Biology subjects

Jetten, M. S. M.

Publications and source records attributed to Jetten, M. S. M..

At least 19 recordsLinked to original sources

bioRxiv2026

ANME-2a drive methane oxidation in brackish coastal sediments via multiple pathways

Methane is a powerful greenhouse gas. Typically, a large fraction of the methane formed in coastal sediments is removed via anaerobic methane oxidation (AOM). Here, we demonstrate the potential for a range of AOM pathways in brackish coastal sediments by ANME-2a archaea. At our study site, geochemical profiles indicate that AOM is primarily restricted to a shallow, metal-oxide-rich sulfate-methane transition zone (SMTZ). ANME-2a were the sole methanotrophs detected, and metatranscriptomics showed the highest expression levels of the ANME-2a genes in the SMTZ. AOM activity was observed in sediment incubations with various electron acceptors, including sulfate, metal oxides, and the organic matter analogue graphene oxide. Highest potential rates were observed in sediments from below the SMTZ, pointing towards fast stimulation of the deeper methanotrophic community when alleviating the electron acceptor limitation. The variety of AOM pathways and persistence of methanotrophs below the SMTZ likely contribute to the resilience of the microbial methane filter in brackish coastal sediments.

microbiology↗

bioRxiv2026

Potential for metal-coupled methane oxidation by Candidatus Methanocomedenaceae in coastal sediments

Anaerobic methanotrophic (ANME) archaea are important players in the microbial methane cycle, mitigating methane emissions from anoxic environments. ANME are found ubiquitously in methane-rich sediments, where they can couple anaerobic methane oxidation (AOM) to different electron acceptors such as sulfate, metal oxides, and natural organic matter (NOM). However, we still lack understanding of the geochemical niches and preferred metabolic pathways of most ANME subclades. Here, we investigated the genomic potential and ecophysiology of ANME-2a with respect to metal-dependent AOM in brackish metal-rich coastal sediments. We assembled several high-quality ANME MAGs from subclades with high strain heterogeneity and analyzed the genomic potential for metal-AOM. Additionally, we monitored long-term enrichments with various electron acceptors from the same sediments. Ultimately, we recovered 8 novel genomes of ANME-2a that clustered with an uncharacterized genus with only 2 representatives in public databases for which we propose the name Candidatus Methanoborealis. The analysis of the MAGs showed two different clusters within this genus; one comprising of MAGs from the Baltic Sea that showed high potential for extracellular electron transfer (EET) required for metal-AOM, and another cluster form more diverse environments with less EET potential. The Baltic Sea Ca. Methanoborealis were the only canonical methanotrophs in the incubations during active methane oxidation and metal reduction. Our results contribute to the understanding of the phylogenomic and metabolic diversity in ANME subclades, which will help to further characterize novel ANME lineages from complex sediment samples.

microbiology↗

bioRxiv2026

Coastal sediments maintain potential for N2O cycling under seasonally varying redox conditions

Coastal eutrophication can lead to deoxygenation and sulfide accumulation in sediments, which could strongly impact the dynamics of the potent greenhouse gas nitrous oxide (N2O). Here, we investigated the effects of oxygen (O2) and sulfide on microbial N2O production and consumption in surface sediments of a seasonally euxinic (anoxic and sulfidic) coastal basin. In spring, these surface sediments are oxygenated, while they are highly sulfidic during stratification of the water column in summer. During oxygenated spring conditions, rapid depletion of the substrates O2 and nitrate (NO3-) in the surface sediment limited net in situ N2O production, despite potential for nitrification and for N2O production through incomplete denitrification as observed in batch incubations. Based on metagenome and metatranscriptome analyses the N2O-consuming microbial community was shown to be highly diverse and dominated by clade II nosZ-possessing Flavobacteriia. Assessing the summer sulfidic conditions in surface sediments via batch incubations, we found that moderate sulfide concentrations (0.2-1 mM) enhanced N2O consumption, whereas high concentrations (4 mM) inhibited all steps of denitrification. These findings highlight the redox controls on N2O dynamics, by indicating that coastal sediments can maintain significant N2O turnover potential despite substrate limitations and elevated sulfide concentrations. Consequently, ecosystem restoration strategies that alter O2, NO3- and sulfide availability may fundamentally impact coastal N2O budgets.

microbiology↗

bioRxiv2025

Long-term euxinia hinders microbial ammonium removal in brackish coastal waters

Anthropogenic activities are key drivers of eutrophication and deoxygenation in coastal marine ecosystems. This stimulates the anaerobic degradation of organic matter and the release of reduced products, such as ammonium, methane, and hydrogen sulfide, which may, in turn, exacerbate eutrophication and deoxygenation. In this study, using a combination of chemical and microbial analyses, we assess the nitrogen dynamics in the water column of a eutrophic coastal system (Stockholm Archipelago) at three sites with contrasting redox conditions (oxic to long-term euxinic). At the oxic site, counter gradients of ammonium and oxygen in the water column, low nitrate {delta}15N values in bottom waters, and the 16S rRNA gene-based presence of nitrifiers indicate nitrification near the sediment-water interface. At the seasonally and long-term euxinic sites, nitrification, as inferred from the water column oxygen and nutrient profiles and the relative abundance of nitrifiers, primarily occurred near the oxycline. At these two sites, nitrate was removed below the oxycline through denitrification linked to sulfide oxidation by Sulfurimonas. Nitrous oxide emissions from surface waters in the archipelago reached up to 40 {micro}mol m-2 d-1 and were not directly related to water column redox conditions, indicating that multiple factors control coastal emissions of this greenhouse gas to the atmosphere. The relative abundance of 16S rRNA genes and of N-cycle genes in metagenomes was highest at the seasonally euxinic site. Importantly, nitrifiers were significantly less abundant at the long-term euxinic site. Our results highlight that prolonged euxinia promotes recycling of ammonium over its removal, likely due to sulfide inhibition of nitrification, which sustains eutrophication and deoxygenation of coastal systems.

microbiology↗

bioRxiv2025

Seasonal dynamics of nitrification in the water column of marine Lake Grevelingen

Coastal ecosystems serve as vital connectors between land and ocean, and their nitrogen cycle and ammonium removal can be affected by various factors. During our seasonal sampling campaign in 2021, the eutrophic marine Lake Grevelingen exhibited high ammonium concentrations and low nitrification rates in the water column, except for a brief period in late summer. Our study revealed ammonium accumulation in the anoxic middle and bottom water layers due to restricted transport caused by water column stratification. Only when ammonium reached the oxic part of the water column, was a short-lived peak in nitrification activity and nitrifier abundance observed at the end of August. Amplicon sequencing indicated very low abundances of Nitrosococcus and Nitrospira (<0.2%) in March, while Nitrosomonas and Nitrospina peaked at the end of August with relative abundances of 2.5% and 1.3%, respectively. Archaea and archaeal ammonium oxidizers were found in very low abundances. Anammox 16S rRNA genes were not detected. Together, these observations suggest a limited role for nitrification in ammonium removal in marine Lake Grevelingen.

microbiology↗

bioRxiv2025

Mini-bacterioferritins: Structural insight into a new type of ferritin-like protein from an anaerobic methane-oxidising archaeon

Ferritins are ubiquitous among life forms, as they are essential for iron homeostasis. Here, we unveiled a novel member of the ferritin family, baptised mini-bacterioferritin. The characterised mini-bacterioferritin was isolated from a microbial enrichment dominated by the methanotrophic archaeon Candidatus Methanoperedens BLZ2. Its atomic resolution crystal structure reveals a 12-mer assembly with a diiron ferroxidase centre located within a four-helix bundle. Redox cycling experiments on protein crystals reveal a shift in iron position at the active site, which follows the established ferritin catalytic cycle. The 12-mer sphere-like structure harboured six Fe-coproporphyrin III ligands, positioned at the interdimeric interface, a characteristic previously only found in 24-mer bacterioferritins. Phylogenetics, together with structure predictions of closely related proteins, revealed that mini-bacterioferritins form a new clade within the ferritin family that might conserve ancestral traits. Future research will need to investigate the physiological roles of these enzymes, which were unsuspectingly widely distributed among prokaryotes. TeaserA novel ferritin family, the heme-binding mini-bacterioferritin, assembles as a dodecamer and is widely distributed among microbes.

biochemistry↗

bioRxiv2025

Sediments from a seasonally euxinic coastal ecosystem show high nitrogen cycling potential

Coastal ecosystems are susceptible to eutrophication and deoxygenation, which may alter their nitrogen cycle dynamics. Here, we investigated the microbial nitrogen cycling potential in the sediment of a seasonally euxinic coastal ecosystem (Lake Grevelingen, NL), in winter and summer. Porewater profiles showed ammonium (NH4+) concentrations exceeding 10 mM and rapid depletion of electron acceptors with depth. Activity tests revealed NH4+ oxidation potential up to 53 {micro}mol g-1 day-1, even in anoxic sediment layers. A nitrifying microbial community was present in both oxic and anoxic sediment sections (up to 1.4% relative abundance). NO-, nitrite (NO2-) and nitrous oxide (N2O) reduction potential were prominent across all sediment sections, with the highest rates (167 {micro}mol NO3- g-1 day-1) in the surface sediment in summer. Denitrification (79.3-98.4%) and dissimilatory nitrate reduction to ammonium (DNRA; 1.6-20.7%) were the major NO3- removal pathways, as supported by the detection of the narG/napA, nirK/nirS, norB, nosZ and nrfA/otr genes in all sediment sections. The DNRA contribution increased with depth and with the addition of electron donors, such as monomethylamine. Anaerobic ammonium oxidation (anammox) was not detected in these eutrophic sediments. Combined, our results show that there is high potential for nitrogen removal in eutrophic coastal ecosystems which may help further restoration measures.

microbiology↗

bioRxiv2024

The clumped isotope signatures of multiple methanogenesis metabolisms

Methane is a potent greenhouse gas, an important energy source, and a potential biosignature on extraterrestrial planetary bodies. The relative abundances of doubly substituted ("clumped") methane isotopologues (13CH3D and 12CH2D2) offer important information on the sources and sinks of methane. However, the clumped isotope signatures of microbially produced methane from different methanogenic pathways lack a systematic investigation. In this study, we provide a dataset encompassing the relative isotopologue abundances produced by hydrogenotrophic, methylotrophic, acetoclastic, and methoxydotrophic methanogenesis. We find that a statistical "combinatorial effect" generates significant differences in 12CH2D2 compositions between hydrogenotrophic methanogenesis and other pathways. The thermodynamic drive of methanogenic reactions and phylogenetic affiliation may also influence the isotope compositions of methane. Our study provides new experimental constraints on the isotope signatures of different microbial methanogenic pathways, and evidence of the mechanisms responsible for the observed differences. TeaserA novel stable isotope tool to track and differentiate sources of biological methane.

microbiology↗

bioRxiv2024

Physiological stress response to sulfide exposure of freshwater anaerobic methanotrophic archaea

Freshwater wetlands and coastal sediments are becoming hotspots for the emission of the greenhouse gas methane. Eutrophication-induced deposition of organic matter leads to elevated methanogenesis and sulfate reduction, thereby increasing the concentrations of methane and toxic sulfide, respectively. However, the effects of sulfide stress on the anaerobic methanotrophic biofilter have not been well explored. Here, we show how an enrichment culture dominated by the freshwater anaerobic methane-oxidizing archaeon Candidatus (Ca.) Methanoperedens responds to short-term and long-term exposure to sulfide in a bioreactor. The methane-oxidizing activity decreased to 45% and 20% but partially recovered to 70% and 30% within 5 days after short- and long-term sulfide exposure, respectively. Metagenomics indicated that Ca. Methanoperedens remained dominant in the enrichment throughout the entire experiment. The first short-term sulfide pulse led to increased expression of genes encoding for sulfide detoxification by low abundant community members, whereas long-term exposure resulted in upregulation of Ca. Methanoperedens genes encoding sulfite reductases of Group III (Dsr-LP). Ca. Methanoperedens consumed Polyhydroxyalkanoates during long-term sulfide exposure, possibly to aid in stress adaptation. Together, these results provide a valuable baseline for understanding fundamental ecophysiological adaptations in sulfate- and nitrate-rich aquatic ecosystems. Short synopsis statementThis study investigated how freshwater anaerobic methanotrophic archaea responded to sulfide exposure, revealing a transient inhibition and physiological adaptation mechanisms.

microbiology↗

bioRxiv2024

Methanotrophic flexibility of Ca. Methanoperedens and its interactions with sulfate-1 reducing bacteria in the sediment of meromictic Lake Cadagno

The greenhouse gas methane is an important contributor to global warming, with freshwater sediments representing important potential methane sources. Anaerobic methane-oxidizing archaea mitigate methane release into the atmosphere by coupling the oxidation of methane to the reduction of extracellular electron acceptors or through interspecies electron transfer with microbial partners. Understanding their metabolic flexibility and microbial interactions is crucial to assess their role in global methane cycling. Here, we investigated anoxic sediments of the meromictic freshwater Lake Cadagno (Switzerland), where Ca. Methanoperedens and sulfate-reducing bacteria co-occur, with metagenomics and long-term incubations. Incubations were performed with different electron acceptors, revealing that manganese oxides supported highest CH4 oxidation potential but enriched for Ca. Methanoperedens phylotypes that were hardly present in the inoculum. Combining data from the inoculum and incubations, we obtained five Ca. Methanoperedens genomes, each harboring different extracellular electron transfer pathways. In a reconstructed Desulfobacterota QYQD01 genome we observed large multi-heme cytochromes, type IV pili, and a putative loss of hydrogenases, suggesting facultative syntrophic interactions with Ca. Methanoperedens. We also screened for putative extrachromosomal elements in the Ca. Methanoperedens genomes, including BORGs. This research deepens our understanding of the metabolic flexibility and potential interspecific interactions of Ca. Methanoperedens in freshwater lakes.

microbiology↗

bioRxiv2024

A ubiquitous and diverse methanogenic community drives microbial methane cycling in eutrophic coastal sediments

Coastal areas are responsible for over 75% of global marine methane emissions and this proportion is predicted to grow due to an increase in anthropogenically induced eutrophication and deoxygenation. Prolonged periods of low oxygen and high organic matter input have been put forward to cause an imbalanced microbial methane cycle, as methane oxidation cannot keep up with methane production. However, it is still unclear what factors affect each process and which microorganisms are responsible. Here we show that methanogenic processes dominate microbial methane cycling in the anoxic sediments of marine Lake Grevelingen (NL) after summer stratification with bottom water anoxia. We observed a shallow and narrow sulfate-methane transition zone between 5 and 15 cm depth, with high methane concentrations (> 5 mM) below this zone. Methanogenesis was dominant over methanotrophy in all investigated layers as active methanogenesis potential was detected down to 60 cm below sea floor, but methane oxidation was only observed in a narrow section of the sulfate-methane transition zone. Based on amplicon sequencing and sediment incubations, we uncovered a metabolically and phylogenetically diverse methanogenic community with distinct niche separation in different sediment layers. ANME archaea and their putative syntrophic sulfate-reducing bacteria were restricted to a narrow zone and were co-occurring with the detected methane oxidation activity. Our results suggest that eutrophication and deoxygenation will further contribute to rising methane emissions in coastal areas, as the microbial methane cycle will be tilted towards increased methanogenesis while the efficiency of the microbial methane filter is expected to decline.

microbiology↗

bioRxiv2023

Seasonal dynamics of the microbial methane filter in the water column of a eutrophic coastal basin

In the water column of coastal waters, methane-oxidizing bacteria (MOB) can form a methane biofilter. This filter can counteract high benthic methane fluxes and thereby lower methane emissions to the atmosphere. Recent metagenomic studies revealed that the metabolism of the MOB in the filter is versatile, and could quickly respond to changing oxygen concentrations. Changes in oxygen availability in coastal basins are largely driven by seasonal stratification and mixing. However, it is still unclear how well the methane biofilter functions throughout the seasons, and how this relates to MOB community composition. Here, we determined water column methane and oxygen depth profiles and the methanotrophic community structure, methane oxidation potential, and methane fluxes of the Scharendijke basin in marine Lake Grevelingen between March and October 2021. In this period, the methane filter mainly consisted of three MOB belonging to Methylomonadaceae. Although in low relative abundance, the methanotrophic community was present in the mixed water column in March and had increased to 9 % by July in the stratified water column, with a distinct vertical niche partitioning in the redoxcline. The methane and oxygen gradients were vertically decoupled in summer upon the formation of a suboxic zone. Surprisingly, this did not affect the vertical distribution or potential methane oxidation of MOB. Moreover, water-air fluxes remained below 0.6 mmol m-2 day-1. Our findings suggest active methane removal by MOB in virtually anoxic water. Weakening of the stratification in September resulted in higher diffusive methane fluxes to the atmosphere (up to 1.6 mmol m-2 day-1). This was likely due to a faster supply of methane, but also a reduction of methane oxidation. Thus, despite the rapid adaptation and versatile genomic potential of the MOB community, seasonal water column dynamics significantly influence methane removal efficiency.

microbiology↗

bioRxiv2023

Mechanisms of extracellular electron transfer in anaerobic methanotrophic archaea

Anaerobic methanotrophic (ANME) archaea are environmentally important uncultivated microorganisms mitigating the release of the potent greenhouse gas methane. During methane oxidation ANME archaea engage in extracellular electron transfer (EET) with other microorganisms, metal oxides, and electrodes, through a currently unknown mechanism. To shed light on this mechanism, we cultivated ANME-2d archaea (Ca. Methanoperedens) in bioelectrochemical systems and observed strong methane-dependent current (91-93% of total current) associated with high enrichment of Ca. Methanoperedens on the anode (up to 82% of the community) determined by metagenomics and transmission electron microscopy. Electrochemistry and metatranscriptomics indicated that the EET mechanism was similar at various electrode potentials pointing to the involvement of an so far uncharacterized short-range electron transport protein complex and OmcZ nanowires, suggesting a unique EET pathway in all ANME-2 archaea. Our findings furthermore indicate that bioelectrochemical cells might be powerful tools for the cultivation, and possibly isolation, of uncultured electroactive microorganisms.

microbiology↗

bioRxiv2022

Versatile methanotrophs form an active methane biofilter in the oxycline of a seasonally stratified coastal basin

The potential and drivers of microbial methane removal in the water column of seasonally stratified coastal ecosystems and the importance of the methanotrophic community composition for ecosystem functioning are not well explored. Here, we combined depth profiles of oxygen and methane with 16S rRNA gene amplicon sequencing, metagenomics, and methane oxidation rates at discrete depths in a stratified coastal marine system (Lake Grevelingen, The Netherlands). Three amplicon sequence variants (ASVs) belonging to different genera of aerobic Methylomonadaceae and the corresponding three methanotrophic metagenome-assembled genomes (MOB-MAGs) were retrieved by 16S rRNA sequencing and metagenomic analysis respectively. The abundances of the different methanotrophic ASVs and MOB-MAGs peaked at different depths along the methane oxygen counter-gradient and the MOB-MAGs show a quite diverse genomic potential regarding oxygen metabolism, partial denitrification, and sulfur metabolism. Moreover, potential aerobic methane oxidation rates indicated high methanotrophic activity throughout the methane oxygen counter-gradient, even at depths with low in situ methane or oxygen concentration. This suggests that niche-partitioning with high genomic versatility of the present Methylomonadaceae might contribute to the functional resilience of the methanotrophic community and ultimately the efficiency of methane removal in the stratified water column of marine Lake Grevelingen.

microbiology↗

bioRxiv2022

Nitrate leaching and its implication for Fe and As mobility in a Southeast Asian aquifer

The drinking water quality of millions of people in South and Southeast Asia is at risk due to arsenic (As) contamination of groundwater and insufficient access to water treatment facilities. Intensive use of nitrogen (N) fertilizer increases the possibility of nitrate (NO3-) leaching into aquifers, yet very little is known about how the N cycle will interact with and affect the iron (Fe) and As mobility in aquifers. We hypothesized that input of NO3- into highly methanogenic aquifers can stimulate nitrate-dependent anaerobic methane oxidation (N-DAMO) and subsequently help to remove NO3- and decrease CH4 emission. We, therefore, investigated the effects of N input into aquifers and its effect on Fe and As mobility, by running a set of microcosm experiments using aquifer sediment from Van Phuc, Vietnam supplemented with 15NO3- and 13CH4. Additionally, we assessed the effect of N-DAMO by inoculating the sediment with two different N-DAMO enrichment cultures (N-DAMO(O) and N-DAMO(V)). We found that native microbial communities and both N-DAMO enrichments could efficiently consume nearly 5 mM NO3- in 5 days. In an uninoculated setup, NO3- was preferentially used over Fe(III) as electron acceptor and consequently inhibited Fe(III) reduction and As mobilization. The addition of N-DAMO(O) and N-DAMO(V) enrichment cultures led to substantial Fe(III) reduction followed by the release of Fe2+ (0.190{+/-}0.002 mM and 0.350{+/-}0.007 mM, respectively) and buildup of sedimentary Fe(II) (11.20{+/-}0.20 mM and 10.91{+/-}0.47 mM, respectively) at the end of the experiment (day 64). Only in the N-DAMO(O) inoculated setup, As was mobilized (27.1{+/-}10.8 g/L), while in the setup inoculated with N-DAMO(V) a significant amount of Mn (24.15{+/-}0.41 mg/L) was released to the water. Methane oxidation and 13CO2 formation were observed only in the inoculated setups, suggesting that the native microbial community did not have sufficient potential for N-DAMO. An increase of NH4+ implied that dissimilatory nitrate reduction to ammonium (DNRA) took place in both inoculated setups. The archaeal community in all treatments was dominated by Ca. Methanoperedens while the bacterial community consisted largely of various denitrifiers. Overall, our results suggest that input of N fertilizers to the aquifer decreases As mobility and that CH4 cannot serve as an electron donor for the native NO3- reducing community. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/511258v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1ac9adborg.highwire.dtl.DTLVardef@eaa3ccorg.highwire.dtl.DTLVardef@a7d1a1org.highwire.dtl.DTLVardef@1b3dee9_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2022

Methanotrophs are vigorous H2S oxidizers using a sulfide:quinone oxidoreductase and a ba3-type terminal oxidase

Hydrogen sulfide (H2S) is produced in a wide range of anoxic environments where sulfate (SO42-) reduction is coupled to decomposition of organic matter. In the same environments, methane (CH4) is the end product of an anaerobic food chain and both H2S and CH4 diffuse upwards into oxic zones where aerobic microorganisms can utilize these gases. Methane-oxidizing bacteria are known to oxidize a major part of the produced CH4 in these ecosystems, mitigating the emissions of this potent greenhouse gas to the atmosphere. However, how methanotrophy is affected by toxic H2S is largely unexplored. Here, we show that a single microorganism can oxidize CH4 and H2S simultaneously. By oxidizing H2S, the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV can alleviate the inhibitory effects on CH4 oxidation. In response to H2S, strain SolV upregulated a type III sulfide:quinone oxidoreductase (SQR) and a sulfide-insensitive ba3-type terminal oxidase to dissipate the reducing equivalents derived from H2S oxidation. Through extensive chemostat cultivation of M. fumariolicum SolV we demonstrate that it converts high loads of H2S to elemental sulfur (S0). Moreover, we show chemolithoautotrophy by tracing 13CO2 fixation into new biomass by using H2S as sole energy source. Molecular surveys revealed several putative SQR sequences in a range of proteobacterial methanotrophs from various environments, suggesting that H2S detoxification is much more widespread in methanotrophs than previously assumed, enabling them to connect carbon and sulfur cycles in new ways.

microbiology↗

bioRxiv2022

Microbial paracetamol degradation involves a high diversity of novel amidase enzyme candidates

Pharmaceuticals are relatively new to nature and often not completely removed in wastewater treatment plants (WWTPs). Consequently, these micropollutants end up in water bodies all around the world posing a great environmental risk. One exception to this recalcitrant conversion is paracetamol, whose full degradation has been linked to several microorganisms. However, the genes and corresponding proteins involved in microbial paracetamol degradation are still elusive. In order to improve our knowledge of the microbial paracetamol degradation pathway, we inoculated a bioreactor with sludge of a hospital WWTP (Pharmafilter, Delft, NL) and fed it with paracetamol as the sole carbon source. Paracetamol was fully degraded without any lag phase and the enriched microbial community was investigated by metagenomic and metatranscriptomic analyses, which demonstrated that the microbial community was very diverse. Dilution and plating on paracetamol-amended agar plates yielded two Pseudomonas sp. isolates: a fast-growing Pseudomonas sp. that degraded 200 mg/L of paracetamol in approximately 10 hours while excreting a dark brown component to the medium, and a slow-growing Pseudomonas sp. that degraded paracetamol without obvious intermediates in more than 90 days. Each Pseudomonas sp. contained a different highly-expressed amidase (31% identity to each other). These amidase genes were not detected in the bioreactor metagenome suggesting that other as-yet uncharacterized amidases may be responsible for the first biodegradation step of paracetamol. Uncharacterized deaminase genes and genes encoding dioxygenase enzymes involved in the catabolism of aromatic compounds and amino acids were the most likely candidates responsible for the degradation of paracetamol intermediates based on their high expression levels in the bioreactor metagenome and the Pseudomonas spp. genomes. Furthermore, cross-feeding between different community members might have occurred to efficiently degrade paracetamol and its intermediates in the bioreactor. This study increases our knowledge about the ongoing microbial evolution towards biodegradation of pharmaceuticals and points to a large diversity of (amidase) enzymes that are likely involved in paracetamol metabolism in WWTPs. HighlightsO_LIParacetamol was fully degraded by activated sludge from hospital wastewater. C_LIO_LILow paracetamol concentrations were removed by a diverse microbial community. C_LIO_LIPseudomonas sp. dominated cultures with high paracetamol concentration. C_LIO_LIUncharacterized amidases are probably involved in degrading paracetamol in WWTPs. C_LIO_LIDeaminases and dioxygenases might be degrading paracetamol transformation products. C_LI

microbiology↗

bioRxiv2022

Sulfide toxicity as key control on anaerobic oxidation of methane in eutrophic coastal sediments

Coastal zones account for significant global marine methane emissions to the atmosphere. In coastal ecosystems, the tight balance between microbial methane production and oxidation in sediments prevents most methane from escaping to the water column. Anthropogenic activities, causing eutrophication and bottom water deoxygenation, could disrupt this balance in the microbial methane cycle and lead to increased methane release from coastal sediments. Here, we combined microbiological and biogeochemical analyses of sediments from three sites along a bottom water redox gradient (oxic-hypoxic-euxinic) in the eutrophic Stockholm Archipelago to investigate the impact of anthropogenically-induced redox shifts on microbial methane cycling. At both the hypoxic and euxinic site, sediments displayed a stronger depletion of terminal electron acceptors at depth and a shoaling of the sulfate-methane transition zone in comparison to the oxic site. Porewater methane and sulfide concentrations and potential methane production rates were also higher at the hypoxic and euxinic site. Analyses of metagenome-assembled genomes and 16S rRNA gene profiling indicated that methanogens became more abundant at the hypoxic and euxinic site, while anaerobic methane-oxidizing archaea (ANME), present in low coverage at the oxic site, increased at the hypoxic site but virtually disappeared at the euxinic site. A 98% complete genome of an ANME-2b Ca. Methanomarinus archaeon had genes encoding a complete reverse methanogenesis pathway, several multiheme cytochromes, and a sulfite reductase predicted to detoxify sulfite. Based on these results, we infer that sulfide exposure at the euxinic site led to toxicity in ANME, which, despite the abundance of substrates at this site, could no longer thrive. These mechanistic insights imply that the development of euxinia, driven by eutrophication, could disrupt the coastal methane biofilter, leading to increased benthic methane release and potential increased methane emissions from coastal zones to the atmosphere.

microbiology↗