Helmut Bürgmann

Helmut Bürgmann
Eawag: Das Wasserforschungs-Institut des ETH-Bereichs | Eawag · Department of Surface Waters Research and Management

Dr.

About

325
Publications
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Introduction
My group investigates the microbial ecology of freshwater systems. We are doing research to link microbial ecology to biogeochemical processes and to test predicitons of ecological theory for microbial communities and theri functions. We currently also do research on the role of antibiotic resistance factors as an emerging environmental contaminant.
Additional affiliations
November 2006 - present
Eawag: Das Wasserforschungs-Institut des ETH-Bereichs
January 2004 - October 2006
University of Georgia
January 1999 - December 2003
ETH Zurich

Publications

Publications (325)
Article
Antibiotic resistance genes (ARGs) are emerging environmental contaminants, known to be continuously discharged into the aquatic environment via human and animal waste. Freshwater aquatic environments represent potential reservoirs for ARG and potentially allow sewage-derived ARG to persist and spread in the environment. This may create increased o...
Article
Full-text available
Antibiotic resistance is a threat to human and animal health worldwide, and key measures are required to reduce the risks posed by antibiotic resistance genes that occur in the environment. These measures include the identification of critical points of control, the development of reliable surveillance and risk assessment procedures, and the implem...
Article
Full-text available
Antibiotic-resistance genes (ARGs) are currently discussed as emerging environmental contaminants. Hospital and municipal sewage are important sources of ARGs for the receiving freshwater bodies. We investigated the spatial distribution of different ARGs (sul1, sul2, tet(B), tet(M), tet(W) and qnrA) in freshwater lake sediments in the vicinity of a...
Article
Glaciated alpine floodplains are responding quickly to climate change through shrinking ice masses. Given the expected future changes in their physicochemical environment, we anticipated variable shifts in structure and ecosystem functioning of hyporheic microbial communities in proglacial alpine streams, depending on present community characterist...
Article
Full-text available
Microbial communities are at the heart of all ecosystems, and yet microbial community behavior in disturbed environments remains difficult to measure and predict. Understanding the drivers of microbial community stability, including resistance (insensitivity to disturbance) and resilience (the rate of recovery after disturbance) is important for pr...
Article
Wastewater-based surveillance (WBS) for disease monitoring is highly promising but requires consistent methodologies that incorporate predetermined objectives, targets, and metrics. Herein, we describe a comprehensive metagenomics-based approach for global surveillance of antibiotic resistance in sewage that enables assessment of 1) which antibioti...
Article
Full-text available
For two decades now, partial nitritation anammox (PNA) systems were suggested to more efficiently remove nitrogen (N) from mainstream municipal wastewater. Yet to date, only a few pilot-scale systems and even fewer full-scale implementations of this technology have been described. Process instability continues to restrict the broad application of P...
Article
Full-text available
In stratified lakes, methane oxidizing bacteria are critical methane converters that significantly reduce emissions of this greenhouse gas to the atmosphere. Efforts to better understand their ecology uncovered a surprising diversity, vertical structure, and seasonal succession. It is an open question how this diversity has to be considered in mode...
Preprint
Full-text available
Background The abundance of clinically important antibiotic resistance determinants in wastewater has raised concerns regarding their dissemination into the environment and transmission to animals and humans. However, the high bacterial diversity and complexity of environmental microbiomes makes it challenging to comprehensively detect and quantify...
Article
Full-text available
Background During wastewater treatment, the wastewater microbiome facilitates the degradation of organic matter, reduction of nutrients, and removal of gut parasites. While the latter function is essential to minimize public health risks, the range of parasites involved and how they are removed is still poorly understood. Results Using shotgun met...
Article
Full-text available
The nitrogen (N) cycle is of global importance, as N is an essential element and a limiting nutrient in terrestrial and aquatic ecosystems. Excessive anthropogenic N fertilizer usage threatens sensitive downstream aquatic ecosystems. Although freshwater lake sediments remove N through various microbially mediated processes, few studies have investi...
Article
Full-text available
Background There is concern that the microbially rich activated sludge environment of wastewater treatment plants (WWTPs) may contribute to the dissemination of antibiotic resistance genes (ARGs). We applied long-read (nanopore) sequencing to profile ARGs and their neighboring genes to illuminate their fate in the activated sludge treatment by comp...
Article
The development of new wastewater treatment processes can assist in reducing the impact of wastewater treatment on the environment. The recently developed partial nitritation anammox (PNA) process, for example, consumes less energy for aeration and reduces nitrate in the effluent without requiring additional organic carbon. However, achieving stabl...
Article
Full-text available
Lachgas (N 2 O) ist ein starkes Treibhausgas und die wichtigste ozonzerstörende Substanz in der Stra- tosphäre. Auf Abwasserreinigungsanlagen wird N 2 O während des biologischen Stickstoff abbaus gebildet, der somit die grösste Treibhausgasquelle während des Reinigungsprozesses darstellt. Reduktionsmassnahmen sind deshalb von grosser Bedeutung und...
Article
Untreated combined sewage (bypass) is often discharged by wastewater treatment plants to receiving rivers during stormwater events, where it may contribute to increased levels of antibiotic resistance genes (ARGs) and multi-resistance risk factors (multi-resistant bacteria and multi-resistance genomic determinants (MGDs)) in the receiving water. Ot...
Article
Full-text available
Many seasonally stratified lakes accumulate substantial amounts of the greenhouse gas methane in the anoxic zone. Methane oxidizing bacteria in the water column act as a converter, oxidizing methane into carbon dioxide and biomass before it reaches the atmosphere. Current observations and estimates of this methane oxidation efficiency are diverging...
Preprint
Full-text available
The nitrogen (N) cycle is of global importance as N is an essential element and a limiting nutrient in terrestrial and aquatic ecosystems. Excessive anthropogenic N fertilizer usage threatens sensitive downstream aquatic ecosystems. Although freshwater lake sediments remove N through various microbial transformation processes, few studies have inve...
Preprint
Wastewater-based epidemiology (WBE) for disease monitoring is highly promising, but requires consistent methodologies that incorporate predetermined objectives, targets, and metrics. We demonstrate a comprehensive metagenomics-based approach for global surveillance of antibiotic resistance in sewage, enabling assessment of: 1) which antibiotic resi...
Article
Full-text available
Mainstream anaerobic ammonium oxidation (anammox) represents one of the most promising energy-efficient mechanisms of fixed nitrogen elimination from wastewaters. However, little is known about the exact processes and drivers of microbial community assembly within the complex microbial biofilms that support anammox in engineered ecosystems. Here, w...
Article
Full-text available
Anaerobic ammonium oxidation (anammox) plays an important role in aquatic systems as a sink of bioavailable nitrogen (N), and in engineered processes by removing ammonium from wastewater. The isotope effects anammox imparts in the N isotope signatures (15N/14N) of ammonium, nitrite, and nitrate can be used to estimate its role in environmental sett...
Article
River networks are one of the main routes by which the public could be exposed to environmental sources of antibiotic resistance, that may be introduced e.g. via treated wastewater. In this study, we applied a comprehensive integrated analysis encompassing mass-flow concepts, chemistry, bacterial plate counts, resistance gene quantification and sho...
Article
Full-text available
Nitrous oxide (N2O) is a strong greenhouse gas and causal for stratospheric ozone depletion. During biological nitrogen removal in wastewater treatment plants (WWTP), high N2O fluxes to the atmosphere can occur, typically exhibiting a seasonal emission pattern. Attempts to explain the peak emission phases in winter and spring using physico-chemical...
Article
Full-text available
Autotrophic nitrogen removal by anaerobic ammonium oxidizing (anammox) bacteria is an energy-efficient nitrogen removal process in wastewater treatment. However, full-scale deployment under mainstream conditions remains challenging for practitioners due to the high stress susceptibility of anammox bacteria towards fluctuations in dissolved oxygen (...
Preprint
The global rise and spread of antibiotic resistance greatly challenge the treatment of bacterial infections. Wastewater treatment plants (WWTPs) harbor and discharge antibiotic resistance genes (ARGs) as environmental contaminants. However, the knowledge gap on the host identity, activity and functionality of ARGs limits transmission and health ris...
Article
Full-text available
The World Health Organization Global Action Plan recommends integrated surveillance programs as crucial strategies for monitoring antibiotic resistance. Although several national surveillance programs are in place for clinical and veterinary settings, no such schemes exist for monitoring antibiotic-resistant bacteria in the environment. In this tra...
Article
Full-text available
In stratified lakes, methane-oxidizing bacteria (MOB) are strongly mitigating methane fluxes to the atmosphere by consuming methane entering the water column from the sediments. MOB communities in lakes are diverse and vertically structured, but their spatio-temporal dynamics along the water column as well as physico-chemical parameters and interac...
Article
Full-text available
In lakes, large amounts of methane are produced in anoxic sediments. Methane-oxidizing bacteria effectively convert this potent greenhouse gas into biomass and carbon dioxide. These bacteria are present throughout the water column, where methane concentrations can range from nanomolar to millimolar. In this study, we tested the hypothesis that meth...
Preprint
Full-text available
Complex microbial biofilms orchestrating mainstream anaerobic ammonium oxida-tion (anammox) represent one of the most promising energy-efficient mechanisms of fixed nitrogen elimination from anthropogenic waste waters. However, little is known about the ecological processes that are driving microbial community assem-bly leading to functional anammo...
Preprint
Aerobic and anaerobic oxidations of ammonium are core biological processes driving the nitrogen cycle in natural and engineered microbial ecosystems. These conversions are tailored in mixed-culture biotechnology to propel partial nitritation and anammox (PN/A) for a complete chemolithoautotrophic removal of nitrogen from wastewater at low resource...
Article
Full-text available
Have you ever sought to use metagenomic DNA sequences reported in scientific publications? Were you successful? Here, we reveal that metagenomes from no fewer than 20% of the papers found in our literature search, published between 2016 and 2019, were not deposited in a repository or were simply inaccessible. The proportion of inaccessible data wit...
Article
Full-text available
Lakes and reservoirs contribute substantially to atmospheric concentrations of the potent greenhouse gas methane. Lake sediments produce large amounts of methane, which accumulate in the oxygen-depleted bottom waters of stratified lakes. Climate change and eutrophication may increase the number of lakes with methane storage in the future. Whether s...
Preprint
Full-text available
With this manuscript we present a novel attempt to investigate microbial stress response on multiple levels in engineered ecosystems. By combining high resolution monitoring of performance parameters with omics-based analysis of community composition, biodiversity and, importantly, gene transcription we aimed to determine biological and ecological...
Preprint
Full-text available
Abstract. In freshwater lakes, large amounts of methane are produced in anoxic sediments. Methane-oxidizing bacteria effectively convert this potent greenhouse gas into biomass and carbon dioxide. These bacteria are present throughout the water column where methane concentrations can range from nanomolar to millimolar concentrations. In this study,...
Article
Lakes are a significant source of atmospheric methane, although methane-oxidizing bacteria consume most methane diffusing upward from anoxic sediments. Diverse methane-oxidizing bacteria form an effective methane filter in the water column of stratified lakes, yet, niche partitioning of different methane-oxidizing bacteria along the oxygen–methane...
Preprint
Lakes and reservoirs contribute substantially to atmospheric concentrations of the potent greenhouse gas methane. Lacustrine sediments produce large amounts of methane, which accumulate in oxygen-depleted hypolimnia of stratified lakes. Due to climate change and progressing eutrophication, the number of lakes with hypolimnetic methane storage may i...
Preprint
Full-text available
Many seasonally stratified lakes accumulate substantial amounts of the greenhouse gas methane in the anoxic zone. Methane oxidizing bacteria in the water column act as a converter, oxidizing methane into carbon dioxide and biomass before it reaches the atmosphere. Current observations and estimates of this methane oxidation efficiency are diverging...
Article
Full-text available
Aerobic methane-oxidizing bacteria (MOB) substantially reduce methane fluxes from freshwater sediments to the atmosphere. Their metalloenzyme methane monooxygenase (MMO) catalyses the first oxidation step converting methane to methanol. Its most prevalent form is the copper-dependent particulate pMMO, however, some MOB are also able to express the...
Article
To compare the performance and antibiotic-resistance character in different process configurations under different levels of antibiotics, anoxic/oxic-membrane bioreactors (MBR) 1#, MBR2# and a sequencing batch reactor (SBR) were operated with identical operating parameters. MBR1# and SBR were operated under high and increasing levels of antibiotics...
Article
Wastewater treatment plants (WWTPs) are implicated as hotspots for the dissemination of antibacterial resistance into the environment. However, the in situ processes governing removal, persistence, and evolution of resistance genes during wastewater treatment remain poorly understood. Here, we used quantitative metagenomic and metatranscriptomic ap...
Article
The fate of dissolved organic carbon (DOC) is partly determined by its availability to microbial degradation. Organisms at upper trophic levels could influence the bioavailability of DOC via cascading effects on primary producers and bacteria. Here we experimentally tested whether the presence of fish in aquatic food webs can indirectly affect the...
Poster
Full-text available
Autotrophic Nitrogen (N) removal by anaerobic ammonium oxidation (anammox) is an important mechanism of fixed N elimination, both in engineered and natural systems. Our aim is to investigate the activity and ecological stability of anammox biofilms, which is crucial for assessing the feasibility of autotrophic N removal in the mainstream treatment...
Article
Full-text available
Aquatic ecosystems serve as a dissemination pathway and a reservoir of both antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARG). In this study, we investigate the role of the bacterial sporobiota to act as a vector for ARG dispersal in aquatic ecosystems. The sporobiota was operationally defined as the resilient fraction of th...
Data
Linear regressions of log-transformed ARG abundance and frequency in relationship to the distance to the WWTP outlet pipe Linear regressions of log-transformed ARG abundance (left) and frequency (right), on the distance to the WWTP outlet pipe (m). Linear regressions calculated for (A) tet(W) and (B) sul1. Blue circles and lines correspond to the s...
Data
Spearman’s correlations coefficient with significance levels for all pairwise comparisons between Corg, Ntot, TMs, and ARG abundance and frequency Values for Corg, Ntot, and TMs were obtained from previous studies (Bueche, 2014; Sauvain et al., 2014). Significance codes of p-values: 0 < ∗∗∗ < 0.001 < ∗∗ < 0.01 < ∗ < 0.05 < . < 0.1.
Data
Composition of the sporobiome community at phylum level in sediments from the Vidy Bay (Lake Geneva) Composition based on 16S rRNA sequencing on spores DNA. Only taxa accounting for at least 0.1% of the total community are shown. Firmicutes was the dominant phylum accounting for at least 85.2% of the sporobiome community. The other main phyla detec...
Data
Principal coordinates analysis (PCoA) triplot of the samples, based on Bray-Curtis dissimilarity and Hellinger transformation of the OTU table OTUs including less than 4 sequences in the whole dataset were removed from the analysis. OTUs were classified at genus level (or higher taxonomic rank if not possible). Colors correspond to different classe...
Data
Blastp results for the Tet(W) protein Summary of the Blastp results for the presence of Tet(W) in the genomes of the close relatives to the 10-most positively correlated OTUs in the dataset (Table 2).
Data
ARG abundance and frequency and relationship to environmental parameters (A) Biplot representing the ARG abundance (copies/g sediment, above) and frequency (copies/ng DNA, below) in each samples. (B) Principal component analysis (PCA, scaling 2) on the environmental parameters, including Corg, Ntot, trace and heavy metals (TMs), the distance to the...
Data
Raw environmental data Organic carbon and nitrogen content. Particulate cadmium, copper, iron, manganese, aluminium, zinc and arsenic concentrations in sediments.
Data
Blast results for the Sul1 protein Summary of the Blastp results for the presence of Sul1 in the genomes of the close relatives to the 10-most positively correlated OTUs in the dataset (Table 2).
Article
Full-text available
Water and sanitation represents a key battlefront in combating the spread of antimicrobial resistance (AMR). Basic water sanitation infrastructure is an essential first step to protecting public health, thereby limiting the spread of pathogens and the need for antibiotics. AMR presents unique human health risks, meriting new risk assessment framewo...
Article
Full-text available
Here we used flow cytometry (FCM) and filtration paired with amplicon sequencing to determine the abundance and composition of small low nucleic acid (LNA)-content bacteria in a variety of freshwater ecosystems. We found that FCM clusters associated with LNA-content bacteria were ubiquitous across several ecosystems, varying from 50 to 90% of aquat...