Competition in nitrate-reducing microbial communities

The biogeochemical nitrogen cycle, including nitrate reduction processes, is highly affected by human activity such as fertilization and ammonia deposition caused by fossil fuel burning. Consequently, gaining a better understanding about the ecophysiology of nitrate-reducing microbial communities is crucial for inferring the impact of anthropogenic nitrogen input. Different nitrate-reducing pathways compete with each other for the electron acceptor nitrate: Denitrifiers reduce nitrate to dinitrogen and nitrous oxide while dissimilatory nitrate reducers reduce nitrate to ammonium. The outcome of this competition has important environmental consequences: denitrification removes fixed nitrogen from the ecosystem, while dissimilatory nitrite reduction to ammonium (DNRA) keeps fixed nitrogen bioavailable. Although a lot of studies have been performed on this topic, no conclusive factors responsible for the dominance of one or the other process could be identified so far. In this thesis, the competition between nitrate reduction pathways was addressed by combining continuous culture incubations of natural microbial communities with stable isotope labeling and metagenomics, complemented with metatranscriptomics and metaproteomics in order to gain insight into the identity, function and interaction of the enriched microbial populations. To be able to make the best use of the obtained metagenomic data a new metagenomic binning procedure was developed. Before the competition between two different nitrate reduction pathways was studied, the relationship between functional and compositional stability over time within one nitrate reduction pathway was investigated: In a heterotrophic denitrifying microbial community, enriched from a marine intertidal flat, strong community dynamics were occurring under constant conditions and during stable conversion of substrates. A stable metabolic interaction between the denitrifying populations and co-enriched fermenting microbes persisted throughout the experiment unaffected by the ongoing population dynamics. This indicated that functional stability was independent of the community composition. Apparently, only the persistence of the overall metabolic potential was important to maintain functional stability. This suggested that stochastic as well as deterministic processes are responsible for the observed community composition. Once the functional stability of denitrification was confirmed and interactions with other microbial guilds were known the competition between DNRA and denitrification was addressed. Several parallel continuous culture incubations that differed in one condition but were otherwise constant led to the identification of the generation time as most important control on the competition between DNRA and denitrification. The organic carbon to nitrate ratio and the kind of electron acceptor supplied (nitrate or nitrite) were identified as further controlling factors that together with the generation time discriminated between the two pathways. The metabolic interaction between nitrate- reducing and fermenting populations was stable under both pathways. One quarter of the nitrate reduction was coupled to the oxidation of sulfide, which was produced in the enrichment culture by microbial sulfate reduction, constituting a strong link between the nitrogen and sulfur cycle. All in all, this thesis provides new insights into the ecophysiology of microbial nitrate reducers by unraveling the driving forces of the competition between different nitrate reduction pathways and by revealing important metabolic interactions with other microbial guilds

Rapid succession of uncultured marine bacterial and archaeal populations in a denitrifying continuous culture.

Kraft B, Tegetmeyer H, Meier D, Geelhoed JS, Strous M. Rapid succession of uncultured marine bacterial and archaeal populations in a denitrifying continuous culture. Environmental Microbiology. 2014;16(10):3275-3286.Marine denitrification constitutes an important part of the global nitrogen cycle and the diversity, abundance and process rates of denitrifying microorganisms have been the focus of many studies. Still, there is little insight in the ecophysiology of marine denitrifying communities. In this study, a heterotrophic denitrifying community from sediments of a marine intertidal flat active in nitrogen cycling was selected in a chemostat and monitored over a period of 50 days. The chemostat enabled the maintenance of constant and well-defined experimental conditions over the time-course of the experiment. Analysis of the microbial community composition by automated ribosomal intergenic spacer analysis (ARISA), Illumina sequencing and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) revealed strong dynamics in community composition over time, while overall denitrification by the enrichment culture was stable. Members of the genera Arcobacter, Pseudomonas, Pseudovibrio, Rhodobacterales and of the phylum Bacteroidetes were identified as the dominant denitrifiers. Among the fermenting organisms co-enriched with the denitrifiers was a novel archaeon affiliated with the recently proposed DPANN-superphylum. The pan-genome of populations affiliated to Pseudovibrio encoded a NirK as well as a NirS nitrite reductase, indicating the rare co-occurrence of both evolutionary unrelated nitrite reductases within coexisting subpopulations

Running to get “lost”? Two types of escapism in recreational running and their relations to exercise dependence and subjective well-being

Escapism is a fundamental motivation in many forms of activity engagements. At its core, escapism is “a habitual diversion of the mind … as an escape from reality or routine”. Accordingly, escapism may entail many adaptive and maladaptive psychological antecedents, covariates, and outcomes. However, few studies have been conducted on escapism as a motivational mindset in running. Here, in a sample of recreational runners (N = 227), we applied a two-dimensional model of escapism, comprising self-expansion (adaptive escapism) and self-suppression (maladaptive escapism), and examined how they were related to exercise dependence and subjective well-being. First, confirmatory factor analyses showed that the escapism dimensions were highly diversifiable in the sample. Then, correlational analyses showed that self-expansion was positively correlated to subjective well-being, whereas self-suppression was negatively related to well-being. Self-suppression was more strongly related to exercise dependence compared to self-expansion. Finally, path analyses evidenced an explanatory role of self-expansion and self-suppression in the inverse relationship between exercise dependence and well-being. In conclusion, the present findings support escapism as a relevant framework for understanding the relationship between exercise dependence in running and subjective well-being

The regulation of oxygen to low concentrations in marine oxygen-minimum zones

The Bay of Bengal hosts persistent, measurable, but sub-micromolar, concentrations of oxygen in its oxygen-minimum zone (OMZ). Such low-oxygen conditions are not necessarily rare in the global ocean and seem also to characterize the OMZ of the Pescadero Basin in the Gulf of California, as well as the outer edges of otherwise anoxic OMZs, such as can be found, for example, in the Eastern Tropical North Pacific. We show here that biological controls on oxygen consumption are required to allow the semistable persistence of low-oxygen conditions in OMZ settings; otherwise, only small changes in physical mixing or rates of primary production would drive the OMZ between anoxic and oxic states with potentially large swings in oxygen concentration. We propose that two controls are active: an oxygen-dependent control on oxygen respiration and an oxygen inhibition of denitrification. These controls, working alone and together, can generate low-oxygen concentrations over a wide variability in ocean mixing parameters. More broadly, we discuss the oxygen regulation of organic matter cycling and N2 production in OMZ settings. Modern biogeochemical models of nitrogen and oxygen cycling in OMZ settings do contain some of the parameterizations that we explore here. However, these models have not been applied to understanding the persistence of low, but measurable, concentrations of oxygen in settings like the Bay of Bengal, nor have they been applied to understanding what biological/physical processes control the transition from a weakly oxygenated state to a “functionally” anoxic state with implications for nitrogen cycling. Therefore, we believe that the approach here illuminates the relationship between oxygen and the biogeochemical cycling of carbon and nitrogen in settings like the Bay of Bengal. Furthermore, we believe that our results could further inform large-scale ocean models seeking to explore how global warming might influence the spread of low-oxygen waters, influencing the cycles of oxygen, carbon, and nitrogen in OMZ settings

Proteogenomic analysis of Georgfuchsia toluolica revealed unexpected concurrent aerobic and anaerobic toluene degradation

Denitrifying Betaproteobacteria play a key role in the anaerobic degradation of monoaromatic hydrocarbons. We performed a multi-omics study to better understand the metabolism of the representative organism Georgfuchsia toluolica strain G5G6 known as a strict anaerobe coupling toluene oxidation with dissimilatory nitrate and Fe(III) reduction. Despite the genomic potential for degradation of different carbon sources, we did not find sugar or organic acid transporters, in line with the inability of strain G5G6 to use these substrates. Using a proteomics analysis, we detected proteins of fumarate-dependent toluene activation, membrane-bound nitrate reductase, and key components of the metal-reducing (Mtr) pathway under both nitrate- and Fe(III)-reducing conditions. High abundance of the multiheme cytochrome MtrC implied that a porincytochrome complex was used for respiratory Fe(III) reduction. Remarkably, strain G5G6 contains a full set of genes for aerobic toluene degradation, and we detected enzymes of aerobic toluene degradation under both nitrate- and Fe(III)-reducing conditions. We further detected an ATP-dependent benzoyl-CoA reductase, reactive oxygen species detoxification proteins, and cytochrome c oxidase indicating a facultative anaerobic lifestyle of strain G5G6. Correspondingly, we found diffusion through the septa a substantial source of oxygen in the cultures enabling concurrent aerobic and anaerobic toluene degradation by strain G5G6.This work was supported by Wageningen University & Research through its investment theme Resilience, the Technology Foundation (STW), the Applied Science Division of the Dutch Research Council (NWO; project 08053), NWO grant 016.Vidi.189.050, and a Gravitation grant of the Netherlands Ministry of Education, Culture and Science and NWO (project 024.002.002 SIAM). B.K. was supported by the Villum foundation, Denmark (VYI Grant 25491).info:eu-repo/semantics/publishedVersio

Impacts of chemical gradients on microbial community structure

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower’. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobic and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems

Genome-Wide Gene-Environment Study Identifies Glutamate Receptor Gene GRIN2A as a Parkinson's Disease Modifier Gene via Interaction with Coffee

Our aim was to identify genes that influence the inverse association of coffee with the risk of developing Parkinson's disease (PD). We used genome-wide genotype data and lifetime caffeinated-coffee-consumption data on 1,458 persons with PD and 931 without PD from the NeuroGenetics Research Consortium (NGRC), and we performed a genome-wide association and interaction study (GWAIS), testing each SNP's main-effect plus its interaction with coffee, adjusting for sex, age, and two principal components. We then stratified subjects as heavy or light coffee-drinkers and performed genome-wide association study (GWAS) in each group. We replicated the most significant SNP. Finally, we imputed the NGRC dataset, increasing genomic coverage to examine the region of interest in detail. The primary analyses (GWAIS, GWAS, Replication) were performed using genotyped data. In GWAIS, the most significant signal came from rs4998386 and the neighboring SNPs in GRIN2A. GRIN2A encodes an NMDA-glutamate-receptor subunit and regulates excitatory neurotransmission in the brain. Achieving P2df = 10−6, GRIN2A surpassed all known PD susceptibility genes in significance in the GWAIS. In stratified GWAS, the GRIN2A signal was present in heavy coffee-drinkers (OR = 0.43; P = 6×10−7) but not in light coffee-drinkers. The a priori Replication hypothesis that “Among heavy coffee-drinkers, rs4998386_T carriers have lower PD risk than rs4998386_CC carriers” was confirmed: ORReplication = 0.59, PReplication = 10−3; ORPooled = 0.51, PPooled = 7×10−8. Compared to light coffee-drinkers with rs4998386_CC genotype, heavy coffee-drinkers with rs4998386_CC genotype had 18% lower risk (P = 3×10−3), whereas heavy coffee-drinkers with rs4998386_TC genotype had 59% lower risk (P = 6×10−13). Imputation revealed a block of SNPs that achieved P2df<5×10−8 in GWAIS, and OR = 0.41, P = 3×10−8 in heavy coffee-drinkers. This study is proof of concept that inclusion of environmental factors can help identify genes that are missed in GWAS. Both adenosine antagonists (caffeine-like) and glutamate antagonists (GRIN2A-related) are being tested in clinical trials for treatment of PD. GRIN2A may be a useful pharmacogenetic marker for subdividing individuals in clinical trials to determine which medications might work best for which patients

Framework and baseline examination of the German National Cohort (NAKO)

The German National Cohort (NAKO) is a multidisciplinary, population-based prospective cohort study that aims to investigate the causes of widespread diseases, identify risk factors and improve early detection and prevention of disease. Specifically, NAKO is designed to identify novel and better characterize established risk and protection factors for the development of cardiovascular diseases, cancer, diabetes, neurodegenerative and psychiatric diseases, musculoskeletal diseases, respiratory and infectious diseases in a random sample of the general population. Between 2014 and 2019, a total of 205,415 men and women aged 19–74 years were recruited and examined in 18 study centres in Germany. The baseline assessment included a face-to-face interview, self-administered questionnaires and a wide range of biomedical examinations. Biomaterials were collected from all participants including serum, EDTA plasma, buffy coats, RNA and erythrocytes, urine, saliva, nasal swabs and stool. In 56,971 participants, an intensified examination programme was implemented. Whole-body 3T magnetic resonance imaging was performed in 30,861 participants on dedicated scanners. NAKO collects follow-up information on incident diseases through a combination of active follow-up using self-report via written questionnaires at 2–3 year intervals and passive follow-up via record linkages. All study participants are invited for re-examinations at the study centres in 4–5 year intervals. Thereby, longitudinal information on changes in risk factor profiles and in vascular, cardiac, metabolic, neurocognitive, pulmonary and sensory function is collected. NAKO is a major resource for population-based epidemiology to identify new and tailored strategies for early detection, prediction, prevention and treatment of major diseases for the next 30 years. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10654-022-00890-5