Biology subjects

Smets, B. F.

Publications and source records attributed to Smets, B. F..

14 recordsLinked to original sources

bioRxiv2026

Viscoelastic flow-integrated Raman spectroscopy platform

We demonstrate the first viscoelastic-based flow-integrated Raman spectroscopy (FIRS) platform using spontaneous Raman spectroscopy with a simplified fluidic design that precisely controls particle transit speed and predicts arrival time to the Raman interrogation region, together with time synchronized triggered acquisition. Using viscoelastic flow focusing and optical detection of velocity for hardware triggering, the setup enables high-throughput, real-time Raman analysis of particles in continuous flow. The system operates with a single pressure pump, two sets of fiber-coupled lasers and detectors, and a microcapillary precisely aligned in a projection micro-stereolithography 3D-printed mount, and ensures detection stability across various flow rates. The demonstrated platform is modular and scalable. Detection rates of up to 80 cells per minute were achieved and dinoflagellate Alexandrium ostenfeldii cultures were analyzed. The integrated optical trigger mechanism supports future extensions such as cell sorting or additional analyses. A user-friendly graphical interface provides full control of fluidics, spectroscopy, and real-time monitoring, making this compact, low-cost FIRS platform accessible across a wide range of laboratory environments.

molecular biology↗

bioRxiv2025

Beyond magnetosomes: ubiquitous and diverse intracellular inclusions expand the role of magnetotactic bacteria in biogeochemical cycling

Magnetotactic bacteria (MTB) are capable of accumulating and storing intercellular pools containing phosphorus, sulfur, nitrogen and carbon. Yet, the metabolic pathways connected with their intracellular storage of polyphosphate, elemental sulfur, nitrate, and calcium carbonate, and the environmental influence on MTB inclusions and their quantitative contribution to sedimentary chemical budgets remain underexplored. Using a combination of chemical characterization, ultrastructural and compositional analyses, and phylogenetic and genomic insights into microbial assemblages, we investigated the influence of geochemical parameters on the diversity, ecophysiology, and distribution of MTB in freshwater and brackish sediments. Special focus is given to intracellular inclusions and their metabolic pathways to uncover functional traits and ecological roles in elemental cycling. Of the 118 examined MTB cells, polyphosphate granules (75%) and nitrate-containing vacuoles (67%) were the most common inclusions followed by sulfur globules (25%) and calcium carbonate granules (8%). The intracellular phosphorus, nitrogen, and sulfur stored in MTB cells were conservatively estimated to account for 0.60%, 0.91%, and 0.23% of the total sedimentary P, N, and S in the investigated freshwater sediments, respectively. The ubiquitous nature and important ecological role of MTB can be explained by their ability to sequester chemical elements into intracellular inclusions, giving them a metabolic advantage in dynamic chemically stratified environments. The extraordinary phylogenetic diversity of MTB, coupled with their capability to hyperaccumulate and store a wide range of elements and compounds, represents a significant resource for biotechnology innovation.

microbiology↗

bioRxiv2025

An integrated meta-omics approach for identifying candidate organic micropollutant degraders in complex microbial communities

Biotransformation is a significant determinant of the fate of organic micropollutants (OMPs) in natural and engineered environments; yet identifying OMP-transforming microorganisms remains challenging. Integrating metagenomics and metatranscriptomics, we searched for correlations between the biotransformation of ammonia and atenolol and the transcriptional activity of metagenome-assembled genomes (MAGs) across five nitrifier-rich cultures in batch experiments. The biotransformation of ammonia correlated with the activity of ammonia-oxidizing bacterium Nitrosomonas europaea but not with the activity of other bacteria, including several ammonia oxidizers. Additionally, the biotransformation of ammonia correlated with the transcript abundance of the ammonia monooxygenase (AMO) expressed by N. europaea but not with the transcript abundance of AMO at the community level. Atenolol biotransformation correlated with the activity of four MAGs representing three heterotrophic genera: Terrimonas, Flavobacterium, and Zeimonas. It did not correlate with the total transcript abundance of any member of a comprehensive set of amidohydrolases, which are predicted to transform this drug. By contrast, it correlated with the expression of the amidohydrolase asparagine synthase (AsnB) identified in the Terrimonas and Flavobacterium MAGs. In summary, we present a novel association-based method for elucidating biotransformation processes robust to variability in enzyme reaction kinetics with implications for OMP control. SynopsisThe fate of organic micropollutants in natural and engineered systems depends greatly on biotransformation by microbes. This study proposes an approach for identifying these microbes with implications for the study and control of organic micropollutant removal. ABSTRACT GRAPHICS O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/639455v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@17c7f1org.highwire.dtl.DTLVardef@147b9eforg.highwire.dtl.DTLVardef@1fffc9eorg.highwire.dtl.DTLVardef@121fd96_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

Potential survival strategies of novel comammox and nitrite-oxidizing Nitrospira present in a reactor treating high-ammonia brackish landfill leachate

Nitrification is mediated by numerous different microorganisms, but knowledge of their ecophysiologies is insufficient. Leachate in the late stages of landfill operation provides a brackish environment with a high ammonia concentration, and methanol is added as an electron donor for denitrification. Such a unique environment may contain novel nitrifiers. Here, we present metagenomic analysis of the microbiome from a closed landfill leachate treatment facility to investigate the identity and functions of nitrifiers. Using a genome-centric approach with metagenomic analysis, we retrieved draft genomes for a novel complete ammonia-oxidizing (comammox) bacterium Nitrospira LAS72; and canonical Nitrospira LAS18, clustered within a novel sub-lineage VII of Nitrospira; Candidatus Nitrosocosmicus LAS21 and Nitrosarchaeum LAS73, belonging to the ammonia-oxidizing archaea (AOA). This is the first evidence of comammox Nitrospira in a high-ammonia-containing brackish environment. Canonical ammonia-oxidizing bacteria were not detected. Given the brackish environment and supplementation of methanol used in the facility, we also investigated the methanol metabolism of these nitrifiers and their potential to produce compatible solutes as osmoprotectants. Uniquely among Nitrospira, comammox Nitrospira LAS72 possesses genes associated with formaldehyde reductase and glycine betaine biosynthesis. Thus, Nitrospira LAS72 may proliferate because of the availability of formaldehyde upstream of carbon metabolism and adapt to fluctuating osmotic pressure by producing a variety of compatible solutes. The discovery of this novel comammox Nitrospira, and canonical Nitrospira forming a new sub-lineage VII in an ammonia-concentrated brackish environment broadens our knowledge of the diversity and functions of nitrifying microorganisms.

microbiology↗

bioRxiv2023

Is it selfish to be filamentous in biofilms? Individual-based modeling links microbial growth strategies with morphology using the new and modular iDynoMiCS 2.0

Microbial communities are found in all habitable environments and often occur in assemblages with self-organized spatial structures developing over time. This complexity can only be understood, predicted, and managed by combining experiments with mathematical modeling. Individual-based models are particularly suited if individual heterogeneity, local interactions, and adaptive behavior are of interest. Here we present the completely overhauled software platform, the individual-based Dynamics of Microbial Communities Simulator, iDynoMiCS 2.0, which enables researchers to specify a range of different models without having to program. Key new features and improvements are: (1) Substantially enhanced ease of use (graphical user interface, editor for model specification, unit conversions, data analysis and visualization and more). (2) Increased performance and scalability enabling simulations of up to 10 million agents in 3D biofilms. (3) Kinetics can be specified with any arithmetic function. (4) Agent properties can be assembled from orthogonal modules for pick and mix flexibility. (5) Force-based mechanical interaction framework enabling attractive forces and non-spherical agent morphologies as an alternative to the shoving algorithm. The new iDynoMiCS 2.0 has undergone intensive testing, from unit tests to a suite of increasingly complex numerical tests and the standard Benchmark 3 based on nitrifying biofilms. A second test case was based on the "biofilms promote altruism" study previously implemented in BacSim because competition outcomes are highly sensitive to the developing spatial structures due to positive feedback between cooperative individuals. We extended this case study by adding morphology to find that (i) filamentous bacteria outcompete spherical bacteria regardless of growth strategy and (ii) non-cooperating filaments outcompete cooperating filaments because filaments can escape the stronger competition between themselves. In conclusion, the new substantially improved iDynoMiCS 2.0 joins a growing number of platforms for individual-based modeling of microbial communities with specific advantages and disadvantages that we discuss, giving users a wider choice. Author summaryMicrobes are fascinating in their own right and play a tremendously important role in ecosystems. They often form complex, self-organized communities with spatial heterogeneity that is changing over time. Such complexity is challenging to understand and manage without the help of mathematical models. Individual-based models are one type of mathematical model that is particularly suited if differences between individual microbes, local interactions and adaptive behavior are important. We have developed a completely overhauled version of iDynoMiCS, a software that allows users to develop, run and analyze a wide range of individual-based models without having to program the software themselves. There are several capability enhancements and numerous small improvements, for example the ability to model different shapes of cells combined with physically realistic mechanical interactions between neighboring cells. We showcase this by simulating the competition between filaments, long chains of cells, with single cells and find that filaments outcompete single cells as they can spread quickly to new territory with higher levels of resources. Users now have a wider choice of platforms so we provide guidance on which platform might be most suitable for a given purpose.

ecology↗

bioRxiv2022

Ancient electrogenic survival metabolism of β-proteobacterial ammonia oxidizers for oxygen deficiency

Oxygen availability is critical for microbes as some are obligatorily dependent on oxygen for energy conservation. However, aerobic microbes that live in environments with varying oxygen concentrations experience pressures over evolutionary time, selecting alternative energy metabolisms that relax the dependence on oxygen. One such capacity is extracellular electron transfer (or EET), which is the ability to transfer electrons from central metabolism to extracellular oxidants such as iron and manganese oxides. We posit that the {beta}-proteobacterial ammonia-oxidizing bacteria, highly specialized lineages heretofore recognized as strict aerobes, can be capable of EET as they have been constantly observed in oxygen-limiting and depleted environments. Here, we show that a strictly aerobic ammonia-oxidizer, Nitrosomonas communis, utilized a poised electrode to maintain metabolic activity in anoxic conditions. The presence and activity of multi-heme cytochromes suggested that direct electron transfer is the mechanism underlying EET. Molecular clock models suggest that the ancestors of {beta}-proteobacterial ammonia oxidizers appeared after the oxygenation of Earth when the oxygen levels were >10-4 pO2 (PAL), suggesting their aerobic origins. Phylogenetic reconciliations of gene and species trees show that the multi-heme c-type EET proteins in Nitrosomonas and Nitrosospira were acquired by gene transfer from {beta}-proteobacteria during oxygen scarcity. The preservation of EET metabolism over billions of years under fluctuating oxygen levels and aspects of EET physiology in {beta}-proteobacterial ammonia oxidizers might explain how they have been coped with oxygen stress and survived under oxygen deprivation. SIGNIFICANCEMetabolic versatility can permit typically aerobic microbes to survive in anaerobic conditions when oxygen is deficient as a terminal electron acceptor. This article demonstrates a previously unidentified anaerobic extracellular electron transfer metabolism that operates in aerobic {beta}-proteobacterial ammonia oxidizers and reconstructs the evolutionary history of this metabolism, linking it to the early history of Earths oxygenation. Our approach contributes to the understanding of metabolisms in the N-cycle and their evolution on Earth, as well as how aerobic microbes manage to retain energy generation under oxygen-limiting or depleted conditions. AUTHOR CONTRIBUTIONSAG designed the physiological research with PRG and the phylogenetic research with GF; AG performed the research, AG analyzed the data with PRG and GF. AG wrote the paper, and all authors edited and approved the manuscript.

evolutionary biology↗

bioRxiv2021

Different autotrophic enrichments yield efficient inocula for biocathodic applications

The uptake of extracellular electrons from cathodes by microbes is a recently discovered phenomenon. However, current knowledge on the diversity of microbes accepting extracellular electrons and populating biocathodes is scarce. Research is required to explore the distribution of extracellular electron uptake metabolism in the tree of life across microbial guilds. Here we characterize the electron uptake ability of microbial guilds enriched on H2, S2O32-, or CH4 and NH4+ from the same inoculum taken from a groundwater treatment sand-filter. We hypothesized that functional microbes having dense outer membrane cytochromes in their native pathway, such as pathways of NH4+, CH4, S2O32- and H2, can perform extracellular electron uptake. We aimed of addressing the following questions: (1) Are there any known microbial member of anticipated function performing extracellular electron transfer? (2) How does electron uptake efficiency vary between the different functional guilds? (3) How is the dissipated electron energy distributed across metabolisms? We developed and applied a novel pipeline to identify taxa utilizing direct electron energy and utilizing secondary microbial products. We report the putative direct electron uptake metabolism of types belonging to Methylomonas, UBA6140, and Nitrosomonas. Furthermore, members of Streptococcaceae, Rhizobiaceae, Streptococcus, Brevundimonas, Chryseobacterium, and Pseudomonas are detected as electroactive taxa. Our results reveal novel insights into the diversity, electrochemical activity, and metabolism of taxa performing direct electron uptake.

ecology↗

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

Extended spectrum β-lactamase and carbapenemase genes are substantially and sequentially reduced during conveyance and treatment of urban sewage

Integrated and quantitative observations of antibiotic resistance genes (ARGs) in urban water systems (UWSs) are lacking. We sampled three UWSs for clinically important extended spectrum {beta}-lactamase (ESBL) and carbapenemase (CP) genes, mobile genetic elements and microbial communities. Sewage - especially from hospitals - carried substantial loads of ESBL and CP genes (106 - 107 per person equivalent), but those loads progressively declined along the UWS, resulting in minimal emissions (101 - 104 copies per person equivalent). Removal was primarily during sewage conveyance (65% {+/-} 36%) rather than within sewage treatment (34% {+/-} 23%). The ARGs clustered in groups based on their persistence; less persistent groups were associated to putative host taxa (especially Enterobacteriaceae and Moraxellaceae), while more persistent groups appear horizontally transferred as they correlated with mobile genetic elements. This first documentation of a substantial ARG reduction during sewage conveyance provides opportunities for antibiotic resistance management and a caution for sewage-based ARG surveillance.

ecology↗

bioRxiv2020

Evolutionary ecology of natural comammox Nitrospira populations

Microbes commonly exists in diverse and complex communities where species interact, and their genomic repertoires evolve over time. Our understanding of species interactions and evolution has increased in the last decades, but most studies of evolutionary dynamics are based on single species in isolation or in experimental systems composed of few interacting species. Here, we use the microbial ecosystem found in groundwater-fed sand filters as a model to avoid this limitation. In these open systems, diverse microbial communities experience relatively stable conditions, and the coupling between chemical and biological processes is generally well defined. Metagenomic analysis of 12 sand filters revealed systematic co-occurrence of at least five comammox Nitrospira species, likely promoted by low ammonium concentrations. These Nitrospira species showed intra-population sequence diversity, although possible clonal expansion was detected in few abundant local comammox populations. They showed low homologous recombination and strong purifying selection, the latter process being especially strong in genes essential in energy metabolism. Positive selection was detected on genes related to resistance to foreign DNA and phages. We found that, compared to other habitats, groundwater-fed sand filters impose strong purifying selection and low recombination on comammox Nitrospira populations. These results suggest that evolutionary processes are more affected by habitat type than by species identity. Together, this study improves our understanding of species interactions and evolution in complex microbial communities, and sheds light on the environmental dependency of evolutionary processes.

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

Plasmids persist in a microbial community by providing fitness benefit to multiple phylotypes

The current epidemic of antibiotic resistance has been facilitated by the wide and rapid horizontal dissemination of antibiotic resistance genes (ARGs) in microbial communities. Indeed, ARGs are often located on plasmids, which can efficiently shuttle genes across diverse taxa. While the existence conditions of plasmids have been extensively studied in a few model bacterial populations, their fate in complex bacterial communities is poorly understood. Here, we coupled plasmid transfer assays with serial growth experiments to investigate the persistence of the broad-host-range IncP-1 plasmid pKJK5 in microbial communities derived from a sewage treatment plant. The cultivation conditions combined different nutrient and oxygen levels, and were non-selective and non-conducive for liquid-phase conjugal transfer. Following initial transfer, the plasmid persisted in almost all conditions during a 10-day serial growth experiment (equivalent to 60 generations), with a transient transconjugant incidence up to 30%. By combining cell enumeration and sorting with amplicon sequencing, we mapped plasmid fitness effects across taxa of the microbial community. Unexpected plasmid fitness benefits were observed in multiple phylotypes of Aeromonas, Pseudomonas and Enterobacteriaceae, which resulted in community-level plasmid persistence. We demonstrate, for the first time, that plasmid fitness effects across community members can be estimated in a high-throughput way without prior isolation. By gaining a fitness benefit when carrying plasmids, members within complex microbial communities might have a hitherto unrecognized potential to maintain plasmids for long-term community-wide access.

ecology↗

bioRxiv2019

Genomic profiling of Nitrospira species reveals ecological success of comammox Nitrospira

Nitrification was long thought to consist in the stepwise oxidation of ammonia to nitrite and of nitrite to nitrate by ammonia oxidizing and nitrite oxidizing microorganisms, respectively. Recently, single microorganisms capable of complete ammonia to nitrate oxidation (comammox) were identified in the Nitrospira genus. This genus, previously considered to only contain canonical nitrite oxidizers is diverse and has a broad environmental distribution. Yet, a global insight into the abundance, niche preference, and genomic diversity of Nitrospira is missing. Here, we established the largest Nitrospira genome database to date, revealing 68 putative species, most without cultivated representatives. We performed a global survey through read recruitment of metagenomic data from various environments against this database that identified that environmental filtering structures species distribution, without large scale biogeographical signal. The ecological success of comammox Nitrospira is evident as they outnumber and are more diverse than canonical Nitrospira in communities from all environments but wastewater treatment plants. We detect a phylogenetic signal in Nitrospira species habitat preference, that is strongest for canonical Nitrospira species. Comammox Nitrospira eco-evolutionary history is more complex with subclades achieving rapid niche divergence via horizontal transfer of genes, including that encoding the hydroxylamine oxidoreductase, one of the key enzymes involved in nitrification.

microbiology↗

bioRxiv2017

Comparative Genomics Sheds Light On Niche Differentiation And The Evolutionary History Of Comammox Nitrospira

The description of comammox Nitrospira spp., performing complete ammonium-to-nitrate oxidation, and their co-occurrence with canonical betaproteobacterial ammonium oxidizing bacteria ({beta}-AOB) in the environment, call into question the metabolic potential of comammox Nitrospira and the evolutionary history of their ammonium oxidation pathway. We report four new comammox Nitrospira genomes, constituting two novel species, and the first comparative genomic analysis on comammox Nitrospira.\n\nComammox Nitrospira has lost the potential to use external nitrite as energy and nitrogen source: compared to strictly nitrite oxidizing Nitrospira; they lack genes for assimilative nitrite reduction and reverse electron transport from nitrite. By contrast, compared to other Nitrospira, their ammonium oxidizer physiology is exemplified by genes for ammonium and urea transporters and copper homeostasis and the lack of cyanate hydratase genes. Two comammox clades are different in their ammonium uptake systems. Contrary to {beta}-AOB, comammox Nitrospira genomes have single copies of the two central ammonium oxidation pathway genes, lack genes involved in nitric oxide reduction, and encode genes that would allow efficient growth at low oxygen concentrations. Hence, comammox Nitrospira seems attuned to oligotrophy and hypoxia compared to {beta}-AOB.\n\n{beta}-AOBs are the clear origin of the ammonium oxidation pathway in comammox Nitrospira: reconciliation analysis indicates two separate early amoA gene transfer events from {beta}-AOB to an ancestor of comammox Nitrospira, followed by clade specific losses. For haoA, one early transfer from {beta}-AOB to comammox Nitrospira is predicted - followed by intra-clade transfers. We postulate that the absence of comammox genes in most Nitrospira genomes is the result of subsequent loss.\n\nSignificanceThe recent discovery of comammox bacteria - members of the Nitrospira genus able to fully oxidize ammonia to nitrate - upset the long-held conviction that nitrification is a two-step process. It also opened key questions on the ecological and evolutionary relations of these bacteria with other nitrifying prokaryotes. Here, we report the first comparative genomic analysis of comammox Nitrospira and related nitrifiers. Ammonium oxidation genes in comammox Nitrospira had a surprisingly complex evolution, originating from ancient transfer from the phylogenetically distantly related ammonia-oxidizing betaproteobacteria, followed by within-lineage transfers and losses. The resulting comammox genomes are uniquely adapted to ammonia oxidation in nutrient-limited and low-oxygen environments and appear to have lost the genetic potential to grow by nitrite oxidation alone.

microbiology↗