Biology subjects

Buergmann, H.

Publications and source records attributed to Buergmann, H..

8 recordsLinked to original sources

bioRxiv2026

Active microbial communities and their extrachromosomal elements link organic matter degradation to methane cycling in anoxic sediments

Anaerobic carbon transformation in freshwater sediments drives substantial methane emissions globally, yet the microbial taxa linking complex carbon degradation to methane production remain poorly characterized. Here, we combined metagenomics with the first metatranscriptomic dataset from the anoxic sediments of meromictic Lake Cadagno (Swiss Alps) to identify the active microbial clades, metabolic pathways, and extrachromosomal elements (ecDNA) across a depth gradient within the upper 56 cm of sediment. We recovered 802 species-level metagenome-assembled genomes (MAGs) spanning 66 phyla and identified a Bacteroidota clade (VadinHA17) as one of the most abundant and transcriptionally active populations in the sediment. This clade encodes and transcribes a broad range of diverse glycoside hydrolases (GH), indicating a central role in complex carbohydrate degradation. Transcriptional profiles suggest that this clade ferments organic substrates to acetate and hydrogen, which are key substrates for methanogenesis. In line with this, the acetoclastic methanogen Methanothrix and hydrogenotrophic Methanoregula were among the most abundant and transcriptionally active archaea in the same depth layers. Beyond microbial genomes, we detected 86,905 viral OTUs (vOTUs) and 2,136 plasmid OTUs (pOTUs), with free viruses and plasmids accounting for 5-10% and 0.2% of all sequencing reads, respectively. Notably, plasmids and viruses associated with Bacteroidota VadinHA17 encode and transcribe GHs that could augment host carbohydrate-degrading capacity. Together, these findings reveal new details on how methane production in anoxic lake sediments emerges from a network spanning primary fermentation, methanogenesis and ecDNA-mediated metabolisms.

ecology↗

bioRxiv2025

Ripples of Resistance: Unveiling Antimicrobial Resistance Dynamics Along Switzerland's Aare River

The global spread of antimicrobial resistance (AMR) is a serious public health concern, driven by widespread antibiotic use and the global environmental circulation of antibiotic-resistant bacteria and resistance genes (ARGs). Wastewater treatment plants (WWTPs) are important sources of anthropogenic AMR entering large rivers, which serve as vital water resources but facilitate downstream dissemination. The drivers and dynamics of AMR propagation along river systems remain poorly understood. As Switzerlands longest and one of its largest rivers, the Aare, situated in the upper Rhine watershed, plays a central role in the water castle of Europe. This study examines the impact of WWTP discharges, some receiving high loads of hospital effluent, on ARG distribution along the 288 km Aare river-continuum. Using quantitative PCR targeting 14 ARGs conferring resistance to eight antibiotic classes, combined with 16S rRNA gene amplicon sequencing, we conducted a high-resolution spatial survey to assess shifts in the riverine ARG content and microbiome. Concentrations of trace metals and nutrients were analyzed as tracers of anthropogenic inputs. Results revealed a progressive increase in ARG abundance downstream, driven by WWTP effluents enriched in ARGs. Effluents had 70-fold higher mean ARG concentrations than upstream waters, raising downstream levels up to 141-fold. Major tributaries such as the Reuss and Limmat sustained elevated ARG levels, while passage through lakes markedly reduced concentrations. This study provides the first detailed baseline for ARG prevalence along a large river system, from pristine headwaters to pollution-affected lower reaches and insights into aquatic AMR dynamics and guidance for future monitoring.

microbiology↗

bioRxiv2023

Disentangling abiotic and biotic effects of treated wastewater on stream biofilm resistomes enables the discovery of a new planctomycete beta-lactamase

BackgroundAntibiotic resistance, which is mediated by environmental reservoirs, poses a threat to human and animal health. Aquatic biofilms impacted by treated wastewater (WW) are known environmental reservoirs for antibiotic resistance, however the specific influence of biotic factors and abiotic factors from WW on the abundance of antibiotic resistance genes (ARGs) within aquatic biofilms remains unclear. Additionally, experimental evidence is limited as to whether genes with low sequence similarity to reference ARGs actually encode for functional ARGs, particularly within complex aquatic microbial communities. ResultsTo disentangle the effects of abiotic and biotic factors on ARG abundances, natural biofilms were previously grown in flume systems with different proportions of stream water and either ultrafiltered or nonultrafiltered WW. In this study, we conducted deep shotgun metagenomic sequencing of 75 biofilm, stream, and WW samples from these flume systems and compared the taxonomic and functional microbiome and resistome composition. Statistical analysis revealed an alignment of the resistome and microbiome composition and a significant association with experimental treatment. Several ARG classes exhibited an increase in metagenomic abundances in biofilms grown with increasing percentages of nonultrafiltered WW. In contrast, sulfonamide and BEL family beta-lactamase ARGs showed greater abundances in biofilms grown in ultrafiltered WW compared to nonultrafiltered WW. Overall, our results pointed toward the dominance of biotic factors over abiotic factors in determining ARG abundances in WW-impacted stream biofilms and suggested gene family-specific mechanisms for ARGs which exhibited divergent abundance patterns. To investigate one of these specific ARG families experimentally, we biochemically characterized a new beta-lactamase from the Planctomycetota (Phycisphaeraceae). This beta-lactamase displayed activity in the cleavage of cephalosporin analog despite sharing low sequence identity with known ARGs. ConclusionsThis discovery of a functional planctomycete beta-lactamase ARG is noteworthy, not only because it was the first beta-lactamase to be biochemically characterized from this phylum, but also because it was not detected by standard homology-based ARG tools. In summary, this study conducted metagenomic analysis on the relative importance of biotic and abiotic factors in the context of WW discharge and their impact on both known and new ARGs in aquatic biofilms.

microbiology↗

bioRxiv2020

Sewage-Borne Pathogens and Indigenous Denitrifiers are Active and Key Multi-Antibiotic Resistant Players in Wastewater Treatment Plants

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 risk assessment of WWTPs resistome. Hereby, a genome-centric quantitative metatranscriptomic approach was exploited to realize high-resolution qualitative and quantitative analyses of bacterial hosts of ARGs (i.e., multi-resistance, pathogenicity, activity and niches) throughout 12 urban WWTPs. We found that [~]45% of 248 recovered genomes expressed ARGs against multiple classes of antibiotics, among which bacitracin and aminoglycoside resistance genes in Proteobacteria was the most prevalent scenario. Both potential pathogens and indigenous denitrifying bacteria were transcriptionally active hosts of ARGs. The almost unchanged relative expression levels of ARGs in the most resistant populations (66.9%) and the surviving ARG hosts including globally emerging pathogens (e.g., Aliarcobacter cryaerophilus) in treated WWTP effluent prioritizes future examination on the health risks related with resistance propagation and human exposure in the receiving environment.

microbiology↗

bioRxiv2020

Distinct growth stages shaped by an interplay of deterministic and neutral processes are indispensable for functional anammox biofilms

Complex microbial biofilms orchestrating mainstream anaerobic ammonium oxidation (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 assembly leading to functional anammox biofilms in engineered ecosystems. Here, we use fluorescence in situ hybridization and 16S rRNA sequencing combined with network modelling to elucidate the contribution of stochastic and deterministic processes during anammox biofilm development from first colonization to maturation in a carrier-based anammox reactor. We find that distinct stages of biofilm development emerge naturally in terms of structure and community composition. These stages are characterized by dynamic succession and an interplay of stochastic and deterministic processes. The staged process of biofilm establishment appears to be the prerequisite for the anticipated growth of anammox bacteria and for reaching a biofilm community structure with the desired metabolic capacities. We discuss the relevance of this improved understanding of anammox community ecology and biofilm development concerning its practical application in the start-up and configuration of anammox biofilm reactors.

microbiology↗

bioRxiv2020

Temperature modulates stress response in anammox reactors

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 and temperature. Here, we investigated the response of microbial biofilms with verified anammox activity to oxygen shocks under favorable and cold temperature regimes. Genome-centric metagenomics and metatranscriptomics were used to investigate the stress response on various biological levels. We show that temperature regime and strength of oxygen perturbations induced divergent responses from the process level down to the transcriptional profile of individual taxa. Temperature induced distinct transcriptional states in compositionally identical communities and transient pulses of dissolved oxygen resulted in the upregulation of stress-response only under favorable temperatures. Anammox species and other key biofilm taxa display different transcriptional responses to the induced stress regimes.

microbiology↗

bioRxiv2019

Growth and rapid succession of methanotrophs effectively limit methane release during lake overturn

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 increase in the future. However, whether stored methane eventually reaches the atmosphere during lake overturn is a matter of controversy and depends critically on the response of the methanotroph assemblage. We show that the methanotroph assemblage in a mixing lake underwent both a substantial bloom and ecological succession. As a result, the methane oxidation capacity of the mixed layer kept pace with the methane supplied from the hypolimnion and most of the stored methane was oxidized. This previously unknown aspect of freshwater methanotroph ecology represents an effective mechanism limiting methane transfer from lakes to the atmosphere.

microbiology↗

bioRxiv2019

Lake overturn as a key driver for methane oxidation

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, especially for the lake overturn period. Here we combine a model of turbulent mixing, gas exchange and microbial growth with a comprehensive data set for autumn mixing to quantify the relevant physical and microbial processes. We show that the microbial methane converter is effectively transforming the increased methane flux during the overturn period. Only rare events of pronounced surface cooling in combination with persistently strong wind can trigger substantial outgassing. In the context of climate change, these results suggest that changes in the frequency of storms may be even more important for methane emissions from temperate lakes than gradual warming.

microbiology↗