Publications in peer reviewed journals

20 Publications found
  • Interleukin-11 drives human and mouse alcohol-related liver disease

    Effenberger M, Widjaja AA, Grabherr F, Schaefer B, Grander C, Mayr L, Schwaerzler J, Enrich B, Moser P, Fink J, Pedrini A, Jaschke N, Kirchmair A, Pfister A, Hausmann B, Bale R, Putzer D, Zoller H, Schafer S, Pjevac P, Trajanoski Z, Oberhuber G, Adolph T Cook S, Tilg H
    2022 - BMJ, in press


    Objective Alcoholic hepatitis (AH) reflects acute exacerbation of alcoholic liver disease (ALD) and is a growing healthcare burden worldwide. Interleukin-11 (IL-11) is a profibrotic, proinflammatory cytokine with increasingly recognised toxicities in parenchymal and epithelial cells. We explored IL-11 serum levels and their prognostic value in patients suffering from AH and cirrhosis of various aetiology and experimental ALD.
    Design IL-11 serum concentration and tissue expression was determined in a cohort comprising 50 patients with AH, 110 patients with cirrhosis and 19 healthy volunteers. Findings were replicated in an independent patient cohort (n=186). Primary human hepatocytes exposed to ethanol were studied in vitro. Ethanol-fed wildtype mice were treated with a neutralising murine IL-11 receptor-antibody (anti-IL11RA) and examined for severity signs and markers of ALD.
    Results IL-11 serum concentration and hepatic expression increased with severity of liver disease, mostly pronounced in AH. In a multivariate Cox-regression, a serum level above 6.4 pg/mL was a model of end-stage liver disease independent risk factor for transplant-free survival in patients with compensated and decompensated cirrhosis. In mice, severity of alcohol-induced liver inflammation correlated with enhanced hepatic IL-11 and IL11RA expression. In vitro and in vivo, anti-IL11RA reduced pathogenic signalling pathways (extracellular signal-regulated kinases, c-Jun N-terminal kinase, NADPH oxidase 4) and protected hepatocytes and murine livers from ethanol-induced inflammation and injury.
    Conclusion Pathogenic IL-11 signalling in hepatocytes plays a crucial role in the pathogenesis of ALD and could serve as an independent prognostic factor for transplant-free survival. Blocking IL-11 signalling might be a therapeutic option in human ALD, particularly AH.
  • Ecology and evolution of chlamydial symbionts of arthropods

    Halter T, Koestlbacher S, Collingro A, Sixt BS, Toenshoff ER, Hendrickx F, Kostanjšek R, Horn M
    2022 - bioRxiv, 10.1101/2022.03.11.4


    The phylum Chlamydiae consists of obligate intracellular bacteria including major human pathogens and diverse environmental representatives. Here we investigated the Rhabdochlamydiaceae, which is predicted to be the largest and most diverse chlamydial family, with the few described members known to infect arthropod hosts. Using published 16S rRNA gene sequence data we identified at least 388 genus-level lineages containing about 14 051 putative species within this family. We show that rhabdochlamydiae are mainly found in freshwater and soil environments, suggesting the existence of diverse, yet unknown hosts. Next, we used a comprehensive genome dataset including metagenome assembled genomes classified as members of the family Rhabdochlamydiaceae, and we added novel complete genome sequences of Rhabdochlamydia porcellionis infecting the woodlouse Porcellio scaber, and of 'Candidatus R. oedothoracis' associated with the linyphiid dwarf spider Oedothorax gibbosus. Comparative analysis of basic genome features and gene content with reference genomes of well-studied chlamydial families with known host ranges, namely Parachlamydiaceae (protist hosts) and Chlamydiaceae (human and other vertebrate hosts) suggested distinct niches for members of the Rhabdochlamydiaceae. We propose that members of the family represent intermediate stages of adaptation of chlamydiae from protists to vertebrate hosts. Within the genus Rhabdochlamydia, pronounced genome size reduction could be observed (1.49-1.93 Mb). The abundance and genomic distribution of transposases suggests transposable element expansion and subsequent gene inactivation as a mechanism of genome streamlining during adaptation to new hosts. This type of genome reduction has never been described before for any member of the phylum Chlamydiae. This study provides new insights into the molecular ecology, genomic diversity, and evolution of representatives of one of the most divergent chlamydial families.

  • How low can they go? Aerobic respiration by microorganisms under apparent anoxia

    Berg J, Ahmerkamp S, Pjevac P, Hausmann B, Milucka J, Kuypers MMM
    2022 - FEMS Microbiology Reviews, in press


    Oxygen (O2) is the ultimate oxidant on Earth and its respiration confers such an energetic advantage that microorganisms have evolved the capacity to scavenge O2 down to nanomolar concentrations. The respiration of O2 at extremely low levels is proving to be common to diverse microbial taxa, including organisms formerly considered strict anaerobes. Motivated by recent advances in O2 sensing and DNA/RNA sequencing technologies, we performed a systematic review of environmental metatranscriptomes revealing that microbial respiration of O2 at nanomolar concentrations is ubiquitous and drives microbial activity in seemingly anoxic aquatic habitats. These habitats were key to the early evolution of life and are projected to become more prevalent in the near future due to anthropogenic-driven environmental change. Here we summarize our current understanding of aerobic microbial respiration under apparent anoxia, including novel processes, their underlying biochemical pathways, the involved microorganisms, and their environmental importance and evolutionary origin.

  • ‘Candidatus Phosphoribacter’, previously identified as Tetrasphaera, is the dominant polyphosphate accumulating lineage in wastewater treatment plants

    Singleton CM, Petriglieri F, Wasmund K, Nierychlo M, Kondrotaite Z, Petersen JF, Peces M, Dueholm MS, Wagner M, Nielsen PH
    2022 - ISME J, in press


    The bacterial genus Tetrasphaera encompasses abundant polyphosphate accumulating organisms (PAOs) that are responsible for enhanced biological phosphorus removal (EBPR) in wastewater treatment plants. Recent analyses of genomes from pure cultures revealed that 16S rRNA genes cannot resolve the lineage, and that Tetrasphaera spp. are from several different genera within the Dermatophilaceae. Here, we examine 14 recently recovered high-quality metagenome-assembled genomes from wastewater treatment plants containing full-length 16S rRNA genes identified as Tetrasphaera, 11 of which belong to the uncultured Tetrasphaera clade 3. We find that this clade represents two distinct genera, named here Ca. Phosphoribacter and Ca. Lutibacillus, and reveal that the widely used model organism Tetrasphaera elongata is less relevant for physiological predictions of this uncultured group. Ca. Phosphoribacter incorporates species diversity unresolved at the 16S rRNA gene level, with the two most abundant and often co-occurring species encoding identical V1-V3 16S rRNA gene amplicon sequence variants but different metabolic capabilities, and possibly, niches. Both Ca. P. hodrii and Ca. P. baldrii were visualised using fluorescence in situ hybridisation (FISH), and PAO capabilities were confirmed with FISH-Raman microspectroscopy and phosphate cycling experiments. Ca. Phosphoribacter represents the most abundant former Tetrasphaera lineage and PAO in EPBR systems in Denmark and globally. 


  • Targeting Gut Bacteria Using Inulin-Conjugated Mesoporous Silica Nanoparticles

    von Baeckmann C, Riva A, Guggenberger P, Kählig H, Han SW, Inan D, Del Favero G, Berry D, Kleitz F
    2022 - Adv Mater Interfaces, 9: 202102558


    To facilitate the creation of novel nanocarrier systems targeting the intestinal microbiome, inulin-conjugated mesoporous silica nanoparticles (MSNs) are described herein for the first time. Surface functionalization is achieved on either hydrophilic or hydrophobic mesoporous nanoparticles using different conjugation methods. The targeting performance of the resulting materials is assessed and compared upon incubation with human stool. It appears that amide formation is the most favorable coupling method on hydrophilic MSNs to achieve the desired bioconjugate. Remarkably, high affinity of gut bacteria to the conjugated particles can be obtained, paving the way to novel targeted drug delivery systems.

  • Individual sweet taste perception influences salivary characteristics after orosensory stimulation with sucrose and non-caloric sweeteners

    Karl CM, Vidakovic A, Pjevac P, Hausmann B, Schleining G, Ley JP, Berry D, Hans J, WEndlin M, Koenig J, Somoza V, Lieder B
    2022 - frontiers in Nutrition, in press


    Emerging evidence suggests a major role for salivary flow and the viscoelastic properties for taste perception and mouthfeel. Sweet-tasting compounds have also been proposed to have an effect on salivary characteristic. However, it is yet not clarified if perceived differences in the sensorial properties of structural diverse sweet tasting compounds contribute to salivary flow and viscoelasticity of saliva as part of mouthfeel and overall taste perception. Here we hypothesized that sensorially diverse sweeteners would affect salivary characteristics differently. Thus, we investigated the salivary flow, viscoelasticity of saliva, and selected influencing factors including the basal oral microbiome from 21 healthy test subjects after orosensory stimulation with sucrose, rebaudioside M (RebM), sucralose, and neohesperidin dihydrochalcone (NHDC) in a cross-over design. All test compounds enhanced the salivary flow by up to 1.51 ± 0.12 g/min for RebM, compared to 1.10 ± 0.09 g/min for water in the first minute after stimulation. The increase in the flow rate was correlated moderately to the individual perceived sweetness (r= 0.3, p< 0.01), but did not differ between the test compounds. The complex viscosity of the saliva was not affected by the test compounds, but analysis of covariance showed that the complex viscosity was associated (p< 0.05) with the concentration of mucin 5B (Muc5B). The oral microbiome showed a typical composition and diversity but was strongly individual-dependent (PERMANOVA: R²=0.76, p< 0.001), and was not associated with the changes in salivary characteristics. In conclusion, the present study indicates an impact of the individual sweetness impression on the flow rate without measurable changes in the complex viscosity of saliva, which may contribute to overall taste perception and mouthfeel of sweet tasting compounds.

  • Sulfur in lucinid bivalves inhibits intake rates of a molluscivore shorebird

    Tim Oortwijn, Jimmy de Fouw, Jillian Petersen, Jan A. van Gils
    2022 - Oecologia, in press


    A forager’s energy intake rate is usually constrained by a combination of handling time, encounter rate and digestion rate. On top of that, food intake may be constrained when a forager can only process a maximum amount of certain toxic compounds. The latter constraint is well described for herbivores with a limited tolerance to plant secondary metabolites. In sulfidic marine ecosystems, many animals host chemoautotrophic endosymbionts, which store sulfur compounds as an energy resource, potentially making their hosts toxic to predators. The red knot Calidris canutus canutus is a molluscivore shorebird that winters on the mudflats of Banc d’Arguin, where the most abundant bivalve prey Loripes orbiculatus hosts sulfide-oxidizing bacteria. In this system, we studied the potential effect of sulfur on the red knots’ intake rates, by offering Loripes with various sulfur content to captive birds. To manipulate toxicity, we starved Loripes for 10 days by removing them from their symbiont’s energy source sulfide. As predicted, we found lower sulfur concentrations in starved Loripes. We also included natural variation in sulfur concentrations by offering Loripes collected at two different locations. In both cases lower sulfur levels in Loripes resulted in higher consumption rates in red knots. Over time the red knots increased their intake rates on Loripes, showing their ability to adjust to a higher intake of sulfur.

  • Global grassland diazotrophic communities are structured by combined abiotic, biotic, and spatial distance factors but resilient to fertilization

    Nepel M, Angel R, Borer ET, Frey B, MacDougall AS, McCulley RL, Risch AC, Schütz M, Seasbloom EW, Woebken D
    2022 - Front Microbiol, 13: 1-12


    Grassland ecosystems cover around 37% of the ice-free land surface on Earth and have critical socioeconomic importance globally. As in many terrestrial ecosystems, biological dinitrogen (N2) fixation represents an essential natural source of nitrogen (N). The ability to fix atmospheric N2 is limited to diazotrophs, a diverse guild of bacteria and archaea. To elucidate the abiotic (climatic, edaphic), biotic (vegetation), and spatial factors that govern diazotrophic community composition in global grassland soils, amplicon sequencing of the dinitrogenase reductase gene—nifH—was performed on samples from a replicated standardized nutrient [N, phosphorus (P)] addition experiment in 23 grassland sites spanning four continents. Sites harbored distinct and diverse diazotrophic communities, with most of reads assigned to diazotrophic taxa within the Alphaproteobacteria (e.g., Rhizobiales), Cyanobacteria (e.g., Nostocales), and Deltaproteobacteria (e.g., Desulforomonadales) groups. Likely because of the wide range of climatic and edaphic conditions and spatial distance among sampling sites, only a few of the taxa were present at all sites. The best model describing the variation among soil diazotrophic communities at the OTU level combined climate seasonality (temperature in the wettest quarter and precipitation in the warmest quarter) with edaphic (C:N ratio, soil texture) and vegetation factors (various perennial plant covers). Additionally, spatial variables (geographic distance) correlated with diazotrophic community variation, suggesting an interplay of environmental variables and spatial distance. The diazotrophic communities appeared to be resilient to elevated nutrient levels, as 2–4 years of chronic N and P additions had little effect on the community composition. However, it remains to be seen, whether changes in the community composition occur after exposure to long-term, chronic fertilization regimes.

  • Omics research on abalone (Haliotis spp.): Current state and perspectives

    Nguyen TV, Alfaro AC, Mundy C, Petersen JM, Ragg NLC
    2022 - Aquaculture, 547: 737438


    The steady increase in abalone aquaculture production throughout the world has attracted growing interest in the application of new technologies, such as omics approaches for abalone research. Many omics techniques, such as genomics, transcriptomics, proteomics, and metabolomics are becoming established in abalone research and are beginning to reveal key molecules and pathways underlying many biological processes, and to identify associated candidate biomarkers of biological or environmental processes. In this contribution, we synthesize the published omics studies on abalone to highlight the current state of knowledge, open questions, and future directions. In addition, we outline the challenges and limitations of each omics field, some of which could be overcome by integrating multiple omics approaches – a future strategy with great potential for contributing to improve abalone production. Full text

  • Elucidating the role of the gut microbiota in the physiological effects of dietary fiber.

    Deehan EC, Zhang Z, Riva A, Armet AM, Perez-Muñoz ME, Nguyen NK, Krysa JA, Seethaler B, Zhao YY, Cole J, Li F, Hausmann B, Spittler A, Nazare JA, Delzenne NM, Curtis JM, Wismer WV, Proctor SD, Bakal JA, Bischoff SC, Knights D, Field CJ, Berry D, Prado CM, Walter J
    2022 - Microbiome, 1: 77


    Dietary fiber is an integral part of a healthy diet, but questions remain about the mechanisms that underlie effects and the causal contributions of the gut microbiota. Here, we performed a 6-week exploratory trial in adults with excess weight (BMI: 25-35 kg/m) to compare the effects of a high-dose (females: 25 g/day; males: 35 g/day) supplement of fermentable corn bran arabinoxylan (AX; n = 15) with that of microbiota-non-accessible microcrystalline cellulose (MCC; n = 16). Obesity-related surrogate endpoints and biomarkers of host-microbiome interactions implicated in the pathophysiology of obesity (trimethylamine N-oxide, gut hormones, cytokines, and measures of intestinal barrier integrity) were assessed. We then determined whether clinical outcomes could be predicted by fecal microbiota features or mechanistic biomarkers.
    AX enhanced satiety after a meal and decreased homeostatic model assessment of insulin resistance (HOMA-IR), while MCC reduced tumor necrosis factor-α and fecal calprotectin. Machine learning models determined that effects on satiety could be predicted by fecal bacterial taxa that utilized AX, as identified by bioorthogonal non-canonical amino acid tagging. Reductions in HOMA-IR and calprotectin were associated with shifts in fecal bile acids, but correlations were negative, suggesting that the benefits of fiber may not be mediated by their effects on bile acid pools. Biomarkers of host-microbiome interactions often linked to bacterial metabolites derived from fiber fermentation (short-chain fatty acids) were not affected by AX supplementation when compared to non-accessible MCC.
    This study demonstrates the efficacy of purified dietary fibers when used as supplements and suggests that satietogenic effects of AX may be linked to bacterial taxa that ferment the fiber or utilize breakdown products. Other effects are likely microbiome independent. The findings provide a basis for fiber-type specific therapeutic applications and their personalization., NCT02322112 , registered on July 3, 2015. Video Abstract.

  • Differential Modulation of the European Sea Bass Gut Microbiota by Distinct Insect Meals.

    Rangel F, Enes P, Gasco L, Gai F, Hausmann B, Berry D, Oliva-Teles A, Serra CR, Pereira FC
    2022 - Front Microbiol, 831034


    The aquaculture industry is one of the fastest-growing sectors in animal food production. However, farming of carnivorous fish strongly relies on the use of wild fish-based meals, a practice that is environmentally and economically unsustainable. Insect-based diets constitute a strong candidate for fishmeal substitution, due to their high nutritional value and low environmental footprint. Nevertheless, data on the impact of insect meal (IM) on the gut microbiome of farmed fish are so far inconclusive, and very scarce in what concerns modulation of microbial-mediated functions. Here we use high-throughput 16S rRNA gene amplicon sequencing and quantitative PCR to evaluate the impact of different IMs on the composition and chitinolytic potential of the European sea bass gut digesta- and mucosa-associated communities. Our results show that insect-based diets of distinct origins differently impact the gut microbiota of the European sea bass (). We detected clear modulatory effects of IM on the gut microbiota, which were more pronounced in the digesta, where communities differed considerably among the diets tested. Major community shifts were associated with the use of black soldier fly larvae (, HM) and pupal exuviae (HEM) feeds and were characterized by an increase in the relative abundance of the Firmicutes families , , and and the Actinobacteria family , which all include taxa considered beneficial for fish health. Modulation of the digesta community by HEM was characterized by a sharp increase in and a decrease of several Gammaproteobacteria and Bacteroidota members. In turn, a mealworm larvae-based diet (, TM) had only a modest impact on microbiota composition. Further, using quantitative PCR, we demonstrate that shifts induced by HEM were accompanied by an increase in copy number of chitinase ChiA-encoding genes, predominantly originating from species with effective chitinolytic activity. Our study reveals an HEM-driven increase in chitin-degrading taxa and associated chitinolytic activity, uncovering potential benefits of adopting exuviae-supplemented diets, a waste product of insect rearing, as a functional ingredient.

  • Individuality of the Extremely Premature Infant Gut Microbiota Is Driven by Ecological Drift.

    Seki D, Schauberger C, Hausmann B, Berger A, Wisgrill L, Berry D
    2022 - mSystems, e0016322


    The initial contact between humans and their colonizing gut microbiota after birth is thought to have expansive and long-lasting consequences for physiology and health. Premature infants are at high risk of suffering from lifelong impairments, due in part to aberrant development of gut microbiota that can contribute to early-life infections and inflammation. Despite their importance to health, the ecological assembly and succession processes governing gut microbiome composition in premature infants remained incompletely understood. Here, we quantified these ecological processes in a spatiotemporally resolved 16S rRNA gene amplicon sequencing data set of 60 extremely premature neonates using an established mathematical framework. We found that gut colonization during the first months of life is predominantly stochastic, whereby interindividual diversification of microbiota is driven by ecological drift. Dispersal limitations are initially small but have increasing influence at later stages of succession. Furthermore, we find similar trends in a cohort of 32 healthy term-born infants. These results suggest that the uniqueness of individual gut microbiota of extremely premature infants is largely due to stochastic assembly. Our knowledge concerning the initial gut microbiome assembly in human neonates is limited, and scientific progression in this interdisciplinary field is hindered due to the individuality in composition of gut microbiota. Our study addresses the ecological processes that result in the observed individuality of microbes in the gastrointestinal tract between extremely premature and term-born infants. We find that initial assembly is mainly driven by neutral ecological processes. Interestingly, while this progression is predominantly random, limitations to the dispersal of microbiota between infants become increasingly important with age and are concomitant features of gut microbiome stability. This indicates that while we cannot predict gut microbiota assembly due to its random nature, we can expect the establishment of certain ecological features that are highly relevant for neonatal health.

  • Ecological Processes Shaping Microbiomes of Extremely Low Birthweight Infants.

    Zioutis C, Seki D, Bauchinger F, Herbold C, Berger A, Wisgrill L, Berry D
    2022 - Front Microbiol, 812136


    The human microbiome has been implicated in affecting health outcomes in premature infants, but the ecological processes governing early life microbiome assembly remain poorly understood. Here, we investigated microbial community assembly and dynamics in extremely low birth weight infants (ELBWI) over the first 2 weeks of life. We profiled the gut, oral cavity and skin microbiomes over time using 16S rRNA gene amplicon sequencing and evaluated the ecological forces shaping these microbiomes. Though microbiomes at all three body sites were characterized by compositional instability over time and had low body-site specificity (PERMANOVA, = 0.09, = 0.001), they could nonetheless be clustered into four discrete community states. Despite the volatility of these communities, deterministic assembly processes were detectable in this period of initial microbial colonization. To further explore these deterministic dynamics, we developed a probabilistic approach in which we modeled microbiome state transitions in each ELBWI as a Markov process, or a "memoryless" shift, from one community state to another. This analysis revealed that microbiomes from different body sites had distinctive dynamics as well as characteristic equilibrium frequencies. Time-resolved microbiome sampling of premature infants may help to refine and inform clinical practices. Additionally, this work provides an analysis framework for microbial community dynamics based on Markov modeling that can facilitate new insights, not only into neonatal microbiomes but also other human-associated or environmental microbiomes.

  • Persistence of the antagonistic effects of a natural mixture of Alternaria mycotoxins on the estrogen-like activity of human feces after anaerobic incubation.

    Crudo F, Aichinger G, Dellafiora L, Kiss E, Mihajlovic J, Del Favero G, Berry D, Dall'Asta C, Marko D
    2022 - Toxicol Lett, 88-99


    Several Alternaria mycotoxins are believed to act as endocrine disruptive chemicals (EDCs), since they are reported to bind estrogen receptors in several experimental models. After ingestion of contaminated food commodities, the mycotoxins reach the intestine, where they come into direct contact with food constituents as well as the gut microbiota. Thus, the aim of the present work was to evaluate the modulatory potential of a complex extract of cultured Alternaria fungi (CE; containing eleven chemically characterized compounds) on the estrogenic signaling cascade of mammalian cells before and after anaerobic incubation with fecal slurries, in order to simulate an in vivo-like condition in the gut. Assessing alkaline phosphatase expression in Ishikawa cells as a measure for estrogenicity, we found the CE to partially quench the intrinsic estrogenic properties of fecal slurries and fecal waters, even after 3 h of fecal incubation. Investigation of the mechanisms underlying the effects observed carried out through an in vitro/in silico approach revealed the ability of the extract to decrease the ERα/ERβ nuclear ratio, while a possible action of the mycotoxins as ER-antagonists was excluded. Our results suggest that Alternaria mycotoxins might act as EDCs in vivo, and warrant further investigation in animal models.

  • Resolving the structure of phage-bacteria interactions in the context of natural diversity.

    Kauffman KM, Chang WK, Brown JM, Hussain FA, Yang J, Polz MF, Kelly L
    2022 - Nat Commun, 1: 372


    Microbial communities are shaped by viral predators. Yet, resolving which viruses (phages) and bacteria are interacting is a major challenge in the context of natural levels of microbial diversity. Thus, fundamental features of how phage-bacteria interactions are structured and evolve in the wild remain poorly resolved. Here we use large-scale isolation of environmental marine Vibrio bacteria and their phages to obtain estimates of strain-level phage predator loads, and use all-by-all host range assays to discover how phage and host genomic diversity shape interactions. We show that lytic interactions in environmental interaction networks (as observed in agar overlay) are sparse-with phage predator loads being low for most bacterial strains, and phages being host-strain-specific. Paradoxically, we also find that although overlap in killing is generally rare between tailed phages, recombination is common. Together, these results suggest that recombination during cryptic co-infections is an important mode of phage evolution in microbial communities. In the development of phages for bioengineering and therapeutics it is important to consider that nucleic acids of introduced phages may spread into local phage populations through recombination, and that the likelihood of transfer is not predictable based on lytic host range.

  • The life cycle-dependent transcriptional profile of the obligate intracellular amoeba symbiont Amoebophilus asiaticus.

    Selberherr E, Penz T, König L, Conrady B, Siegl A, Horn M, Schmitz-Esser S
    2022 - FEMS Microbiol Ecol, in press


    Free-living amoebae often harbor obligate intracellular bacterial symbionts. Amoebophilus (A.) asiaticus is a representative of a lineage of amoeba symbionts in the phylum Bacteroidota. Here, we analyze the transcriptome of A. asiaticus strain 5a2 at four time points during its infection cycle and replication within the Acanthamoeba host using RNA sequencing. Our results reveal a dynamic transcriptional landscape throughout different A. asiaticus life cycle stages. Many intracellular bacteria and pathogens utilize eukaryotic-like proteins (ELPs) for host cell interaction and the A. asiaticus 5a2 genome shows a particularly high abundance of ELPs. We show the expression of all genes encoding ELPs and found many ELPs to be differentially expressed. At the replicative stage of A. asiaticus, ankyrin repeat proteins and tetratricopeptide/Sel1-like repeat proteins were upregulated. At the later time points, high expression levels of a type 6 secretion system that likely prepares for a new infection cycle after lysing its host, were found. This study reveals comprehensive insights into the intracellular lifestyle of A. asiaticus and highlights candidate genes for host cell interaction. The results from this study have implications for other intracellular bacteria such as other amoeba-associated bacteria and the arthropod symbionts forming the sister lineage of A. asiaticus.

  • Genus-specific carbon fixation activity measurements reveal distinct responses to oxygen among hydrothermal vent Campylobacteria

    McNichol J, Dyksma S, Mussmann M, Seewald JS, Sylva SP, Sievert SM
    2022 - Appl Environ Microbiol, 2: e0208321


    Molecular surveys of low temperature deep-sea hydrothermal vent fluids have shown that Campylobacteria (previously Epsilonproteobacteria) often dominate the microbial community and that three genera, ArcobacterSulfurimonas, and Sulfurovum, frequently coexist. In this study, we used replicated radiocarbon incubations of deep-sea hydrothermal fluids to investigate activity of each genus under three experimental conditions. To quantify genus-specific radiocarbon incorporation, we used newly designed oligonucleotide probes for ArcobacterSulfurimonas, and Sulfurovum to quantify their activity using catalyzed-reporter deposition fluorescence in situhybridization (CARD-FISH) combined with fluorescence-activated cell sorting. All three genera actively fixed CO2 in short-term (∼ 20 h) incubations, but responded differently to the additions of nitrate and oxygen. Oxygen additions had the largest effect on community composition, and caused a pronounced shift in community composition at the amplicon sequence variant (ASV) level after only 20 h of incubation. The effect of oxygen on carbon fixation rates appeared to depend on the initial starting community. The presented results support the hypothesis that these chemoautotrophic genera possess functionally redundant core metabolic capabilities, but also reveal finer-scale differences in growth likely reflecting adaptation of physiologically-distinct phylotypes to varying oxygen concentrations in situ. Overall, our study provides new insights into how oxygen controls community composition and total chemoautotrophic activity, and underscores how quickly deep-sea vent microbial communities respond to disturbances. IMPORTANCE Sulfidic environments worldwide are often dominated by sulfur-oxidizing, carbon-fixing Campylobacteria. Environmental factors associated with this group's dominance are now understood, but far less is known about the ecology and physiology of members of subgroups of chemoautotrophic Campylobacteria. In this study, we used a novel method to differentiate the genus-specific chemoautotrophic activity of three subtypes of Campylobacteria. In combination with evidence from microscopic counts, chemical consumption/production during incubations, and DNA-based measurements, our data show that oxygen concentration affects both community composition and chemoautotrophic function in situ. These results help us better understand factors controlling microbial diversity at deep-sea hydrothermal vents, and provide first-order insights into the ecophysiological differences between these distinct microbial taxa.

  • Lipid synthesis at the trophic base as the source for energy management to build complex structures.

    Schnorr SL, Berry D
    2022 - Curr Opin Biotechnol, 364-373


    The review explores the ecological basis for bacterial lipid metabolism in marine and terrestrial ecosystems. We discuss ecosystem stressors that provoked early organisms to modify their lipid membrane structures, and where these stressors are found across a variety of environments. A major role of lipid membranes is to manage cellular energy utility, including how energy is used for signal propagation. As different environments are imbued with properties that necessitate variation in energy regulation, bacterial lipid synthesis has undergone incalculable permutations of functional trial and error. This may hold clues for how biotechnology can improvise a short-hand version of the evolutionary gauntlet to stimulate latent functional competences for the synthesis of rare lipids. Reducing human reliance on marine resources and deriving solutions for production of essential nutrients is a pressing problem in sustainable agriculture and aquaculture, as well as timely considering the increasing fragility of human health in an aging population.

  • Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities.

    Jung MY, Sedlacek CJ, Kits KD, Mueller AJ, Rhee SK, Hink L, Nicol GW, Bayer B, Lehtovirta-Morley L, Wright C, De La Torre JR, Herbold CW, Pjevac P, Daims H, Wagner M
    2022 - ISME J, 1: 272-283
    Kinetics of nitrifiers


    Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co-occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major cultivated phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest affinity for both ammonia and total ammonium of any characterized AOA, and these values are similar to previously determined ammonia and total ammonium affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values supports the hypothesis that-like for AOB-ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.

  • Evolutionarily recent dual obligatory symbiosis among adelgids indicates a transition between fungus- and insect-associated lifestyles.

    Szabó G, Schulz F, Manzano-Marín A, Toenshoff ER, Horn M
    2022 - ISME J, 1: 247-256


    Adelgids (Insecta: Hemiptera: Adelgidae) form a small group of insects but harbor a surprisingly diverse set of bacteriocyte-associated endosymbionts, which suggest multiple replacement and acquisition of symbionts over evolutionary time. Specific pairs of symbionts have been associated with adelgid lineages specialized on different secondary host conifers. Using a metagenomic approach, we investigated the symbiosis of the Adelges laricis/Adelges tardus species complex containing betaproteobacterial ("Candidatus Vallotia tarda") and gammaproteobacterial ("Candidatus Profftia tarda") symbionts. Genomic characteristics and metabolic pathway reconstructions revealed that Vallotia and Profftia are evolutionary young endosymbionts, which complement each other's role in essential amino acid production. Phylogenomic analyses and a high level of genomic synteny indicate an origin of the betaproteobacterial symbiont from endosymbionts of Rhizopus fungi. This evolutionary transition was accompanied with substantial loss of functions related to transcription regulation, secondary metabolite production, bacterial defense mechanisms, host infection, and manipulation. The transition from fungus to insect endosymbionts extends our current framework about evolutionary trajectories of host-associated microbes.

Book chapters and other publications

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