and composition were observed between GIT sections and sample types. Streptococcus was a predominant genus in the digesta and mucosa of the small intestine, and novel insights into the stomach’s microbial community were uncovered. WGS metagenomic sequencing of the digesta samples revealed functional shifts along the GIT, with specific metabolic pathways related to “Amino acid metabolism” and “Metabolism of other amino acids”, being differentially abundant in the duodenum, indicating an anabolic contribution to protein metabolism. These results offer a deeper knowledge of the microbial community in the digesta and mucosa across different GIT sections and its contribution to nutrient metabolism. The categorization of samples into enterotype-like clusters, and their correlation with microbial composition in digesta samples indicates a possible link between enterotype-like clusters and gastrointestinal microbial composition.
This work explores the microbiome's impact on the complex interactions between gut microbiota and protein utilization but also provides a foundation for developing subsequent strategies to improve sustainability in pig production.