Staff

Helmut Bürgmann

Dr. Helmut Bürgmann

Microbial Ecology

Department Surface Waters Research & Management

About Me

Function
Senior research scientist. Head of the Microbial Ecology research group in the Surface Waters - Research and Management department

Research interests
Dissemination and evolution of antimicrobial resistance in the aquatic environment.
Microbial nitrogen, carbon, and sulfur cycling.
Structure - function relationships in microbial communities.
Linking gene expression to biochemical processes in environmental microbial communities.
Microbial interaction with ecosystem processes on various scales.

Recent research grants
2018 Fate of antibiotic resistance in post-ozonation biofilter treatment. H. Bürgmann. FOEN contract # 00.519.PZ/R114-1489 (64 kCHF)
2016 Swiss River Resistome. H. Bürgmann. National Research Program NFP72 “Antimicrobial Resistance” project (479 kCHF)
2016 Advanced understanding of autotrophic nitrogen removal and associated N2O emissions in mixed nitritation-anammox systems through combined stable ISOtopic and MOLecular constraints (ISOMOL). M. Lehmann (U. Basel), H. Bürgmann, A. Joss, J. Mohn. Swiss National Science Foundation SINERGIA grant (1.484 kCHF)
2016 The regulation of nitrogen turnover in lakes. B. Müller, H. Bürgmann. Swiss National Science Foundation grant (450 kCHF)
2015 Antimicrobial resistance in Swiss drinking water sources and drinking water. SVGW / FOWA: Forschungs, Enwicklungs- und Förderungsfonds der Schweizer Wasserversorgungsbranche. H. Bürgmann (30 kCHF) 
2015 Understanding resistance gene flow during passage of wastewater treatment (RESIST-Flow). H. Bürgmann, A. Johnson, C. McArdell. Eawag Discretionary Funds project (176 kCHF)
2015 Understanding the diversity of aerobic methane oxidizing bacteria in lacustrine oxyclines using community ecology and trait-based modeling (MOBtrait). H. Bürgmann, A. Brandt (460 kCHF) 



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Projects

Wastewater is a source of antibiotic resistant bacteria. We study their dissemination in the aquatic environment, and strategies to remove them.

Antibiotic resistance as an emerging environmental contaminant
Niches and traits of methanotroph bacteria in stratified lakes are studied with the ultimate goal to improve process models.

MOBtrait: Methanotrophs in stratified lakes

Copper and Methane Oxidation
We study the ecological stability of anammox biofilms, which are responsible for the autotrophic Nitrogen removal in mixed nitritation-anammox systems.

Ecological stability of anammox biofilms
How is nitrate removed from lakes?

The Cycle of Nitrogen in Lakes

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Curriculum Vitae

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Selected publications

Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange, and upregulated expression in the effluent microbiomes

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 approaches to achieve a broad-spectrum view of the flow and expression of genes related to antibacterial resistance to over 20 classes of antibiotics, 65 biocides, and 22 metals. All compartments of 12 WWTPs share persistent resistance genes with detectable transcriptional activities that were comparatively higher in the secondary effluent, where mobility genes also show higher relative abundance and expression ratios. The richness and abundance of resistance genes vary greatly across metagenomes from different treatment compartments, and their relative and absolute abundances correlate with bacterial community composition and biomass concentration. No strong drivers of resistome composition could be identified among the chemical stressors analyzed, although the sub-inhibitory concentration (hundreds of ng/L) of macrolide antibiotics in wastewater correlates with macrolide and vancomycin resistance genes. Contig-based analysis shows considerable co-localization between resistance and mobility genes and implies a history of substantial horizontal resistance transfer involving human bacterial pathogens. Based on these findings, we propose future inclusion of mobility incidence (M%) and host pathogenicity of antibiotic resistance genes in their quantitative health risk ranking models with an ultimate goal to assess the biological significance of wastewater resistomes with regard to disease control in humans or domestic livestock.
Ju, F.; Beck, K.; Yin, X.; Maccagnan, A.; McArdell, C. S.; Singer, H. P.; Johnson, D. R.; Zhang, T.; Bürgmann, H. (2019) Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange, and upregulated expression in the effluent microbiomes, ISME Journal, 13(2), 346-360, doi:10.1038/s41396-018-0277-8, Institutional Repository

Water and sanitation: an essential battlefront in the war on antimicrobial resistance

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 frameworks specifically adapted to water and sanitation-borne AMR. There are numerous exposure routes to AMR originating from human waste, each of which must be quantified for its relative risk to human health. Wastewater treatment plants (WWTPs) play a vital role in centralized collection and treatment of human sewage, but there are numerous unresolved questions in terms of the microbial ecological processes occurring within and the extent to which they attenuate or amplify AMR. Research is needed to advance understanding of the fate of resistant bacteria and antibiotic resistance genes (ARGs) in various waste management systems, depending on the local constraints and intended re-use applications. WHO and national AMR action plans would benefit from a more holistic 'One Water' understanding. Here we provide a framework for research, policy, practice, and public engagement aimed at limiting the spread of AMR from water and sanitation in both low-, medium- and high-income countries, alike.
Bürgmann, H.; Frigon, D.; Gaze, W.; Manaia, C.; Pruden, A.; Singer, A. C.; Smets, B.; Zhang, T. (2018) Water and sanitation: an essential battlefront in the war on antimicrobial resistance, FEMS Microbiology Ecology, 94(9), fiy101 (14 pp.), doi:10.1093/femsec/fiy101, Institutional Repository

Towards a comprehensive strategy to mitigate dissemination of environmental sources of antibiotic resistance

Antibiotic resistance is a pervasive global health threat. To combat the spread of resistance, it is necessary to consider all possible sources and understand the pathways and mechanisms by which resistance disseminates. Best management practices are urgently needed to provide barriers to the spread of resistance and maximize the lifespan of antibiotics as a precious resource. Herein we advise upon the need for coordinated national and international strategies, highlighting three essential components: 1) Monitoring, 2) Risk Assessment, and 3) Mitigation of antibiotic resistance. Central to all three components is What exactly to monitor, assess, and mitigate? We address this question within an environmental framework, drawing from fundamental microbial ecological processes driving the spread of resistance.
Vikesland, P. J.; Pruden, A.; Alvarez, P. J. J.; Aga, D. S.; Buergmann, H.; Li, X.; Manaia, C. M.; Nambi, I. M.; Wigginton, K. R.; Zhang, T.; Zhu, Y.-G. (2017) Towards a comprehensive strategy to mitigate dissemination of environmental sources of antibiotic resistance, Environmental Science and Technology, 51(22), 13061-13069, doi:10.1021/acs.est.7b03623, Institutional Repository

Bacteria-induced mixing in natural waters

Swimming organisms can enhance mixing in their natural environments by creating eddies in their wake and by dragging water along. However, these mixing mechanisms are inefficient for microorganisms, because swimming-induced variations in velocity, temperature, and dissolved substances are evened out before they can be advected. In bioconvection, however, microorganisms induce water movement not by propulsion directly but by locally changing the fluid density, which drives convection. Observations of bioconvection have so far mainly been limited to laboratory settings. We report the first observation and quantification of bioconvection within a stratified natural water body. Using in situ measurements, laboratory experiments, and numerical simulations, we demonstrate that the bacterium Chromatium okenii is capable of mixing 0.3 to 1.2 m thick water layers at around 12 m water depth in the Alpine Lake Cadagno (Switzerland). As many species are capable of driving bioconvection, this phenomenon potentially plays a role in species distributions and influences large-scale phenomena like algal blooms.
Sommer, T.; Danza, F.; Berg, J.; Sengupta, A.; Constantinescu, G.; Tokyay, T.; Bürgmann, H.; Dressler, Y.; Sepúlveda Steiner, O.; Schubert, C. J.; Tonolla, M.; Wüest, A. (2017) Bacteria-induced mixing in natural waters, Geophysical Research Letters, 44(18), 9424-9432, doi:10.1002/2017GL074868, Institutional Repository

Antibiotikaresistenzen im Wasserkreislauf. Ein Überblick über die Situation in der Schweiz

Obwohl in der Schweiz vergleichsweise wenig Antibiotika in der Humanmedizin eingesetzt werden und die Verbrauchszahlen in der Veterinärmedizin seit 2008 stetig sinken, werden auch hierzulande Resistenzen in der aquatischen Umwelt beobachtet. Dieser Artikel stellt Fallstudien zur Verbreitung von Antibiotikaresistenzen in Abwasser und Fliessgewässern in der Schweiz und daraus resultierende Risiken vor. Es wird diskutiert, inwiefern neuartige Technologien in der Abwasserbehandlung (Ozonung, Ultrafiltration) diese biologischen Verunreinigungen reduzieren können.
Czekalski, N.; von Gunten, U.; Bürgmann, H. (2016) Antibiotikaresistenzen im Wasserkreislauf. Ein Überblick über die Situation in der Schweiz, Aqua & Gas, 96(9), 72-80, Institutional Repository

Tackling antibiotic resistance: the environmental framework

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 implementation of technological solutions that can prevent environmental contamination with antibiotic resistant bacteria and genes. In this Opinion article, we discuss the main knowledge gaps, the future research needs and the policy and management options that should be prioritized to tackle antibiotic resistance in the environment.
Berendonk, T. U.; Manaia, C. M.; Merlin, C.; Fatta-Kassinos, D.; Cytryn, E.; Walsh, F.; Bürgmann, H.; Sørum, H.; Norström, M.; Pons, M.-N.; Kreuzinger, N.; Huovinen, P.; Stefani, S.; Schwartz, T.; Kisand, V.; Baquero, F.; Martinez, J. L. (2015) Tackling antibiotic resistance: the environmental framework, Nature Reviews Microbiology, 13(5), 310-317, doi:10.1038/nrmicro3439, Institutional Repository

Does human activity impact the natural antibiotic resistance background? Abundance of antibiotic resistance genes in 21 Swiss lakes

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 opportunities for an eventual contact with, and gene transfer to, human and animal pathogens via the food chain or drinking water. However, assessment of this risk requires a better understanding of the level and variability of the natural resistance background and the extent of the human impact. We have analyzed water samples from 21 Swiss lakes, taken at sampling points that were not under the direct influence of local contamination sources and analyzed the relative abundance of ARG using quantitative real-time PCR. Copy numbers of genes mediating resistance to three different broad-spectrum antibiotic classes (sulfonamides: sul1, sul2, tetracyclines: tet(B), tet(M), tet(W) and fluoroquinolones: qnrA) were normalized to copy numbers of bacterial 16S rRNA genes. We used multiple linear regression to assess if ARG abundance is related to human activities in the catchment, microbial community composition and the eutrophication status of the lakes. Sul genes were detected in all sampled lakes, whereas only four lakes contained quantifiable numbers of tet genes, and qnrA remained below detection in all lakes. Our data indicate higher abundance of sul1 in lakes with increasing number and capacity of wastewater treatment plants (WWTPs) in the catchment. sul2 abundance was rather related to long water residence times and eutrophication status. Our study demonstrates the potential of freshwater lakes to preserve antibiotic resistance genes, and provides a reference for ARG abundance from lake systems with low human impact as a baseline for assessing ARG contamination in lake water.
Czekalski, N.; Sigdel, R.; Birtel, J.; Matthews, B.; Bürgmann, H. (2015) Does human activity impact the natural antibiotic resistance background? Abundance of antibiotic resistance genes in 21 Swiss lakes, Environment International, 81, 45-55, doi:10.1016/j.envint.2015.04.005, Institutional Repository

Wastewater as a point source of antibiotic-resistance genes in the sediment of a freshwater lake

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 point source of treated wastewater. ARG contamination of Vidy Bay, Lake Geneva, Switzerland was quantified using real-time PCR and compared with total mercury (THg), a frequently particle-bound inorganic contaminant with known natural background levels. Two-dimensional mapping of the investigated contaminants in lake sediments with geostatistical tools revealed total and relative abundance of ARGs in close proximity of the sewage discharge point were up to 200-fold above levels measured at a remote reference site (center of the lake) and decreased exponentially with distance. Similar trends were observed in the spatial distribution of different ARGs, whereas distributions of ARGs and THg were only moderately correlated, indicating differences in the transport and fate of these pollutants or additional sources of ARG contamination. The spatial pattern of ARG contamination and supporting data suggest that deposition of particle-associated wastewater bacteria rather than co-selection by, for example, heavy metals was the main cause of sediment ARG contamination.
Czekalski, N.; Díez, E. G.; Bürgmann, H. (2014) Wastewater as a point source of antibiotic-resistance genes in the sediment of a freshwater lake, ISME Journal, 8(7), 1381-1390, doi:10.1038/ismej.2014.8, Institutional Repository

Bacterial structures and ecosystem functions in glaciated floodplains: contemporary states and potential future shifts

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 characteristics and landscape structures. We examined microbial structure and functioning during different hydrologic periods in glacial (kryal) streams and, as contrasting systems, groundwater-fed (krenal) streams. Three catchments were chosen to cover an array of landscape features, including interconnected lakes, differences in local geology and degree of deglaciation. Community structure was assessed by automated ribosomal intergenic spacer analysis and microbial function by potential enzyme activities. We found each catchment to contain a distinct bacterial community structure and different degrees of separation in structure and functioning that were linked to the physicochemical properties of the waters within each catchment. Bacterial communities showed high functional plasticity, although achieved by different strategies in each system. Typical kryal communities showed a strong linkage of structure and function that indicated a major prevalence of specialists, whereas krenal sediments were dominated by generalists. With the rapid retreat of glaciers and therefore altered ecohydrological characteristics, lotic microbial structure and functioning are likely to change substantially in proglacial floodplains in the future. The trajectory of these changes will vary depending on contemporary bacterial community characteristics and landscape structures that ultimately determine the sustainability of ecosystem functioning.
Freimann, R.; Bürgmann, H.; Findlay, S. E. G.; Robinson, C. T. (2013) Bacterial structures and ecosystem functions in glaciated floodplains: contemporary states and potential future shifts, ISME Journal, 7(12), 2361-2373, doi:10.1038/ismej.2013.114, Institutional Repository

Impact of particulate organic matter composition and degradation state on the vertical structure of particle-associated and planktonic lacustrine bacteria

In order to determine how concentration, composition, and degradation states of particulate organic matter (POM) influence lacustrine bacteria, we analyzed changes in bacterial community (BC) structure and total bacterial cell abundance throughout the water columns of 2 contrasting deep lakes in Switzerland. Lake Brienz is oligotrophic and fully oxic while Lake Zug is eutrophic and partially anoxic. The community composition of the particle-associated (>5 µm) and free-living (>0.2, <5 µm) bacteria was analyzed by automated ribosomal intergenic spacer analysis (ARISA). Cluster analysis showed that the lakes comprised distinct BCs. However, the BCs of both lakes were structured with depth. Although particulate amino compounds appeared to impact the number of ARISA-operational taxonomic units of the particle-associated BCs throughout the lake water columns, the compositional dynamics of this bacterial fraction were affected more strongly by the sampling date and physico-chemical parameters, such as pH. For the free-living BCs, the chlorin index (CI), an indicator for the degradation state of primary produced POM, appeared to significantly impact the vertical community shifts. The vertical changes of the total bacterial cell abundance were also significantly determined by the CI and by shifts in particulate amino compounds. The present study shows that not only bulk environmental parameters but also POM composition and degradation state shape the abundance and composition of lacustrine BCs.
Köllner, K. E.; Carstens, D.; Schubert, C. J.; Zeyer, J.; Bürgmann, H. (2013) Impact of particulate organic matter composition and degradation state on the vertical structure of particle-associated and planktonic lacustrine bacteria, Aquatic Microbial Ecology, 69(1), 81-92, doi:10.3354/ame01623, Institutional Repository

Bacterial chitin hydrolysis in two lakes with contrasting trophic statuses

Chitin, which is a biopolymer of the amino sugar glucosamine (GlcN), is highly abundant in aquatic ecosystems, and its degradation is assigned a key role in the recycling of carbon and nitrogen. In order to study the significance of chitin decomposition in two temperate freshwater lakes with contrasting trophic and redox conditions, we measured the turnover rate of the chitin analog methylumbelliferyl-N,N′-diacetylchitobioside (MUF-DC) and the presence of chitinase (chiA) genes in zooplankton, water, and sediment samples. In contrast to the eutrophic and partially anoxic lake, chiA gene fragments were detectable throughout the oligotrophic water column and chiA copy numbers per ml of water were up to 15 times higher than in the eutrophic waters. For both lakes, the highest chiA abundance was found in the euphotic zone—the main habitat of zooplankton, but also the site of production of easily degradable algal chitin. The bulk of chitinase activity was measured in zooplankton samples and the sediments, where recalcitrant chitin is deposited. Both, chiA abundance and chitinase activity correlated well with organic carbon, nitrogen, and concentrations of particulate GlcN. Our findings show that chitin, although its overall contribution to the total organic carbon is small (∼0.01 to 0.1%), constitutes an important microbial growth substrate in these temperate freshwater lakes, particularly where other easily degradable carbon sources are scarce.
Köllner, K. E.; Carstens, D.; Keller, E.; Vazquez, F.; Schubert, C. J.; Zeyer, J.; Bürgmann, H. (2012) Bacterial chitin hydrolysis in two lakes with contrasting trophic statuses, Applied and Environmental Microbiology, 78(3), 695-704, doi:10.1128/AEM.06330-11, Institutional Repository

Methane sources and sinks in Lake Kivu

Unique worldwide, Lake Kivu stores enormous amounts of CH4 and CO2. A recent study reported that CH4 concentrations in the lake have increased by up to 15% in the last 30 years and that accumulation at this rate could lead to catastrophic outgassing by ∼2100. This study investigates the present-day CH4 formation and oxidation in Lake Kivu. Analyses of 14C and 13C in CH4 and potential carbon sources revealed that below 260 m, an unusually high ∼65% of the CH4 originates either from reduction of geogenic CO2 with mostly geogenic H2 or from direct inflows of geogenic CH4. Aerobic CH4 oxidation, performed by close relatives of type X CH4-oxidizing bacteria, is the main process preventing CH4 from escaping to the atmosphere. Anaerobic CH4 oxidation, carried out by CH4-oxidizing archaea in the SO42−-reducing zone, was also detected but is limited by the availability of sulfate. Changes in 14CCH4 and 13CCH4 since the 1970s suggest that the amount of CH4 produced from degrading organic material has increased due to higher accumulation of organic matter. This, as well as the sudden onset of carbonates in the 1960s, has previously been explained by three environmental changes: (1) introduction of nonnative fish, (2) amplified subaquatic inflows following hydrological changes, and (3) increased external inputs due to the fast growing population. The resulting enhancement of primary production and organic matter sedimentation likely caused CH4 to increase. However, given the large proportion of old CH4 carbon, we cannot exclude an increased inflow of geogenic H2 or CH4.
Pasche, N.; Schmid, M.; Vazquez, F.; Schubert, C. J.; Wüest, A.; Kessler, J. D.; Pack, M. A.; Reeburgh, W. S.; Bürgmann, H. (2011) Methane sources and sinks in Lake Kivu, Journal of Geophysical Research G: Biogeosciences, 116(G3), G03006 (16 pp.), doi:10.1029/2011JG001690, Institutional Repository

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Address

E-Mail: helmut.buergmann@eawag.ch
Phone: +41 58 765 2165
Fax: +41 58 765 2168
Address: Eawag
Seestrasse 79
6047 Kastanienbaum
Office: CA B11
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Research Group

Microbial Ecology

Dept. Surface Waters

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Research Focus

Microbial Ecology of Freshwaters

Resistance and Resilience of microbial communities

Antimicrobial resistance in environmental bacteria

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