Biology subjects

Luecker, S.

Publications and source records attributed to Luecker, S..

8 recordsLinked to original sources

bioRxiv2024

Metagenomic analysis of age-dependent microbial dynamics in dual-media rapid sand filters treating groundwater

Biofiltration using rapid sand filters is an often used and highly effective method to produce drinking water from anoxic groundwater, yet the microbial processes underlying contaminant removal remain poorly understood. This study used metagenomic sequencing to analyze the microbial communities of dual-media filters of varying ages, yielding 34 high-quality and 177 medium-quality metagenome-assembled genomes (MAGs), including 102 MAGs harboring genes involved in methane, iron or manganese oxidation, and nitrification. Methanotrophic bacteria from the Methylomonadaceae family were abundant in both the youngest and oldest anthracite layers. The dominant methanotroph shifted from a MAG possessing both soluble and particulate methane monooxygenases in the two-month-old filters to MAGs only containing particulate methane monooxygenases in older filters, possibly due to changes in copper availability. Iron oxidation was restricted to the anthracite layer and linked predominantly to Gallionella, which encoded cluster 1 outer membrane cytochromes Cyc2. Gallionella MAGs also became more abundant with filter age, indicating increasing relevance of biological iron oxidation in mature filters. The nitrifying community was dominated by Nitrosomonas and Candidatus Nitrotoga in the two-month-old filter, with the latter being replaced by Nitrospira as the most abundant NOB in older filters. Canonical Nitrospira far exceeded comammox Nitrospira in abundance, except in the oldest sand layers. These results challenge the previously posed assumption that Nitrospira dominance in rapid sand filters is primarily due to comammox activity. Furthermore, it indicates that long operational times are required for comammox Nitrospira to achieve significant abundance. Intriguingly, Nitrospira MAGs contained multi-copper oxidase-type putative manganese oxidases and cluster 3 cyc2 genes. Phylogenetic analysis could not conclusively link the Nitrospira Cyc2 to iron or manganese oxidation, warranting further study of their role in the removal of these compounds. Overall, these findings reveal dynamic, age-dependent changes in microbial communities and their functions within rapid sand filters, offering new targets for physiological studies of bacteria involved in contaminant removal from anoxic groundwater during drinking water production. HIGHLIGHTSO_LIMethanotrophic community shifts between young and mature rapid sand filters. C_LIO_LICluster 1 Cyc2-encoding Gallionella mediate biological iron oxidation. C_LIO_LICandidatus Nitrotoga and Nitrosomonas dominate nitrification in young filters. C_LIO_LIComammox Nitrospira become abundant after prolonged operational periods. C_LIO_LICanonical Nitrospira, not comammox, constitute high Nitrospira abundances. C_LIO_LIAbundant cluster 3 Cyc2-containing Nitrospira might catalyze metal oxidation. C_LI

microbiology↗

bioRxiv2023

Unveiling unique microbial nitrogen cycling and novel nitrification drivers in coastal Antarctica

Although microbial nitrogen (N) cycling plays a pivotal role in Antarctic ecosystems, its underlying mechanisms are largely uncharted. In this study, we unravel the biological origin of nitrate via triple oxygen isotopic composition analysis and systematically profile functional N-cycling genes within soil and lake sediment samples from the ice-free areas of East Antarctica. We successfully reconstruct 1,968 metagenome-assembled genomes (MAGs) spanning 29 microbial phyla, enabling the analysis of the presence or absence of 52 diverse metabolic marker genes. Consistent with quantitative data, our metagenomic analyses confirm the active processes of microbial nitrogen fixation, nitrification, and denitrification. We find no detectable anaerobic ammonium oxidation (anammox) processes, underscoring a unique microbial N-cycling dynamic in the region. Notably, we identify the predominance of complete ammonia-oxidizing (comammox) Nitrospira, a recently discovered bacterial guild capable of performing the entire nitrification process within a single organism. Further genomic investigations reveal their adaptive strategies in the Antarctic environment. These strategies likely involve the synthesis of trehalose to counteract cold stress, high substrate affinity to efficiently utilize available resources, and alternative metabolic pathways to adapt to nutrient-scarce conditions. Their significant role in the nitrification process is validated through 13C-DNA-based stable isotope probing (DNA-SIP). This research provides a comprehensive illustration of nitrifications crucial contribution to the nitrogen budget in coastal Antarctica, highlighting comammox Nitrospira clade B as a novel nitrifying agent and shedding new light on the complex biogeochemical processes of nitrogen cycling in coastal Antarctica.

microbiology↗

bioRxiv2023

Optimizing microbial community metagenomic hybrid assembly correction and polishing approaches informed by reference-independent analyses

Hybrid metagenomic assembly, leveraging both long- and short-read sequencing technologies, of microbial communities is becoming an increasingly accessible approach, yet its widespread application faces several challenges. High-quality references may not be available for assembly accuracy comparisons common for benchmarking, and certain aspects of hybrid assembly may require dataset-dependent, empirically-guided optimization rather than application of a uniform approach. In this study, several simple, reference-free characteristics - gene lengths and read recruitment - were analyzed as reliable proxies of assembly quality to guide hybrid assembly optimization. These characteristics were further explored in relation to reference-dependent genome- and gene-centric analyses that are common for microbial community metagenomic studies. Here, two laboratory-scale bioreactors were sequenced with short and long read platforms, and assembled with commonly used software packages. Following long read assembly, long read correction and short read polishing were iterated to resolve errors. Each iteration in this process was shown so have a substantial effect on gene- and genome-centric community composition. Simple, reference-free assembly characteristics, specifically changes in gene fragmentation and short read recruitment, explored throughout this process replicated patterns of more advanced analyses seen in published comparative studies, and therefore are suitable proxies for hybrid metagenome assembly accuracy to save computational resources. Hybrid metagenomic sequencing approaches will likely remain relevant due to the low costs of short read sequencing, therefore it is imperative that users are equipped to estimate assembly accuracy prior to downstream gene- and genome-centric analyses.

bioinformatics↗

bioRxiv2022

Meta-omics profiling of full-scale groundwater rapid sand filters explains stratification of iron, ammonium and manganese removals

Rapid sand filters (RSF) are an established and widely applied technology for groundwater treatment. Yet, the underlying interwoven biological and physical-chemical reactions controlling the sequential removal of iron, ammonia and manganese remain poorly understood. To resolve the contribution and interactions between the individual reactions, we studied two full-scale drinking water treatment plant configurations, namely (i) one dual-media (anthracite and quartz sand) filter and (ii) two single-media (quartz sand) filters in series. In situ and ex situ activity tests were combined with mineral coating characterization and metagenome-guided metaproteomics along the depth of each filter. Both plants exhibited comparable performances and process compartmentalization, with most of ammonium and manganese removal occurring only after complete iron depletion. Within each compartment, the homogeneity of the media coating and genome-based microbial composition highlighted the effect of backwashing on filter media mixing. In stark contrast, intra-compartment contaminant removal was highly stratified following decreasing substrate availability along the filter height. This apparent and long-standing conflict was resolved by quantifying the expressed proteome at different filter heights, revealing a consistent stratification of proteins catalysing ammonia oxidation and protein-based relative abundances of nitrifying genera. This implies that microorganisms adapt their protein pool to the available nutrient load at a faster rate than the backwash mixing frequency. Ultimately, these results show the unique and complementary potential of metaproteomics to understand metabolic adaptations and interactions in highly dynamic ecosystems.

microbiology↗

bioRxiv2021

An activity-based labelling method for the detection of ammonia and methane-oxidizing bacteria.

The advance of metagenomics in combination with intricate cultivation approaches has facilitated the discovery of novel ammonia- and methane-oxidizing microorganisms, indicating that our understanding of the microbial biodiversity within the biogeochemical nitrogen and carbon cycles still is incomplete. However, the in situ detection and phylogenetic identification of novel ammonia- and methane-oxidizing bacteria remains a challenge. Here, we describe an activity-based protein profiling protocol allowing cultivation-independent unveiling of ammonia- and methane-oxidizing bacteria. In this protocol, 1,7-octadiyne is used as a bifunctional enzyme probe that, in combination with a highly specific alkyne-azide cycloaddition reaction, enables the fluorescent or biotin labelling of cells harboring active ammonia and methane monooxygenases. The biotinylation of these enzymes in combination with immunogold labelling reveals the subcellular localization of the tagged proteins, while the fluorescent labelling of cells harboring active ammonia or methane monooxygenases provides a direct link of these functional lifestyles to phylogenetic identification when combined with fluorescence in situ hybridization. Furthermore, we show that this activity-based labelling protocol can be successfully coupled with fluorescence-activated cell sorting for the enrichment of nitrifiers and methanotrophs from complex environmental samples, facilitating the retrieval of their high quality metagenome-assembled genomes. In conclusion, this study demonstrates a novel, functional tagging technique for the reliable detection, identification, and enrichment of ammonia- and methane-oxidizing bacteria present in complex microbial communities.

microbiology↗

bioRxiv2020

Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions

The genus Nitrospira is the most widespread group of chemolithoautotrophic nitrite-oxidizing bacteria that thrive in diverse natural and engineered ecosystems. Nitrospira marina Nb-295T represents the type genus and was isolated from the oceanic water column over 30 years ago, however, its genome has not yet been analyzed. Here, we analyzed the complete genome sequence of N. marina and performed select physiological experiments to test genome-derived hypotheses. Our data confirm that N. marina benefits from additions of undefined organic carbon substrates, has adaptations to combat oxidative, osmotic and UV-light induced stress and low dissolved pCO2, and is able to grow chemoorganotrophically on formate. We further investigated the metabolic response of N. marina to low (∼5.6 µM) O2 concentrations commonly encountered in marine environments with high nitrite concentrations. In response to O2-limited conditions, the abundance of a potentially more efficient CO2-fixing pyruvate:ferredoxin oxidoreductase (POR) complex and a high affinity cbb3-type terminal oxidase increased, suggesting a role in sustaining nitrite oxidation-driven autotrophy under O2 limitation. Additionally, a Cu/Zn-binding superoxide dismutase increased in abundance potentially protecting this putatively more O2-sensitive POR complex from oxidative damage. An increase in abundance of proteins involved in alternative energy metabolisms, including type 3b [NiFe] hydrogenase and formate dehydrogenase, indicate a high metabolic versatility to survive conditions unfavorable for aerobic nitrite oxidation. In summary, the genome and proteome of the first marine Nitrospira isolate identifies adaptations to life in the oxic ocean and provides important insights into the metabolic diversity and niche differentiation of NOB in marine environments.Competing Interest StatementThe authors have declared no competing interest.View Full Text

ecology↗

bioRxiv2020

Metagenomic profiling of ammonia- and methane-oxidizing microorganisms in a Dutch drinking water treatment plant

Elevated concentrations of ammonium and methane in groundwater can cause severe problems during drinking water production. To avoid their accumulation, raw water in the Netherlands, and many other countries, is purified by sand filtration. These drinking water filtration systems select for microbial communities that mediate the biodegradation of organic and inorganic compounds. In this study, the active layers and wall biofilm of a Dutch drinking water treatment plant (DWTP) were sampled at different locations along the filtration units of the plant over three years. We used high-throughput sequencing in combination with differential coverage and sequence composition-based binning to recover 56 near-complete metagenome-assembled genomes (MAGs) with an estimated completion of [≥]70% and with [≤]10% redundancy. These MAGs were used to characterize the microbial communities involved in the conversion of ammonia and methane. The methanotrophic microbial communities colonizing the wall biofilm (WB) and the granular material of the primary rapid sand filter (P-RSF) were dominated by members of the Methylococcaceae and Methylophilaceae. The abundance of these bacteria drastically decreased in the secondary rapid sand filter (S-RSF) samples. In all samples, complete ammonia-oxidizing (comammox) Nitrospira were the most abundant nitrifying guild. Clade A comammox Nitrospira dominated the P-RSF, while clade B was most abundant in WB and S-RSF, where ammonium concentrations were much lower. In conclusion, the knowledge obtained in this study contributes to understanding the role of microorganisms in the removal of carbon and nitrogen compounds during drinking water production. We furthermore found that drinking water treatment plants represent valuable model systems to study microbial community function and interaction. HighlightsO_LIMicrobial distribution was mainly influenced by sampling location within the DWTP C_LIO_LIClade A comammox Nitrospira were the dominant nitrifiers in the primary sand filter C_LIO_LIClade B was most abundant in samples from wall biofilm and the secondary filter C_LIO_LIA novel Methylophilaceae-affiliated methanotroph dominated the primary sand filter C_LI

microbiology↗

bioRxiv2019

Chemosymbiotic bivalves contribute to the nitrogen budget of seagrass ecosystems

In many seagrass sediments, lucinid bivalves and their sulfur-oxidizing symbionts are thought to underpin key ecosystem functions, but little is known about their role in nutrient cycles, particularly nitrogen. We used natural stable isotopes, elemental analyses, and stable isotope probing to study the ecological stoichiometry of a lucinid symbiosis in spring and fall. Chemoautotrophy appeared to dominate in fall, when chemoautotrophic carbon fixation rates were up to one order of magnitude higher as compared to the spring, suggesting a flexible nutritional mutualism. In fall, an isotope pool dilution experiment revealed carbon limitation of the symbiosis and ammonium excretion rates up to 10-fold higher compared to fluxes reported for non-symbiotic marine bivalves. These results provide evidence that lucinid bivalves can contribute substantial amounts of ammonium to the ecosystem. Given the preference of seagrasses for this nitrogen source, lucinid bivalves contribution may boost productivity of these important blue carbon ecosystems.

ecology↗