Publications in peer reviewed journals

38 Publications found
  • Abiotic factors influence patterns of bacterial diversity and community composition in the Dry Valleys of Antarctica

    Bottos EM, Laughlin DC, Herbold CW, Lee CK, McDonald IR, Cary SC
    2020 - FEMS Microbiology Ecology, 96: in press


    The Dry Valleys of Antarctica are a unique ecosystem of simple trophic structure, where the abiotic factors that influence soil bacterial communities can be resolved in the absence of extensive biotic interactions. This study evaluated the degree to which aspects of topographic, physicochemical and spatial variation explain patterns of bacterial richness and community composition in 471 soil samples collected across a 220 square kilometer landscape in Southern Victoria Land. Richness was most strongly influenced by physicochemical soil properties, particularly soil conductivity, though significant trends with several topographic and spatial variables were also observed. Structural equation modeling (SEM) supported a final model in which variation in community composition was best explained by physicochemical variables, particularly soil water content, and where the effects of topographic variation were largely mediated through their influence on physicochemical variables. Community dissimilarity increased with distance between samples, and though most of this variation was explained by topographic and physicochemical variation, a small but significant relationship remained after controlling for this environmental variation. As the largest survey of terrestrial bacterial communities of Antarctica completed to date, this work provides fundamental knowledge of the Dry Valleys ecosystem, and has implications globally for understanding environmental factors that influence bacterial distributions.

  • Co-infection of chicken layers with Histomonas meleagridis and avian pathogenic Escherichia coli is associated with dysbiosis, cecal colonization and translocation of the bacteria from the gut lumen

    Abdelhamid MK, Quijada NM, Dzieciol M, Hatfaludi T, Bilic I, Selberherr E, Liebhart D, Hess C, Hess M, Paudel S
    2020 - Front Microbiol, 11: 586437


    Histomonosis in chickens often appears together with colibacillosis in the field. Thus, we have experimentally investigated consequences of the co-infection of birds with Histomonas meleagridisand avian pathogenic Escherichia coli (APEC) on the pathology, host microbiota and bacterial translocation from the gut. Commercial chicken layers were infected via oral and cloacal routes with lux-tagged APEC with or without H. meleagridis whereas negative controls were left uninfected. Except one bird, which died due to colibacillosis, no clinical signs were recorded in birds infected with bioluminescence lux gene tagged E. coli. In co-infected birds, depression and ruffled feathers were observed in 4 birds and average body weight gain significantly decreased. Typhlitis caused by H. meleagridis was present only in co-infected birds, which also had pronounced microscopic lesions in systemic organs such as liver, heart and spleen. The 16S rRNA gene amplicon sequencing showed that in co-infected birds, corresponding to the severity of cecal lesions, microbial species richness and diversity in caeca greatly decreased and the abundance of the Escherichia group, Helicobacter and Bacteroides was relatively higher with a reduction of commensals. Most of the shared Amplicon Sequencing Variants between cecum and blood in co-infected birds belonged to Pseudomonas, Staphylococcus, and members of Enterobacteriaceae while those assigned as Lactobacillus and members of Ruminococcaceae and Lachnospiraceae were found mainly in negative controls. In infected birds, E. coli in the cecal lumen penetrated into deeper layers, a phenomenon noticed with higher incidence in the dead and co-infected birds. Furthermore, numbers of lux-tagged E. coli in caeca were significantly higher at every sampling date in co-infected birds. Altogether, infection of layers with H. meleagridis and E. coli resulted in more severe pathological changes, dramatic shift in the cecal mucosa-associated microbiota, higher tissue colonization of pathogenic bacteria such as avian pathogenic E. coli in the gut and increased penetration of E. coli from the cecal lumen toward peritoneum. This study provides novel insights into the parasite-bacteria interaction in vivohighlighting the role of H. meleagridis to support E. coli in the pathogenesis of colibacillosis in chickens.

  • Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms

    Sharma K, Palatinszky M, Nikolov G, Berry D, Shank EA
    2020 - Elife, 9: e56275


    Microscale processes are critically important to soil ecology and biogeochemistry yet are difficult to study due to soil’s opacity and complexity. To advance the study of soil processes, we constructed transparent soil microcosms that enable the visualization of microbes via fluorescence microscopy and the non-destructive measurement of microbial activity and carbon uptake in situ via Raman microspectroscopy. We assessed the polymer Nafion and the crystal cryolite as optically transparent soil substrates. We demonstrated that both substrates enable the growth, maintenance, and visualization of microbial cells in three dimensions over time, and are compatible with stable isotope probing using Raman. We applied this system to ascertain that after a dry-down/rewetting cycle, bacteria on and near dead fungal hyphae were more metabolically active than those far from hyphae. These data underscore the impact fungi have facilitating bacterial survival in fluctuating conditions and how these microcosms can yield insights into microscale microbial activities.

  • Acidobacteria are active and abundant members of diverse atmospheric H2-oxidizing communities detected in temperate soils

    Giguere AT, Eichorst SA, Meier D, Herbold CW, Richter A, Greening C, Woebken D
    2020 - ISME J, in press


    Significant rates of atmospheric H2 consumption have been observed in temperate soils due to the activity of high-affinity enzymes, such as the group 1h [NiFe]-hydrogenase. We designed broadly inclusive primers targeting the large subunit gene (hhyL) of group 1h [NiFe]-hydrogenases for long-read sequencing to explore its taxonomic distribution across soils. This approach revealed a diverse collection of microorganisms harboring hhyL, including previously unknown groups and taxonomically not assignable sequences. Acidobacterial group 1h [NiFe]-hydrogenases genes were abundant and expressed in temperate soils. To support the participation of acidobacteria in H2 consumption, we studied two representative mesophilic soil acidobacteria, which expressed group 1h [NiFe]-hydrogenases and consumed atmospheric H2 during carbon starvation. This is the first time mesophilic acidobacteria, which are abundant in ubiquitous temperate soils, have been shown to oxidize H2 down to below atmospheric concentrations. As this physiology allows bacteria to survive periods of carbon starvation, it could explain the success of soil acidobacteria. With our long-read sequencing approach of group 1h [NiFe]-hydrogenases genes, we show that the ability to oxidize atmospheric levels of His more widely distributed among soil bacteria than previously recognized and could represent a common mechanism enabling bacteria to persist during periods of carbon deprivation.

  • Conversion of Rutin, a Prevalent Dietary Flavonol, by the Human Gut Microbiota

    Riva A, Kolimar D, Spittler A, Wisgrill L, Herbold CW, Abrankó L, Berry D
    2020 - Frontiers in microbiology, in press


    The gut microbiota plays a pivotal role in the conversion of dietary flavonoids, which can affect their bioavailability and bioactivity and thereby their health-promoting properties. The ability of flavonoids to metabolically-activate the microbiota has, however, not been systematically evaluated. In the present study, we used a fluorescence-based single-cell activity measure [biorthogonal non-canonical ammino acid-tagging (BONCAT)] combined with fluorescence activated cell sorting (FACS) to determine which microorganisms are metabolically-active after amendment of the flavonoid rutin. We performed anaerobic incubations of human fecal microbiota amended with rutin and in the presence of the cellular activity marker L-azidohomoalanine (AHA) to detect metabolically-active cells. We found that 7.3% of cells in the gut microbiota were active after a 6 h incubation and 26.9% after 24 h. We then sorted BONCAT-positive cells and observed an enrichment of Lachnospiraceae (Lachnoclostridium and Eisenbergiella), Enterobacteriaceae, Tannerellaceae, and Erysipelotrichaceae species in the rutin-responsive fraction of the microbiota. There was marked inter-individual variability in the appearance of rutin conversion products after incubation with rutin. Consistent with this, there was substantial variability in the abundance of rutin-responsive microbiota among different individuals. Specifically, we observed that Enterobacteriaceae were associated with conversion of rutin into quercetin-3-glucoside (Q-glc) and Lachnospiraceae were associated with quercetin (Q) production. This suggests that individual microbiotas differ in their ability to metabolize rutin and utilize different conversion pathways.

  • Polyphenol Exposure, Metabolism, and Analysis: A Global Exposomics Perspective.

    Oesterle I, Braun D, Berry D, Wisgrill L, Rompel A, Warth B
    2020 - Annu Rev Food Sci Technol, in press


    Polyphenols are generally known for their health benefits and estimating actual exposure levels in health-related studies can be improved by human biomonitoring. Here, the application of newly available exposomic and metabolomic technology, notably high-resolution mass spectrometry, in the context of polyphenols and their biotransformation products, is reviewed. Comprehensive workflows for investigating these important bioactives in biological fluids or microbiome-related experiments are scarce. Consequently, this new era of nontargeted analysis and omic-scale exposure assessment offers a unique chance for better assessing exposure to, as well as metabolism of, polyphenols. In clinical and nutritional trials, polyphenols can be investigated simultaneously with the plethora of other chemicals to which we are exposed, i.e., the exposome, which may interact abundantly and modulate bioactivity. This research direction aims at ultimately eluting into a true systems biology/toxicology evaluation of health effects associated with polyphenol exposure, especially during early life, to unravel their potential for preventing chronic diseases. Expected final online publication date for the , Volume 12 is March 2021. Please see for revised estimates.

  • Virulence characterization and comparative genomics of Listeria monocytogenes sequence type 155 strains.

    Wagner E, Zaiser A, Leitner R, Quijada NM, Pracser N, Pietzka A, Ruppitsch W, Schmitz-Esser S, Wagner Ma, Rychli K
    2020 - BMC Genomics, 21: 847


    Listeria (L.) monocytogenes strains show a high diversity regarding stress tolerance and virulence potential. Genome studies have mainly focused on specific sequence types (STs) predominantly associated with either food or human listeriosis. This study focused on the prevalent ST155, showing equal distribution among clinical and food isolates. We evaluated the virulence potential of 20 ST155 strains and performed comparative genomic analysis of 130 ST155 strains isolated from food, food processing environments and human listeriosis cases in different countries and years.
    The in vitro virulence assays using human intestinal epithelial Caco2 and hepatocytic HEPG2 cells showed an impaired virulence phenotype for six of the 20 selected ST155 strains. Genome analysis revealed no distinct clustering of strains from the same source category (food, food processing environment, and clinical isolates). All strains harbored an intact inlA and inlB locus, except four strains, which had an internal deletion in the inlA gene. All strains harbored LIPI-1, but prfA was present in a longer variant in six strains, all showing impaired virulence. The longer PrfA variant resulted in lower expression of inlA, inlB, and prfA, and no expression of hly and actA. Regarding stress-related gene content, SSI-1 was present, whereas qacH was absent in all strains. 34.6% of the strains harbored a plasmid. All but one ST155 plasmids showed high conservation and harbored cadA2, bcrABC, and a triphenylmethane reductase.
    This study contributes to an enhanced understanding of L. monocytogenes ST155 strains, being equally distributed among isolates from humans, food, and food processing environments. The conservation of the present genetic traits and the absence of unique inherent genetic features makes these types of STs especially interesting since they are apparently equally adapted to the conditions in food processing environments, as well as in food as to the human host environment. However, a ST155-specific mutation resulting in a longer PrfA variant impaired the virulence potential of several ST155 strains.

  • Redox-informed models of global biogeochemical cycles.

    Zakem EJ, Polz MF, Follows MJ
    2020 - Nat Commun, 1: 5680


    Microbial activity mediates the fluxes of greenhouse gases. However, in the global models of the marine and terrestrial biospheres used for climate change projections, typically only photosynthetic microbial activity is resolved mechanistically. To move forward, we argue that global biogeochemical models need a theoretically grounded framework with which to constrain parameterizations of diverse microbial metabolisms. Here, we explain how the key redox chemistry underlying metabolisms provides a path towards this goal. Using this first-principles approach, the presence or absence of metabolic functional types emerges dynamically from ecological interactions, expanding model applicability to unobserved environments."Nothing is less real than realism. It is only by selection, by elimination, by emphasis, that we get at the real meaning of things." -Georgia O'Keefe.

  • Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities

    Waite DW, Chuvochina M, Pelikan C, Parks DH, Yilmaz P, Wagner M, Loy A, Naganuma T, Nakai R, Whitman WB, Hahn MW, Kuever J, Hugenholtz P
    2020 - Int J Syst Evol Microbiol, 11: 5972-6016


    The class comprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylum , it rarely affiliates with other proteobacterial classes and is frequently not recovered as a monophyletic unit in phylogenetic analyses. Indeed, one branch of the class encompassing like predators was recently reclassified into a separate proteobacterial class, the . Here we systematically explore the phylogeny of taxa currently assigned to these classes using 120 conserved single-copy marker genes as well as rRNA genes. The overwhelming majority of markers reject the inclusion of the classes and in the phylum . Instead, the great majority of currently recognized members of the class are better classified into four novel phylum-level lineages. We propose the names phyl. nov. and phyl. nov. for two of these phyla, based on the oldest validly published names in each lineage, and retain the placeholder name SAR324 for the third phylum pending formal description of type material. Members of the class represent a separate phylum for which we propose the name phyl. nov. based on priority in the literature and general recognition of the genus phyl. nov. includes the taxa previously classified in the phylum , and these reclassifications imply that the ability of sulphate reduction was vertically inherited in the rather than laterally acquired as previously inferred. Our analysis also indicates the independent acquisition of predatory behaviour in the phyla and , which is consistent with their distinct modes of action. This work represents a stable reclassification of one of the most taxonomically challenging areas of the bacterial tree and provides a robust framework for future ecological and systematic studies.

  • Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization.

    Pereira FC, Wasmund K, Cobankovic I, Jehmlich N, Herbold CW, Lee KS, Sziranyi B, Vesely C, Decker T, Stocker R, Warth B, von Bergen M, Wagner M, Berry D
    2020 - Nat Commun, 1: 5104


    Many intestinal pathogens, including Clostridioides difficile, use mucus-derived sugars as crucial nutrients in the gut. Commensals that compete with pathogens for such nutrients are therefore ecological gatekeepers in healthy guts, and are attractive candidates for therapeutic interventions. Nevertheless, there is a poor understanding of which commensals use mucin-derived sugars in situ as well as their potential to impede pathogen colonization. Here, we identify mouse gut commensals that utilize mucus-derived monosaccharides within complex communities using single-cell stable isotope probing, Raman-activated cell sorting and mini-metagenomics. Sequencing of cell-sorted fractions reveals members of the underexplored family Muribaculaceae as major mucin monosaccharide foragers, followed by members of Lachnospiraceae, Rikenellaceae, and Bacteroidaceae families. Using this information, we assembled a five-member consortium of sialic acid and N-acetylglucosamine utilizers that impedes C. difficile's access to these mucosal sugars and impairs pathogen colonization in antibiotic-treated mice. Our findings underscore the value of targeted approaches to identify organisms utilizing key nutrients and to rationally design effective probiotic mixtures.

  • Environmental and intestinal phylum Firmicutes bacteria metabolize the plant sugar sulfoquinovose via a 6-deoxy-6-sulfofructose transaldolase pathway

    Frommeyer B, Fiedler AW, Oehler SR, Hanson BT, Loy A, Franchini P, Spiteller D, Schleheck D
    2020 - iScience, 23: 101510


    Bacterial degradation of the sugar sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose) produced by plants, algae and cyanobacteria, is an important component of the biogeochemical carbon and sulfur cycles. Here, we reveal a third biochemical pathway for primary SQ degradation in an aerobic Bacillus aryabhattaistrain. An isomerase converts SQ to 6-deoxy-6-sulfofructose (SF). A novel transaldolase enzyme cleaves the SF to 3-sulfolactaldehyde (SLA), while the non-sulfonated C3-(glycerone)-moiety is transferred to an acceptor molecule, glyceraldehyde phosphate (GAP), yielding fructose-6-phosphate (F6P). Intestinal anaerobic bacteria such as Enterococcus gilvus, Clostridium symbiosum and Eubacterium rectale strains also express transaldolase-pathway gene clusters during fermentative growth with SQ. The now three known biochemical strategies for SQ catabolism reflect adaptations to the aerobic or anaerobic life-style of the different bacteria. The occurrence of these pathways in intestinal (family) Enterobacteriaceae and (phylum) Firmicutes strains further highlights a potential importance of metabolism of green-diet SQ by gut microbial communities to, ultimately, hydrogen sulfide.

  • A refined set of rRNA-targeted oligonucleotide probes for in situ detection and quantification of ammonia-oxidizing bacteria

    Lukumbuzya M, Kristensen JM, Kitzinger K, Pommerening-Roser A, Nielsen PH, Wagner M, Daims H, Pjevac P
    2020 - Water Res., 186: 116372
    ammonia oxidizing bacteria FISH picture


    Ammonia-oxidizing bacteria (AOB) of the betaproteobacterial genera Nitrosomonas and Nitrosospira are key nitrifying microorganisms in many natural and engineered ecosystems. Since many AOB remain uncultured, fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes has been one of the most widely used approaches to study the community composition, abundance, and other features of AOB directly in environmental samples. However, the established and widely used AOB-specific 16S rRNA-targeted FISH probes were designed up to two decades ago, based on much smaller rRNA gene sequence datasets than available today. Several of these probes cover their target AOB lineages incompletely and suffer from a weak target specificity, which causes cross-hybridization of probes that should detect different AOB lineages. Here, a set of new highly specific 16S rRNA-targeted oligonucleotide probes was developed and experimentally evaluated that complements the existing probes and enables the specific detection and differentiation of the known, major phylogenetic clusters of betaproteobacterial AOB. The new probes were successfully applied to visualize and quantify AOB in activated sludge and biofilm samples from seven pilot- and full-scale wastewater treatment systems. Based on its improved target group coverage and specificity, the refined probe set will facilitate future in situ analyses of AOB.

  • Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment

    Buongiorno J, Sipes K, Wasmund K, Loy A, Lloyd K
    2020 - PLoS One, 15: e0234839


    Distinct lineages of Gammaproteobacteria clade Woeseiales are globally distributed in marine sediments, based on metagenomic and 16S rRNA gene analysis. Yet little is known about why they are dominant or their ecological role in Arctic fjord sediments, where glacial retreat is rapidly imposing change. This study combined 16S rRNA gene analysis, metagenome-assembled genomes (MAGs), and genome-resolved metatranscriptomics uncovered the in situ abundance and transcriptional activity of Woeseiales with burial in four shallow sediment sites of Kongsfjorden and Van Keulenfjorden of Svalbard (79°N). We present five novel Woeseiales MAGs and show transcriptional evidence for metabolic plasticity during burial, including sulfur oxidation with reverse dissimilatory sulfite reductase (dsrAB) down to 4 cm depth and nitrite reduction down to 6 cm depth. A single stress protein, spore protein SP21 (hspA), had a tenfold higher mRNA abundance than any other transcript, and was a hundredfold higher on average than other transcripts. At three out of the four sites, SP21 transcript abundance increased with depth, while total mRNA abundance and richness decreased, indicating a shift in investment from metabolism and other cellular processes to build-up of spore protein SP21. The SP21 gene in MAGs was often flanked by genes involved in membrane-associated stress response. The ability of Woeseiales to shift from sulfur oxidation to nitrite reduction with burial into marine sediments with decreasing access to overlying oxic bottom waters, as well as enter into a dormant state dominated by SP21, may account for its ubiquity and high abundance in marine sediments worldwide, including those of the rapidly shifting Arctic.

  • It Takes a Village: Discovering and Isolating the Nitrifiers.

    2020 - Front Microbiol, 1900


    It has been almost 150 years since Jean-Jacques Schloesing and Achille Müntz discovered that the process of nitrification, the oxidation of ammonium to nitrate, is a biological process carried out by microorganisms. In the following 15 years, numerous researchers independently contributed paradigm shifting discoveries that formed the foundation of nitrification and nitrification-related research. One of them was Sergei Winogradsky, whose major accomplishments include the discovery of both lithotrophy (in sulfur-oxidizing bacteria) and chemoautotrophy (in nitrifying bacteria). However, Winogradsky often receives most of the credit for many other foundational nitrification discoveries made by his contemporaries. This accumulation of credit over time is at least in part due to the increased attention, Winogradsky receives in the scientific literature and textbooks as a "founder of microbiology" and "the founder of microbial ecology." Here, some light is shed on several other researchers who are often overlooked, but whose work was instrumental to the emerging field of nitrification and to the work of Winogradsky himself. Specifically, the discovery of the biological process of nitrification by Schloesing and Müntz, the isolation of the first nitrifier by Grace and Percy Frankland, and the observation that nitrification is carried out by two distinct groups of microorganisms by Robert Warington are highlighted. Finally, the more recent discoveries of the chemolithoautotrophic ammonia-oxidizing archaea and complete ammonia oxidizers are put into this historical context.

  • Dietary Supplementation with Sugar Beet Fructooligosaccharides and Garlic Residues Promotes Growth of Beneficial Bacteria and Increases Weight Gain in Neonatal Lambs.

    Quijada NM, Bodas R, Lorenzo JM, Schmitz-Esser S, Rodríguez-Lázaro D, Hernández M
    2020 - Biomolecules, 8: in press


    The proper development of the early gastrointestinal tract (GIT) microbiota is critical for newborn ruminants. This microbiota is susceptible to modification by diverse external factors (such as diet) that can lead to long-lasting results when occurring in young ruminants. Dietary supplementation with prebiotics, ingredients nondigestible and nonabsorbable by the host that stimulate the growth of beneficial GIT bacteria, has been applied worldwide as a potential approach in order to improve ruminant health and production yields. However, how prebiotics affect the GIT microbiota during ruminants' early life is still poorly understood. We investigated the effect of milk supplementation with a combination of two well-known prebiotics, fructooligosaccharides (FOS) from sugar beet and garlic residues (all together named as "additive"), exerted on preweaned lamb growth and the composition of their fecal microbiota, by using 16S rRNA gene amplicon high-throughput sequencing. The results showed a significant increase in the mean daily weight gain of lambs fed with the additive. Lamb fecal microbiota was also influenced by the additive intake, as additive-diet lambs showed lower bacterial diversity and were significantly more abundant in , , and . These bacteria have been previously reported to confer beneficial properties to the ruminant, including promotion of growth and health status, and our results showed that they were strongly linked to the additive intake and the increased weight gain of lambs. This study points out the combination of FOS from sugar beet and garlic residues as a potential prebiotic to be used in young ruminants' nutrition in order to improve production yields.

  • Molecular causes of an evolutionary shift along the parasitism-mutualism continuum in a bacterial symbiont.

    Herrera P, Schuster L, Wentrup C, König L, Kempinger T, Na H, Schwarz J, Köstlbacher S, Wascher F, Zojer M, Rattei T, Horn M
    2020 - Proc. Natl. Acad. Sci. U.S.A., 117: 21658-21666


    Symbiosis with microbes is a ubiquitous phenomenon with a massive impact on all living organisms, shaping the world around us today. Theoretical and experimental studies show that vertical transmission of symbionts leads to the evolution of mutualistic traits, whereas horizontal transmission facilitates the emergence of parasitic features. However, these studies focused on phenotypic data, and we know little about underlying molecular changes at the genomic level. Here, we combined an experimental evolution approach with infection assays, genome resequencing, and global gene expression analysis to study the effect of transmission mode on an obligate intracellular bacterial symbiont. We show that a dramatic shift in the frequency of genetic variants, coupled with major changes in gene expression, allow the symbiont to alter its position in the parasitism-mutualism continuum depending on the mode of between-host transmission. We found that increased parasitism in horizontally transmitted chlamydiae residing in amoebae was a result of processes occurring at the infectious stage of the symbiont's developmental cycle. Specifically, genes involved in energy production required for extracellular survival and the type III secretion system-the symbiont's primary virulence mechanism-were significantly up-regulated. Our results identify the genomic and transcriptional dynamics sufficient to favor parasitic or mutualistic strategies.

  • Composition and activity of nitrifier communities in soil are unresponsive to elevated temperature and CO, but strongly affected by drought.

    Séneca J, Pjevac P, Canarini A, Herbold CW, Zioutis C, Dietrich M, Simon E, Prommer J, Bahn M, Pötsch EM, Wagner M, Wanek W, Richter A
    2020 - ISME J, 12: 3038-3053
    soil nitrifier response to climate change


    Nitrification is a fundamental process in terrestrial nitrogen cycling. However, detailed information on how climate change affects the structure of nitrifier communities is lacking, specifically from experiments in which multiple climate change factors are manipulated simultaneously. Consequently, our ability to predict how soil nitrogen (N) cycling will change in a future climate is limited. We conducted a field experiment in a managed grassland and simultaneously tested the effects of elevated atmospheric CO, temperature, and drought on the abundance of active ammonia-oxidizing bacteria (AOB) and archaea (AOA), comammox (CMX) Nitrospira, and nitrite-oxidizing bacteria (NOB), and on gross mineralization and nitrification rates. We found that N transformation processes, as well as gene and transcript abundances, and nitrifier community composition were remarkably resistant to individual and interactive effects of elevated CO and temperature. During drought however, process rates were increased or at least maintained. At the same time, the abundance of active AOB increased probably due to higher NH availability. Both, AOA and comammox Nitrospira decreased in response to drought and the active community composition of AOA and NOB was also significantly affected. In summary, our findings suggest that warming and elevated CO have only minor effects on nitrifier communities and soil biogeochemical variables in managed grasslands, whereas drought favors AOB and increases nitrification rates. This highlights the overriding importance of drought as a global change driver impacting on soil microbial community structure and its consequences for N cycling.

  • Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira.

    Daebeler A, Kitzinger K, Koch H, Herbold CW, Steinfeder M, Schwarz J, Zechmeister T, Karst SM, Albertsen M, Nielsen PH, Wagner M, Daims H
    2020 - ISME J, 12: 2967-2979
    Ca. N. alkalitolerans


    Nitrite-oxidizing bacteria of the genus Nitrospira are key players of the biogeochemical nitrogen cycle. However, little is known about their occurrence and survival strategies in extreme pH environments. Here, we report on the discovery of physiologically versatile, haloalkalitolerant Nitrospira that drive nitrite oxidation at exceptionally high pH. Nitrospira distribution, diversity, and ecophysiology were studied in hypo- and subsaline (1.3-12.8 g salt/l), highly alkaline (pH 8.9-10.3) lakes by amplicon sequencing, metagenomics, and cultivation-based approaches. Surprisingly, not only were Nitrospira populations detected, but they were also considerably diverse with presence of members from  Nitrospira lineages I, II and IV. Furthermore, the ability of Nitrospira enrichment cultures to oxidize nitrite at neutral to highly alkaline pH of 10.5 was demonstrated. Metagenomic analysis of a newly enriched Nitrospira lineage IV species, "Candidatus Nitrospira alkalitolerans", revealed numerous adaptive features of this organism to its extreme environment. Among them were a sodium-dependent N-type ATPase and NADH:quinone oxidoreductase next to the proton-driven forms usually found in Nitrospira. Other functions aid in pH and cation homeostasis and osmotic stress defense. "Ca. Nitrospira alkalitolerans" also possesses group 2a and 3b [NiFe] hydrogenases, suggesting it can use hydrogen as alternative energy source. These results reveal how Nitrospira cope with strongly fluctuating pH and salinity conditions and expand our knowledge of nitrogen cycling in extreme habitats.

  • Gut microbiota and undigested food constituents modify toxin composition and suppress the genotoxicity of a naturally occurring mixture of Alternaria toxins in vitro.

    Crudo F, Aichinger G, Mihajlovic J, Dellafiora L, Varga E, Puntscher H, Warth B, Dall'Asta C, Berry D, Marko D
    2020 - Arch. Toxicol., in press


    Molds of the genus Alternaria produce several mycotoxins, some of which may pose a threat for health due to their genotoxicity. Due to the lack of adequate toxicological and occurrence data, they are currently not regulated. Interactions between mycotoxins, gut microbiota and food constituents might occur after food ingestion, modifying the bioavailability and, therefore, overall toxicity of mycotoxins. The present work aimed to investigate the impact of in vitro short-term fecal incubation on the in vitro DNA-damaging effects exerted by 5 µg/mL of an Alternaria alternata extract, containing, among others, 15 nM alternariol, 12 nM alternariol monomethyl ether, 241 nM altertoxin II and 301 nM stemphyltoxin III, all of which are known as genotoxic. The involvement of microorganisms, undigested food constituents and soluble substances of human fecal samples in modifying the composition and the genotoxicity of the extract was investigated through the application of LC-MS/MS analysis and comet assays in HT-29 cells. Results showed that the potential of the mycotoxins to induce DNA strand breaks was almost completely quenched, even before anaerobic incubation, by contact with the different fractions of the fecal samples, while the potency to induce formamidopyrimidine DNA glycosylase (FPG)-sensitive sites was only slightly reduced. These effects were in line with a reduction of mycotoxin concentrations found in samples analyzed by LC-MS/MS. Although a direct correlation between the metabolic activity of the gut microbiota and modifications in mycotoxin contents was not clearly observed, adsorptive phenomena to bacterial cells and to undigested food constituents might explain the observed modifications.

  • Microbiome definition re-visited: old concepts and new challenges.

    Berg G, Rybakova D, Fischer D, Cernava T, Vergès MC, Charles T, Chen X, Cocolin L, Eversole K, Corral GH, Kazou M, Kinkel L, Lange L, Lima N, Loy A, Macklin JA, Maguin E, Mauchline T, McClure R, Mitter B, Ryan M, Sarand I, Smidt H, Schelkle B, Roume H, Kiran GS, Selvin J, Souza RSC, van Overbeek L, Singh BK, Wagner M, Walsh A, Sessitsch A, Schloter M
    2020 - Microbiome, 1: 103


    The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term "microbiome." Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role. Video Abstract.

  • Chlamydiae in the Environment.

    Collingro A, Köstlbacher S, Horn M
    2020 - Trends Microbiol, 11: 877-888



  • Roadmap for naming uncultivated Archaea and Bacteria.

    Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rosselló-Móra R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Hedlund BP, Reysenbach AL
    2020 - Nat Microbiol, 8: 987-994
    Roadmap for naming uncultured microbes


    The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.

  • The role of metal contamination in shaping microbial communities in heavily polluted marine sediments

    Di Cesare A, Pjevac P, Eckert E, Curkov N, Miko Šparica M, Corno G, Orlić S
    2020 - Environ. Pollut., 265: 114823


    Microorganisms in coastal sediments are fundamental for ecosystem functioning, and regulate processes relevant in global biogeochemical cycles. Still, our understanding of the effects anthropogenic perturbation and pollution can have on microbial communities in marine sediments is limited. We surveyed the microbial diversity, and the occurrence and abundance of metal and antibiotic resistance genes is sediments collected from the Pula Bay (Croatia), one of the most significantly polluted sites along the Croatian coast. With a collection of 14 samples from the bay area, we were able to generate a detailed status quo picture of a site that only recently started a cleaning and remediation process (closing of sewage pipes and reduction of industrial activity). The concentrations of heavy metals in Pula Bay sediments are significantly higher than in pristine sediments from the Adriatic Sea, and in some cases, manifold exceed international sediment quality guidelines. While the sedimentary concentrations of heavy metals did significantly influence the abundance of the tested metal resistance genes, no strong effect of heavy metal pollution on the overall microbial community composition was observed. Like in many other marine sediments, Gammaproteobacteria, Bacteroidota and Desulfobacterota dominated the microbial community composition in most samples, and community assembly was primarily driven by water column depth and nutrient (carbon and nitrogen) availability, regardless of the degree of heavy metal pollution.

  • Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan.

    Sichert A, Corzett CH, Schechter MS, Unfried F, Markert S, Becher D, Fernandez-Guerra A, Liebeke M, Schweder T, Polz MF, Hehemann JH
    2020 - Nat Microbiol, 8: 1026-1039


    Brown algae are important players in the global carbon cycle by fixing carbon dioxide into 1 Gt of biomass annually, yet the fate of fucoidan-their major cell wall polysaccharide-remains poorly understood. Microbial degradation of fucoidans is slower than that of other polysaccharides, suggesting that fucoidans are more recalcitrant and may sequester carbon in the ocean. This may be due to the complex, branched and highly sulfated structure of fucoidans, which also varies among species of brown algae. Here, we show that 'Lentimonas' sp. CC4, belonging to the Verrucomicrobia, acquired a remarkably complex machinery for the degradation of six different fucoidans. The strain accumulated 284 putative fucoidanases, including glycoside hydrolases, sulfatases and carbohydrate esterases, which are primarily located on a 0.89-megabase pair plasmid. Proteomics reveals that these enzymes assemble into substrate-specific pathways requiring about 100 enzymes per fucoidan from different species of brown algae. These enzymes depolymerize fucoidan into fucose, which is metabolized in a proteome-costly bacterial microcompartment that spatially constrains the metabolism of the toxic intermediate lactaldehyde. Marine metagenomes and microbial genomes show that Verrucomicrobia including 'Lentimonas' are abundant and highly specialized degraders of fucoidans and other complex polysaccharides. Overall, the complexity of the pathways underscores why fucoidans are probably recalcitrant and more slowly degraded, since only highly specialized organisms can effectively degrade them in the ocean.

  • Crypt residing bacteria and proximal colonic carcinogenesis in a mouse model of Lynch syndrome.

    Lang M, Baumgartner M, Rożalska A, Frick A, Riva A, Jarek M, Berry D, Gasche C
    2020 - Int. J. Cancer, 8: 2316-2326


    Colorectal cancer is a multifactorial disease involving inherited DNA mutations, environmental factors, gut inflammation and intestinal microbiota. Certain germline mutations within the DNA mismatch repair system are associated with Lynch syndrome tumors including right-sided colorectal cancer with mucinous phenotype and presence of an inflammatory infiltrate. Such tumors are more often associated with bacterial biofilms, which may contribute to disease onset and progression. Inflammatory bowel diseases are also associated with colorectal cancer and intestinal dysbiosis. Herein we addressed the question, whether inflammation can aggravate colorectal cancer development under mismatch repair deficiency. MSH2 mice were crossed into the IL-10 background to study the importance of inflammation and mucosal bacteria as a driver of tumorigenesis in a Lynch syndrome mouse model. An increase in large bowel tumorigenesis was found in double knockout mice both under conventional housing and under specific pathogen-free conditions. This increase was mostly due to the development of proximal tumors, a hotspot for tumorigenesis in Lynch syndrome, and was associated with a higher degree of inflammation. Additionally, bacterial invasion into the mucus of tumor crypts was observed in the proximal tumors. Inflammation shifted fecal and mucosal microbiota composition and was associated with enrichment in Escherichia-Shigella as well as Akkermansia, Bacteroides and Parabacteroides genera in fecal samples. Tumor-bearing double knockout mice showed a similar enrichment for Escherichia-Shigella and Parabacteroides. Lactobacilli, Lachnospiraceae and Muribaculaceae family members were depleted upon inflammation. In summary, chronic inflammation aggravates colonic tumorigenesis under mismatch repair deficiency and is associated with a shift in microbiota composition.

  • Energetic Basis of Microbial Growth and Persistence in Desert Ecosystems.

    Leung PM, Bay SK, Meier DV, Chiri E, Cowan DA, Gillor O, Woebken D, Greening C
    2020 - mSystems, 2: in press


    Microbial life is surprisingly abundant and diverse in global desert ecosystems. In these environments, microorganisms endure a multitude of physicochemical stresses, including low water potential, carbon and nitrogen starvation, and extreme temperatures. In this review, we summarize our current understanding of the energetic mechanisms and trophic dynamics that underpin microbial function in desert ecosystems. Accumulating evidence suggests that dormancy is a common strategy that facilitates microbial survival in response to water and carbon limitation. Whereas photoautotrophs are restricted to specific niches in extreme deserts, metabolically versatile heterotrophs persist even in the hyper-arid topsoils of the Atacama Desert and Antarctica. At least three distinct strategies appear to allow such microorganisms to conserve energy in these oligotrophic environments: degradation of organic energy reserves, rhodopsin- and bacteriochlorophyll-dependent light harvesting, and oxidation of the atmospheric trace gases hydrogen and carbon monoxide. In turn, these principles are relevant for understanding the composition, functionality, and resilience of desert ecosystems, as well as predicting responses to the growing problem of desertification.

  • Activity and metabolic versatility of complete ammonia oxidizers in full-scale wastewater treatment systems.

    Yang Y, Daims H, Liu Y, Herbold CW, Pjevac P, Lin JG, Li M, Gu JD
    2020 - mBio, 11: e03175-19


    The recent discovery of complete ammonia oxidizers (comammox) contradicts the paradigm that chemolithoautotrophic nitrification is always catalyzed by two different microorganisms. However, our knowledge of the survival strategies of comammox in complex ecosystems, such as full-scale wastewater treatment plants (WWTPs), remains limited. Analyses of genomes and transcriptomes of four comammox organisms from two full-scale WWTPs revealed that comammox were active and showed a surprisingly high metabolic versatility. A gene cluster for the utilization of urea and a gene encoding cyanase suggest that comammox may use diverse organic nitrogen compounds in addition to free ammonia as the substrates. The comammox organisms also encoded the genomic potential for multiple alternative energy metabolisms, including respiration with hydrogen, formate, and sulfite as electron donors. Pathways for the biosynthesis and degradation of polyphosphate, glycogen, and polyhydroxyalkanoates as intracellular storage compounds likely help comammox survive unfavorable conditions and facilitate switches between lifestyles in fluctuating environments. One of the comammox strains acquired from the anaerobic tank encoded and transcribed genes involved in homoacetate fermentation or in the utilization of exogenous acetate, both pathways being unexpected in a nitrifying bacterium. Surprisingly, this strain also encoded a respiratory nitrate reductase which has not yet been found in any other genome and might confer a selective advantage to this strain over other strains in anoxic conditions. The discovery of comammox in the genus changes our perception of nitrification. However, genomes of comammox organisms have not been acquired from full-scale WWTPs, and very little is known about their survival strategies and potential metabolisms in complex wastewater treatment systems. Here, four comammox metagenome-assembled genomes and metatranscriptomic data sets were retrieved from two full-scale WWTPs. Their impressive and-among nitrifiers-unsurpassed ecophysiological versatility could make comammox an interesting target for optimizing nitrification in current and future bioreactor configurations.

  • Raman-based sorting of microbial cells to link functions to their genes.

    Lee KS, Wagner M, Stocker R
    2020 - Microb Cell, 3: 62-65


    In our recent work, we developed an optofluidic platform that allows a direct link to be made between the phenotypes (functions) and the genotypes (genes) of microbial cells within natural communities. By combining stable isotope probing, optical tweezers, Raman microspectroscopy, and microfluidics, the platform performs automated Raman-based sorting of taxa from within a complex community in terms of their functional properties. In comparison with manual sorting approaches, our method provides high throughput (up to 500 cells per hour) and very high sorting accuracy (98.3 ± 1.7%), and significantly reduces the human labour required. The system provides an efficient manner to untangle the contributions of individual members within environmental and host-associated microbiomes. In this News and Thoughts, we provide an overview of our platform, describe potential applications, suggest ways in which the system could be improved, and discuss future directions in which Raman-based analysis of microbial populations might be developed.

  • Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil.

    Alteio LV, Schulz F, Seshadri R, Varghese N, Rodriguez-Reillo W, Ryan E, Goudeau D, Eichorst SA, Malmstrom RR, Bowers RM, Katz LA, Blanchard JL, Woyke T
    2020 - mSystems, 2: in press


    Soil ecosystems harbor diverse microorganisms and yet remain only partially characterized as neither single-cell sequencing nor whole-community sequencing offers a complete picture of these complex communities. Thus, the genetic and metabolic potential of this "uncultivated majority" remains underexplored. To address these challenges, we applied a pooled-cell-sorting-based mini-metagenomics approach and compared the results to bulk metagenomics. Informatic binning of these data produced 200 mini-metagenome assembled genomes (sorted-MAGs) and 29 bulk metagenome assembled genomes (MAGs). The sorted and bulk MAGs increased the known phylogenetic diversity of soil taxa by 7.2% with respect to the Joint Genome Institute IMG/M database and showed clade-specific sequence recruitment patterns across diverse terrestrial soil metagenomes. Additionally, sorted-MAGs expanded the rare biosphere not captured through MAGs from bulk sequences, exemplified through phylogenetic and functional analyses of members of the phylum Analysis of 67 sorted-MAGs showed conserved patterns of carbon metabolism across four clades. These results indicate that mini-metagenomics enables genome-resolved investigation of predicted metabolism and demonstrates the utility of combining metagenomics methods to tap into the diversity of heterogeneous microbial assemblages. Microbial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of untapped genetic diversity. To address some of the challenges associated with bulk metagenomics as well as low throughput of single-cell genomics, we applied flow cytometry-enabled mini-metagenomics to capture expanded microbial diversity from forest soil and compare it to soil bulk metagenomics. Our resulting data from this pooled-cell sorting approach combined with bulk metagenomics revealed increased phylogenetic diversity through novel soil taxa and rare biosphere members. In-depth analysis of genomes within the highly represented phylum provided insights into conserved and clade-specific patterns of carbon metabolism.

  • Using Colonization Assays and Comparative Genomics To Discover Symbiosis Behaviors and Factors in Vibrio fischeri.

    Bongrand C, Moriano-Gutierrez S, Arevalo P, McFall-Ngai M, Visick KL, Polz M, Ruby EG
    2020 - mBio, 2: in press


    The luminous marine Gram-negative bacterium () is the natural light organ symbiont of several squid species, including the Hawaiian bobtail squid, , and the Japanese bobtail squid, Work with has shown how the bacteria establish their niche in the light organ of the newly hatched host. Two types of strains have been distinguished based upon their behavior in cocolonization competition assays in juvenile , i.e., (i) niche-sharing or (ii) niche-dominant behavior. This study aimed to determine whether these behaviors are observed with other strains or whether they are specific to those isolated from light organs. Cocolonization competition assays between strains isolated from the congeneric squid or from other marine animals revealed the same sharing or dominant behaviors. In addition, whole-genome sequencing of these strains showed that the dominant behavior is polyphyletic and not associated with the presence or absence of a single gene or genes. Comparative genomics of 44 squid light organ isolates from around the globe led to the identification of symbiosis-specific candidates in the genomes of these strains. Colonization assays using genetic derivatives with deletions of these candidates established the importance of two such genes in colonization. This study has allowed us to expand the concept of distinct colonization behaviors to strains isolated from a number of squid and fish hosts. There is an increasing recognition of the importance of strain differences in the ecology of a symbiotic bacterial species and, in particular, how these differences underlie crucial interactions with their host. Nevertheless, little is known about the genetic bases for these differences, how they manifest themselves in specific behaviors, and their distribution among symbionts of different host species. In this study, we sequenced the genomes of isolated from the tissues of squids and fishes and applied comparative genomics approaches to look for patterns between symbiont lineages and host colonization behavior. In addition, we identified the only two genes that were exclusively present in all strains isolated from the light organs of sepiolid squid species. Mutational studies of these genes indicated that they both played a role in colonization of the squid light organ, emphasizing the value of applying a comparative genomics approach in the study of symbioses.

  • The Signal and the Noise: Characteristics of Antisense RNA in Complex Microbial Communities.

    Michaelsen TY, Brandt J, Singleton CM, Kirkegaard RH, Wiesinger J, Segata N, Albertsen M
    2020 - mSystems, 1: in press



  • Diarrhoeal events can trigger long-term Clostridium difficile colonization with recurrent blooms.

    VanInsberghe D, Elsherbini JA, Varian B, Poutahidis T, Erdman S, Polz MF
    2020 - Nat Microbiol, 4: 642-650


    Although Clostridium difficile is widely considered an antibiotic- and hospital-associated pathogen, recent evidence indicates that this is an insufficient depiction of the risks and reservoirs. A common thread that links all major risk factors of infection is their association with gastrointestinal disturbances, but this relationship to C. difficile colonization has never been tested directly. Here, we show that disturbances caused by diarrhoeal events trigger susceptibility to C. difficile colonization. Using survey data of the human gut microbiome, we detected C. difficile colonization and blooms in people recovering from food poisoning and Vibrio cholerae infections. Carriers remained colonized for year-long time scales and experienced highly variable patterns of C. difficile abundance, where increased shedding over short periods of 1-2 d interrupted week-long periods in which C. difficile was undetectable. Given that short shedding events were often linked to gastrointestinal disturbances, our results help explain why C. difficile is frequently detected as a co-infecting pathogen in patients with diarrhoea. To directly test the impact of diarrhoea on susceptibility to colonization, we developed a mouse model of variable disturbance intensity, which allowed us to monitor colonization in the absence of disease. As mice exposed to avirulent C. difficile spores ingested increasing quantities of laxatives, more individuals experienced C. difficile blooms. Our results indicate that the likelihood of colonization is highest in the days immediately following acute disturbances, suggesting that this could be an important window during which transmission could be interrupted and the incidence of infection lowered.

  • Single cell analyses reveal contrasting life strategies of the two main nitrifiers in the ocean.

    Kitzinger K, Marchant HK, Bristow LA, Herbold CW, Padilla CC, Kidane AT, Littmann S, Daims H, Pjevac P, Stewart FJ, Wagner M, Kuypers MMM
    2020 - Nat Commun, 1: 767
    Nitrospina AOA in situ growth rates


    Nitrification, the oxidation of ammonia via nitrite to nitrate, is a key process in marine nitrogen (N) cycling. Although oceanic ammonia and nitrite oxidation are balanced, ammonia-oxidizing archaea (AOA) vastly outnumber the main nitrite oxidizers, the bacterial Nitrospinae. The ecophysiological reasons for this discrepancy in abundance are unclear. Here, we compare substrate utilization and growth of Nitrospinae to AOA in the Gulf of Mexico. Based on our results, more than half of the Nitrospinae cellular N-demand is met by the organic-N compounds urea and cyanate, while AOA mainly assimilate ammonium. Nitrospinae have, under in situ conditions, around four-times higher biomass yield and five-times higher growth rates than AOA, despite their ten-fold lower abundance. Our combined results indicate that differences in mortality between Nitrospinae and AOA, rather than thermodynamics, biomass yield and cell size, determine the abundances of these main marine nitrifiers. Furthermore, there is no need to invoke yet undiscovered, abundant nitrite oxidizers to explain nitrification rates in the ocean.

  • Culture-independent tracking of Vibrio cholerae lineages reveals complex spatiotemporal dynamics in a natural population.

    Kirchberger PC, Orata FD, Nasreen T, Kauffman KM, Tarr CL, Case RJ, Polz MF, Boucher YF
    2020 - Environ. Microbiol., in press


    Populations of the bacterium Vibrio cholerae consist of dozens of distinct lineages, with primarily (but not exclusively) members of the pandemic generating lineage capable of causing the diarrhoeal disease cholera. Assessing the composition and temporal dynamics of such populations requires extensive isolation efforts and thus only rarely covers large geographic areas or timeframes exhaustively. We developed a culture-independent amplicon sequencing strategy based on the protein-coding gene viuB (vibriobactin utilization) to study the structure of a V. cholerae population over the course of a summer. We show that the 26 co-occurring V. cholerae lineages continuously compete for limited space on nutrient-rich particles where only a few of them can grow to large numbers. Differential abundance of lineages between locations and size-fractions associated with a particle-attached or free-swimming lifestyle could reflect adaptation to various environmental niches. In particular, a major V. cholerae lineage occasionally grows to large numbers on particles but remain undetectable using isolation-based methods, indicating selective culturability for some members of the species. We thus demonstrate that isolation-based studies may not accurately reflect the structure and complex dynamics of V. cholerae populations and provide a scalable high-throughput method for both epidemiological and ecological approaches to studying this species.

  • Transcriptomic Response of Nitrosomonas europaea Transitioned from Ammonia- to Oxygen-Limited Steady-State Growth.

    Sedlacek CJ, Giguere AT, Dobie MD, Mellbye BL, Ferrell RV, Woebken D, Sayavedra-Soto LA, Bottomley PJ, Daims H, Wagner M, Pjevac P
    2020 - mSystems, 1: e00562-19
    N. europaea electron flow


    Ammonia-oxidizing microorganisms perform the first step of nitrification, the oxidation of ammonia to nitrite. The bacterium is the best-characterized ammonia oxidizer to date. Exposure to hypoxic conditions has a profound effect on the physiology of , e.g., by inducing nitrifier denitrification, resulting in increased nitric and nitrous oxide production. This metabolic shift is of major significance in agricultural soils, as it contributes to fertilizer loss and global climate change. Previous studies investigating the effect of oxygen limitation on have focused on the transcriptional regulation of genes involved in nitrification and nitrifier denitrification. Here, we combine steady-state cultivation with whole-genome transcriptomics to investigate the overall effect of oxygen limitation on Under oxygen-limited conditions, growth yield was reduced and ammonia-to-nitrite conversion was not stoichiometric, suggesting the production of nitrogenous gases. However, the transcription of the principal nitric oxide reductase (cNOR) did not change significantly during oxygen-limited growth, while the transcription of the nitrite reductase-encoding gene () was significantly lower. In contrast, both heme-copper-containing cytochrome oxidases encoded by were upregulated during oxygen-limited growth. Particularly striking was the significant increase in transcription of the B-type heme-copper oxidase, proposed to function as a nitric oxide reductase (sNOR) in ammonia-oxidizing bacteria. In the context of previous physiological studies, as well as the evolutionary placement of sNOR with regard to other heme-copper oxidases, these results suggest sNOR may function as a high-affinity terminal oxidase in and other ammonia-oxidizing bacteria. Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, , growing under oxygen-limited conditions.

  • The role of gut microbiota, butyrate and proton pump inhibitors in amyotrophic lateral sclerosis: a systematic review.

    Erber AC, Cetin H, Berry D, Schernhammer ES
    2020 - Int. J. Neurosci., 7: 727-735


    We conducted a systematic review on existing literature in humans and animals, linking the gut microbiome with amyotrophic lateral sclerosis (ALS). Additionally, we sought to explore the role of the bacterially produced metabolite butyrate as well as of proton pump inhibitors (PPIs) in these associations. Following PRISMA guidelines for systematic literature reviews, four databases (Medline, Scopus, Embase and Web of Science) were searched and screened by two independent reviewers against defined inclusion criteria. Six studies in humans and six animal studies were identified, summarized and reviewed. Overall, the evidence accrued to date is supportive of changes in the gut microbiome being associated with ALS risk, and potentially progression, though observational studies are small (describing a total of 145 patients with ALS across all published studies), and not entirely conclusive. With emerging studies beginning to apply metagenome sequencing, more clarity regarding the importance and promise of the gut microbiome in ALS can be expected. Future studies may also help establish the therapeutic potential of butyrate, and the role of PPIs in these associations.

  • Archaeal nitrification is constrained by copper complexation with organic matter in municipal wastewater treatment plants.

    Gwak JH, Jung MY, Hong H, Kim JG, Quan ZX, Reinfelder JR, Spasov E, Neufeld JD, Wagner M, Rhee SK
    2020 - ISME J, 2: 335-346


    Consistent with the observation that ammonia-oxidizing bacteria (AOB) outnumber ammonia-oxidizing archaea (AOA) in many eutrophic ecosystems globally, AOB typically dominate activated sludge aeration basins from municipal wastewater treatment plants (WWTPs). In this study, we demonstrate that the growth of AOA strains inoculated into sterile-filtered wastewater was inhibited significantly, in contrast to uninhibited growth of a reference AOB strain. In order to identify possible mechanisms underlying AOA-specific inhibition, we show that complex mixtures of organic compounds, such as yeast extract, were highly inhibitory to all AOA strains but not to the AOB strain. By testing individual organic compounds, we reveal strong inhibitory effects of organic compounds with high metal complexation potentials implying that the inhibitory mechanism for AOA can be explained by the reduced bioavailability of an essential metal. Our results further demonstrate that the inhibitory effect on AOA can be alleviated by copper supplementation, which we observed for pure AOA cultures in a defined medium and for AOA inoculated into nitrifying sludge. Our study offers a novel mechanistic explanation for the relatively low abundance of AOA in most WWTPs and provides a basis for modulating the composition of nitrifying communities in both engineered systems and naturally occurring environments.


    Assié A, Leisch N, Meier DV, Gruber-Vodicka H, Tegetmeyer HE, Meyerdierks A, Kleiner M, Hinzke T, Joye S, Saxton M, Dubilier N, Petersen JM
    2020 - ISME J, 1: 104-122


    Most autotrophs use the Calvin-Benson-Bassham (CBB) cycle for carbon fixation. In contrast, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts ("Candidatus Thiobarba") of deep-sea mussels that have acquired a complete CBB cycle and may have lost most key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB cycle genes suggest they were acquired in multiple transfers from Gammaproteobacteria closely related to sulfur-oxidizing endosymbionts associated with the mussels, as well as from Betaproteobacteria. We hypothesize that "Ca. Thiobarba" switched from the rTCA cycle to a fully functional CBB cycle during its evolution, by acquiring genes from multiple sources, including co-occurring symbionts. We also found key CBB cycle genes in free-living Campylobacterota, suggesting that the CBB cycle may be more widespread in this phylum than previously known. Metatranscriptomics and metaproteomics confirmed high expression of CBB cycle genes in mussel-associated "Ca. Thiobarba". Direct stable isotope fingerprinting showed that "Ca. Thiobarba" has typical CBB signatures, suggesting that it uses this cycle for carbon fixation. Our discovery calls into question current assumptions about the distribution of carbon fixation pathways in microbial lineages, and the interpretation of stable isotope measurements in the environment.

Book chapters and other publications

7 Publications found
  • STILLLEBEN with Symbionts

    Athanassakis I, Berry D
    2020 - Performance Research, 25: 83-87


    STILLLEBEN. Becoming Symbionts’ proposes to value milk and its microbial constituents as primordial assets and currencies - along with cells, sperm, blood, water, and oxygen. The latest scientific research, which has suggested that there is an intimate unseen interplay between mothers and their babies via the transfer of breast milk and microbes, which actually increases the value of the currency with each exchange. The co-operation of Irini Athanassakis and David Berry is an invitation to perceive the transfer of milk not only as an interaction visible to the naked eye, but also on the microscopic level of cells and bacteria. In order to challenge us with this unseen perspective, Athanassakis encourages us to step forward and take a performative and procreative role in expanding our perception. As we are home to billions of microscopic entities, we continuously cast this part of ourselves into our surroundings, impacting and interacting with everything around us. We leave a microbial trace, a lingering residue of cells on the objects, rooms, and people that we encounter. Breast milk and formula are part of such an exchange process. If we look at the logic of microbial exchange in nursing as ‘giving’ and knowledge about symbionts for a future holo-economy based on co-operation and mutualism for collective survival.

  • Is too much fertilizer a problem?

    Sedlacek CJ, Giguere AT, Pjevac P
    2020 - Frontiers for Young Minds, 8: 63


    Fertilizers are added to crops in order to produce enough food to feed the human population. Fertilizers provide crops with nutrients like potassium, phosphorus, and nitrogen, which allow crops to grow bigger, faster, and to produce more food. Nitrogen in particular is an essential nutrient for the growth of every organismon Earth.Nitrogen is all around us and makes up about 78% of the air you breathe. However, plants and animals cannot use the nitrogen gas in the air. To grow, plants require nitrogen compounds fromthe soil,which can be produced naturally or be provided by fertilizers. However, applying excessive amounts of fertilizer leads to the release of harmful greenhouse gases into the atmosphere and the eutrophication of our waterways. Scientists are currently trying to find solutions to reduce the environmentally harmful effects of fertilizers, without reducing the amount of food we can produce when using them.

  • Thinking outside the Chlamydia box

    A Taylor-Brown, T Halter, A Polkinghorne, M Horn
    2020 - 429-458. in Chlamydia Biology. (M Tan, JH Hegemann, C Sütterlin). Caister Academic Press


    Chlamydiae have long been studied exclusively in the context of disease. Yet, accumulating evidence over nearly three decades shows that chlamydiae are ubiquitous in the environment, thriving as symbionts of unicellular eukaryotes such as amoeba and infecting a broad range of animal hosts. These chlamydiae share the characteristic chlamydial developmental cycle and other chlamydial hallmarks. Their discovery fundamentally changed our perspective on chlamydial diversity. Instead of a single genus, Chlamydia, including closely related pathogens, the chlamydiae comprise hundreds of families and genera. Investigating isolates and non-cultured representatives provided insights into features that are in common with or divergent from known Chlamydia species, and suggested that some of these chlamydiae may also be considered pathogens. Importantly, these studies have contributed to a better understanding of the biology of all chlamydiae, and they provide a framework for investigating the evolution of the chlamydial intracellular lifestyle and pathogenicity.

  • One complete and seven draft genome sequences of subdivision 1 and 3 Acidobacteria from soil

    Eichorst SA, Trojan D, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Goodwin LA, Shapiro N, Ivanova N, Kyrpides N, Woyke T, Woebken D
    2020 - Microbiology Resource Announcements, 9: 1-4


    We report eight genomes from representatives of the phylum Acidobacteriasubdivisions 1 and 3, isolated from soils. The genome sizes range from 4.9 to 6.7 Mb. Genomic analysis reveals putative genes for low- and high-affinity respiratory oxygen reductases, high-affinity hydrogenases, and the capacity to use a diverse collection of carbohydrates.

  • A genomic catalog of Earth's microbiomes

    Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, Kirton E, Faria JP, Edirisinghe JN, Henry CS, Jungbluth SP, Chivian D, Dehal P, Wood-Charlson EM, Arkin AP, Tringe SG, Visel A, IMG/M Data Consortium, Woyke T, Mouncey NJ, Ivanova NN, Kyrpides NC, Eloe-Fadrosh EA
    2020 - Nat Biotechnol, In press


    The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth's continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.

  • The genetic law of the minimum.

    Polz MF, Cordero OX
    2020 - Science, 6517: 655-656

    2020 - Microbiol Resour Announc, 9: e00220-20

