Biology subjects

Sparmann, S.

Publications and source records attributed to Sparmann, S..

8 recordsLinked to original sources

bioRxiv2025

Fermentation of Agricultural By-products and Zinc Supplementation: A Synergistic Approach to Mealworm Microbiome Optimization

The increasing world population has put pressure on food industry to swiftly come up with initiatives that can sustain an increase in the demand for food, which have led to environmentally unsustainable practices. Insects, such as Tenebrio molitor (TM) larvae, have been widely proposed as sustainable alternative sources of protein with less environmental footprint. Insects can be reared with diets featuring low-cost agricultural side-streams, promoting circular economical practices, which can also be fermented to promote the development of probiotic microbiota. The inclusion of probiotics in the diets of insects during rearing has recently been explored to mitigate potential exposure to pathogens, potentially serving as alternatives to antibiotics. The focus of this study was the fermentation of spinach to naturally develop complex probiotic populations to enrich the diet of mealworms, promoting host health, thus resulting in a more nutritious food/feed source, featuring a safer microbiome profile. Sequencing revealed that fermented spinach had increased lactic acid bacteria (LAB), while repressing Pseudomonas. LAB species have been acknowledged and used as probiotics, whereas Pseudomonas populations are often associated with opportunistic resistant infections. Moreover, zinc is an essential element for bacterial microbiomes of many organisms, including insects. As the effects of dietary zinc on insect gut microbiome have been scarcely investigated, we have supplemented our formulated diets with this trace element and fed it to TM larvae for 35 days. While various diet compositions did not affect mealworm mortality, larvae fed spinach-based and zinc-rich diets gained less weight than that of control. Furthermore, higher dosage of zinc-supplementation resulted in significantly higher accumulation in TM larvae and a lower bioaccumulation factor. Sequencing of larvae fed diets supplemented with fermented spinach revealed increased presence of probiotic-associated genera, Lactococcus and Weissella. It was also found that supplementing diets with spinach and zinc significantly modulated the microbiome of larvae.

microbiology↗

bioRxiv2025

Cytochrome c oxidase I deep amplicon sequencing for metabarcoding of equine strongyle communities: unexpectedly high Strongylus spp. burden in treated horses

Equines are parasitized by complex communities of Strongylidae (Nematoda) comprising multi-species infections. Currently, the Cyathostominae are most prevalent, while the Strongylus species are only rarely detected. Since eggs and, in most cases, infective larvae cannot be differentiated to species level, with the exception of Strongylus spp., species-specific knowledge of the pathology, epidemiology and ecology of these parasitic nematodes is limited. Reference sequence data for several cyathostomin species are limited or missing. Deep amplicon sequencing of internal transcribed spacer 2 (ITS-2) regions of nematodes has been used in equines previously, although barcoding studies demonstrate a better species resolution for the cytochrome c oxidase subunit I (COI) region. The present study introduces a nemabiome method based on the sequencing of COI fragments. This method was applied to compare third stage larvae, representing strongyle communities, derived from regularly treated (RT) and never treated (NT) equine populations from Brazil, France (only RT), Germany, Ukraine, the UK, and the USA. Samples were predominantly from horses, but some were obtained from Przewalskis horses (Ukraine), donkeys (Germany, Ukraine) and kulans (Ukraine). Most sequence reads (87.7%) were identified to the species level, but unclassified reads occurred more frequently in donkeys and kulans than horses. No obvious difference in species diversity and richness was observed between RT and NT equines. However, there were significant differences in species composition between the RT and NT groups. While Strongylus spp. were significantly more abundant in the NT groups, Cylicocyclus nassatus, Cylicostephanus longibursatus, and Cyathostomum catinatum were more abundant in the RT group, suggesting that strongyle communities in domestic equines may have been shaped by anthelmintic treatments in the last decades. The decreased classification success for reads from non-caballine equines suggests that there are more strongyle species specific for this rarely-investigated group and that additional efforts are needed to improve the sequence database, particularly for these hosts. Author summaryThis study shows that long-term deworming treatments have influenced strongyle nematode communities in equines. Our findings showed that regular deworming does not always reduce species richness and diversity. Noteworthy, we observed that the more pathogenic species such as Strongylus vulgaris and Strongylus edentatus were still present but in low abundance in equines. Due to their low abundance, less sensitive diagnostic methods, such as morphological examination of larval cultures might not detect these species, which would lead to an underestimated threat in equine herds. We applied an effective metabarcoding approach based on a reliable gene marker region to accurately detect these and other strongyle species in equines. The detection of various species was more effective for horse samples than for those from donkeys and kulans. An expansion of the current database that includes more specimens from more rare species obtained from different equine species can improve identification and understanding of these complex multi-species communities in the future. In summary, the study underscores the importance of continuing monitoring equine herds based on sensitive methods such as metabarcoding to evaluate the current nematode communities and to adapt and develop treatment strategies for managing strongyle infections in equines.

microbiology↗

bioRxiv2025

Immune-mediated indirect interaction between gut microbiota and bacterial pathogens

BackgroundOrganism survival depends on the ability to orchestrate interactions between the host immune system and gut microbiota in response to pathogenic infections. These tripartite interactions shape pathogen virulence evolution. A key regulator of the immune system and, hence, bipartite interactions (in insects) is the immune deficiency (Imd) pathway, which modulates gut microbiota and pathogens by synthesizing antimicrobial peptides (AMPs). However, whether Imd-dependent AMPs mediate indirect interactions between gut microbiota and pathogens in a tripartite context remains unclear. Using RNAi-mediated knockdown of Tenebrio molitor Relish (TmRelish), we hypothesized that Imd-dependent AMPs influence indirect interaction between Providencia burhodogranaria_B infection and the gut microbiota. ResultsWhile TmRelish-knockdown altered bipartite interactions, disrupting gut microbiota load and composition and increasing pathogen load and virulence through higher host mortality, it did not support our tripartite hypothesis. Instead of Imd-dependent AMPs, gut microbiota and pathogen were influenced by Imd-independent AMPs expression, suggesting alternative regulatory pathways. Nevertheless, our investigations of tripartite interactions showed a positive effect of P. b_B infection on gut microbiota load, while survival analysis further revealed a negative effect of gut microbiota on pathogens infection, suggesting microbiota- mediated immune priming. ConclusionsThese findings suggest that while Imd-dependent AMPs may not mediate tripartite interactions, microbiota-host interactions, such as microbiota-mediated immune priming and changes in microbiota load, can shape infection outcomes. These effects on infection outcomes almost certainly exert important selective pressures on the evolution of bacterial virulence.

immunology↗

bioRxiv2025

Abrupt versus gradual application of pesticides: effects on soil bacterial and fungal communities

Pesticides are a major anthropogenic input to the environment and a factor in global change that puts pressure on soil microbial communities. However, the effects of different rates of pesticide application on soils remain poorly understood. This study investigates how abrupt versus gradual pesticide applications influence soil bacterial and fungal communities. Employing high-throughput sequencing, we examined the microbial diversity and community composition in response to ten commonly used pesticides. Bacterial communities exhibited minimal changes across treatments, whereas fungal communities responded strongly to pesticide exposure. Gradual applications reduced the relative abundance of dominant fungal taxa, resulting in an overall increase in community evenness. This effect was particularly pronounced for two herbicides and a triazole fungicide, which induced substantial shifts in fungal composition. Conversely, abrupt pesticide applications resulted in transient disruptions but did not promote the long-term proliferation of rare fungal variants. These findings suggest that prolonged exposure to pesticides exerts strong selective pressures on fungi, potentially altering fundamental soil functions such as nutrient cycling and decomposition. Future research should focus on the long-term responses of soil microbial communities to pesticide application and the cumulative effects of chronic low-dose exposure to provide a more comprehensive understanding of how they shape microbial communities. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/644867v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@8660a8org.highwire.dtl.DTLVardef@33ce7borg.highwire.dtl.DTLVardef@139113eorg.highwire.dtl.DTLVardef@19b388b_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIFungal communities were more responsive to pesticides than bacterial communities C_LIO_LIHerbicides caused strong non-target effects, similar to those of fungicides C_LIO_LIGradual pesticide applications altered fungal diversity and community composition C_LIO_LIRare fungal taxa proliferated under gradual exposure, increasing evenness C_LIO_LIProlonged exposure exerted greater selective pressure than abrupt application C_LI

ecology↗

bioRxiv2024

The ancient evolution of far-red light photoacclimation in cyanobacteria

Cyanobacteria oxygenated the atmosphere of early Earth and continue to be key players in global carbon and nitrogen cycles. A phylogenetically diverse subset of extant cyanobacteria can perform photosynthesis with far-red light through a process called far-red light photoacclimation, or FaRLiP. This phenotype is enabled by a cluster of [~]20 genes, and involves the synthesis of red-shifted chlorophylls f and d, together with paralogues of the ubiquitous photosynthetic machinery used in visible light. The FaRLiP gene cluster is present in diverse, environmentally important cyanobacterial groups but its origin, evolutionary history, and connection to early biotic environments have remained unclear. This study takes advantage of the recent increase in (meta)genomic data to clarify this issue; sequence data mining, metagenomic assembly, and phylogenetic tree networks were used to recover more than 600 new FaRLiP gene sequences, corresponding to 52 new gene clusters. These data enable high-resolution phylogenetics and - by relying on multiple gene trees, together with gene arrangement conservation - support FaRLiP appearing early in cyanobacterial evolution. Sampling information shows that considerable FaRLiP diversity can be observed in microbialites to the present day, and the process may have been associated with microbial mats and stromatolite formation in the early Paleoproterozoic. The ancestral FaRLiP cluster was reconstructed, revealing a conserved intergenic regulatory sequence that has been maintained for billions of years. Taken together, our results indicate that oxygenic photosynthesis using far-red light may have played a significant role in Earths early history.

evolutionary biology↗

bioRxiv2024

Inbreeding depression depends on the body size and environmental conditions in a threatened songbird, the aquatic warbler Acrocephalus paludicola

While inbreeding is known to affect individual fitness and thus population extinction risk, studies have under-represented non-model species of conservation concern, and rarely sought conditionality of inbreeding depression. Here, using SNPs identified with RAD-seq, we determined inbreeding depression in a threatened bird, the aquatic warbler Acrocephalus paludicola, and whether its magnitude depends on phenotypic and environmental factors. We found that the inbreeding coefficient (F) of adults with small tarsi was negatively associated with the seasonal breeding success (in males) and clutch size (in females), with the respective decrease in fitness in the most inbred relative to the least inbred individuals of ~89% and ~12%. In contrast, in adult males, for the average tarsus, wing and mass, support was low for F to be related to the long-term return rate to breeding grounds. For mean phenotypic covariates and male density, we also found low evidence that F is associated with the annual breeding success. Likewise, there was little support that mother F is related to egg hatch success and nestling survival, and - for average phenotypic traits, rainfall, temperature and nest density, and accounting for breeding peak - to clutch and fledged brood sizes. For nestlings, animal models showed that F is more negatively related to tarsus under higher temperatures and its effect varies by study year. However, for average brood size, temperature, rainfall and prey abundance, and when controlling for nestling sex, breeding peak and mother F, evidence for nestling F and tarsus association was weak. We conclude that (1) inbreeding depression on fitness components is stronger in smaller-bodied individuals, (2) considering interaction with phenotypic and environmental variables enables more accurate estimation of inbreeding depression, and (3) the inbreeding depression estimates will inform extinction risk analysis and conservation actions for the aquatic warbler.

evolutionary biology↗

bioRxiv2023

Microbial Associates of the Elm Leaf Beetle: Uncovering the Absence of Resident Bacteria and the Influence of Fungi on Insect Performance

Microbial symbionts play crucial roles in the biology of many insects. While bacteria have been the primary focus of research on insect-microbe symbiosis, recent studies suggest that fungal symbionts may be just as important. The elm leaf beetle (ELB, Xanthogaleruca luteola) is a serious pest species of elm (Ulmus minor). Using culture-dependent and independent methods, we investigated the abundance and species richness of bacteria and fungi throughout various ELB life stages and generations, while concurrently analysing microbial communities on elm leaves. No persistent bacterial community was found to be associated with the ELB or elm leaves. By contrast, fungi were persistently present in the beetles feeding life stages and on elm leaves. Fungal community sequencing revealed a predominance of the genera Penicillium and Aspergillus in insects and on leaves. Culture-dependent surveys showed a high prevalence of two fungal colony morphotypes closely related to Penicillium lanosocoeruleum and Aspergillus flavus. Among these, the Penicillium morphotype was significantly more abundant on feeding-damaged compared to intact leaves, suggesting that the fungus thrives in the presence of the ELB. We assessed whether the detected prevalent fungal morphotypes influenced ELBs performance by rearing insects on i) surface-sterilised leaves, ii) leaves inoculated with Penicillium spores, and iii) leaves inoculated with Aspergillus spores. Insects feeding on Penicillium-inoculated leaves gained more biomass and tended to lay larger egg clutches than those consuming surface-sterilised leaves or Aspergillus-inoculated leaves. Our results demonstrate that the ELB does not harbour resident bacteria and that it might benefit from associating with Penicillium fungi. ImportanceOur study provides insights into the still understudied role of microbial symbionts in the biology of the ELB, a major pest of elms. Contrary to expectations, we found no persistent bacterial symbionts associated with the ELB or elm leaves. Our research thus contributes to the growing body of knowledge that not all insects rely on bacterial symbionts. While no persistent bacterial symbionts were detectable in the ELB and elm leaf samples, our analyses revealed the persistent presence of fungi, particularly Penicillium and Aspergillus on both elm leaves and in the feeding ELB stages. Moreover, when ELB were fed with fungus-treated elm leaves, we detected a potentially beneficial effect of Penicillium on the ELBs development and fecundity. Our results highlight the significance of fungal symbionts in the biology of this insect.

ecology↗

bioRxiv2023

Non-destructive DNA metabarcoding of arthropods using collection medium from passive traps

BackgroundBroad-scale monitoring of arthropods is often carried out with passive traps (e.g. Malaise traps) that can collect thousands of specimens per sample. The identification of individual specimens requires time and taxonomic expertise, limiting the geographical and temporal scale of research and monitoring studies. DNA metabarcoding of bulk-sample homogenates is faster and has been found to be efficient and reliable, but is destructive and prevents a posteriori validation of species occurrences and/or relative abundances. Non-destructive DNA metabarcoding from the collection medium has been applied in a limited number of studies, but further tests of efficiency are required in a broader range of circumstances to assess the consistency of the method. MethodsWe quantified the detection rate of arthropod species when applying non-destructive DNA metabarcoding with a short (127-bp) fragment of mitochondrial COI on two types of passive traps and collection media: 1) water with monopropylene glycol (H2O-MPG) used in window-flight traps (WFT, 53 in total); 2) ethanol with monopropylene glycol (EtOH-MPG) used in Malaise traps (MT, 27 in total). We then compared our results with those obtained for the same samples using morphological identification (for WFTs) or destructive metabarcoding of bulk homogenate (for MTs). This comparison was applied as part of a larger study of arthropod species richness in silver fir (Abies alba) stands across a range of climate-induced tree dieback levels and forest management strategies. ResultsOf the 53 H2O-MPG samples from WFTs, 16 produced no metabarcoding results, while the remaining 37 samples yielded 77 arthropod MOTUs in total. None of those MOTUs were shared species with the 389 morphological taxa (343 of which were Coleoptera) obtained from the same traps. Metabarcoding of 26 EtOH-MPG samples from MTs detected more arthropod MOTUs (233) and insect orders (11) than destructive metabarcoding of homogenate (146 MOTUs, 8 orders). Arachnida and Collembola were more diverse in EtOH-MPG samples, but Hymenoptera, Coleoptera and Lepidoptera were less represented than in homogenate. Overall, MOTU richness per trap similar for EtOH-MPG (21.81 MOTUs) than for homogenate (32.4 MOTUs). Arthropod communities from EtOH-MPG and homogenate metabarcoding were relatively distinct, with 162 MOTUs (53%) unique to the collection medium and only 71 MOTUs (23%) present in both treatments. Finally, collection medium did not reveal any significant changes in arthropod richness along a disturbance gradient in silver fir forests. We conclude that DNA metabarcoding of collection medium can be used to complement homogenate metabarcoding in inventories to favour the detection of soft-bodied arthropods like spiders.

molecular biology↗