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Abstract Anaerobic methanotrophic (ANME) archaea are environmentally important, uncultivated microorganisms that oxidize the potent greenhouse gas methane. During methane oxidation, ANME archaea engage in extracellular electron transfer (EET) with other microbes, metal oxides, and electrodes through unclear mechanisms. Here, we cultivate ANME-2d archaea (‘Ca. Methanoperedens’) in bioelectrochemical systems and observe 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), as determined by metagenomics and transmission electron microscopy. Electrochemical and metatranscriptomic analyses suggest that the EET mechanism is similar at various electrode potentials, with the possible involvement of an uncharacterized short-range electron transport protein complex and OmcZ nanowires.

Anaerobic methanotrophic (ANME) archaea obtain energy from the breakdown of methane, yet their extrachromosomal genetic elements are little understood. Here we describe large plasmids associated with ANME archaea of the Methanoperedens genus in enrichment cultures and other natural anoxic environments. By manual curation we show that two of the plasmids are large (155,605 bp and 191,912 bp), circular, and may replicate bidirectionally. The plasmids occur in the same copy number as the main chromosome, and plasmid genes are actively transcribed. One of the plasmids encodes three tRNAs, ribosomal protein uL16 and elongation factor eEF2; these genes appear to be missing in the host Methanoperedens genome, suggesting an obligate interdependence between plasmid and host. Our work opens the way for the development of genetic vectors to shed light on the physiology and biochemistry of Methanoperedens, and potentially genetically edit them to enhance growth and accelerate methane oxidation rates.

Anaerobic methanotrophic (ANME) archaea obtain energy from the breakdown of methane. Here, Schoelmerich et al. describe large plasmids associated with ANME archaea of the Methanoperedens genus in enrichment cultures and other natural anoxic environments, opening the way for development of genetic vectors for research on these poorly understood organisms.

BACKGROUND Due to their immunoregulatory and tissue regenerative features, mesenchymal stromal cells (MSCs) are a promising novel tool for the management of ulcerative proctitis (UP). Here we report on a phase IIa clinical study that evaluated the impact of local MSC therapy on UP.METHODS Thirteen refractory UP patients, with an endoscopic Mayo score (EMS) of 2 or 3, were included. Seven patients received 20–40 million allogeneic MSCs (cohort 1), while 6 patients received 40–80 million MSCs (cohort 2). Adverse events (AEs) were assessed at baseline and on weeks 2, 6, 12, and 24. Clinical, endoscopic, and biochemical parameters were assessed at baseline and on weeks 2 and 6. Furthermore, we evaluated the engraftment of MSCs, the presence of donor-specific human leukocyte antigen (HLA) antibodies (DSAs), and we determined the impact of MSC therapy on the local immune compartment.RESULTS No serious AEs were observed. The clinical Mayo score was significantly improved on weeks 2 and 6, and the EMS was significantly improved on week 6, compared with baseline. On week 6, donor MSCs were still detectable in rectal biopsies from 4 of 9 patients and DSAs against both HLA class I and class II were found. Mass cytometry showed a reduction in activated CD8+ T cells and CD16+ monocytes and an enrichment in mononuclear phagocytes and natural killer cells in biopsies after local MSC therapy.CONCLUSION Local administration of allogeneic MSCs is safe, tolerable, and feasible for treatment of refractory UP and shows encouraging signs of clinical efficacy and modulation of local immune responses. This sets the stage for larger clinical trials.TRIAL REGISTRATION EU Clinical Trials Register (EudraCT, 2017-003524-75) and the Dutch Trial Register (NTR7205).FUNDING ECCO grant 2020.

As one of the most famous delta cities in the world, Amsterdam exemplifies how decisions and narratives from the past can be the driving force for present-day actions and more effective design principles for future city planning. Water management in Amsterdam has often been, and frequently still is, reactive in response to water hazards, flooding, droughts, pollution and disease. While contemporary pressures urge water managers to redesign the living environment in harmony with changing water cycles, the centuries-long history of water awareness, cumulative knowledge and long-term spatial planning has led to gradual improvement throughout Amsterdam. Many solutions are still relevant today and are essential in decision making as we design a new climate-resilient future and deal with challenges such as sea-level rise and demographic change. Despite residing below sea level, the people of the delta city of Amsterdam exhibit a profound sense of confidence and security against flooding. Moreover, the material and immaterial dimensions of the water network serve as a tangible reminder of our ancestors’ deltaic identity, highlighting their contributions to our current living environment. Therefore, the water system plays a vital role in preserving Amsterdam’s urban landscapes, cultural heritage and historical significance, which also helps strengthen this delta city’s future water management and urban planning.

Adding Place to Balance People, Planet, Prosperity, Peace and Partnership (toward 6Ps of SDGs): The Dutch landscape contains unique elements resulting from both natural processes and human interventions. To truly understand the Dutch water system, we need to consider how human interventions have impacted it throughout history. This is especially important when it comes to addressing current water challenges as part of the United Nations’ Sustainable Development Goals (SDGs). However, the SDGs are not just isolated goals. They should be perceived as interdependent spheres of action, with “place” being a particularly important new pillar to consider. The concept of “place” forces an integrated approach between the five pillars of SDGs (5Ps of SDGs) – people, planet, prosperity, peace and the unique historic characteristics of specific spaces. By acknowledging and understanding the unique historic characteristics of different places and fostering mutual understanding through the sharing of narratives and building partnerships, we can effectively work together to find solutions that address future challenges.

Chronic intestinal inflammation underlies inflammatory bowel disease (IBD). Previous studies indicated alterations in the cellular immune system; however, it has been challenging to interrogate the role of all immune cell subsets simultaneously. Therefore, we aimed to identify immune cell types associated with inflammation in IBD using high-dimensional mass cytometry. We analyzed 188 intestinal biopsies and paired blood samples of newly-diagnosed, treatment-naive patients (n=42) and controls (n=26) in two independent cohorts. We applied mass cytometry (36-antibody panel) to resolve single cells and analyzed the data with unbiased Hierarchical-SNE. In addition, imaging-mass cytometry (IMC) was performed to reveal the spatial distribution of the immune subsets in the tissue. We identified 44 distinct immune subsets. Correlation network analysis identified a network of inflammation-associated subsets, including HLA-DR+CD38+ EM CD4+ T cells, T regulatory-like cells, PD1+ EM CD8+ T cells, neutrophils, CD27+ TCRγδ cells and NK cells. All disease-associated subsets were validated in a second cohort. This network was abundant in a subset of patients, independent of IBD subtype, severity or intestinal location. Putative disease-associated CD4+ T cells were detectable in blood. Finally, imaging-mass cytometry revealed the spatial colocalization of neutrophils, memory CD4+ T cells and myeloid cells in the inflamed intestine. Our study indicates that a cellular network of both innate and adaptive immune cells colocalizes in inflamed biopsies from a subset of patients. These results contribute to dissecting disease heterogeneity and may guide the development of targeted therapeutics in IBD.

Eutrophication of water bodies has been a problem causing severe degradation of water quality in cities. To gain mechanistic understanding of the temporal dynamics of nitrogen (N) and phosphorus (P) in a groundwater-fed low-lying urban polder, we applied high-frequency monitoring in Geuzenveld, a polder in the city of Amsterdam. The high-frequency monitoring equipment was installed at the pumping station where water leaves the polder. From March 2016 to June 2017, total phosphorus (TP), ammonium (NH4), turbidity, electrical conductivity (EC), and water temperature were measured at intervals of less than 20 min. This paper discusses the results at three timescales: annual scale, rain event scale, and single pumping event scale. Mixing of upwelling groundwater (main source of N and P) and runoff from precipitation on pavements and roofs was the dominant hydrological process governing the temporal pattern of the EC, while N and P fluxes from the polder were also regulated by primary production and iron transformations. In our groundwater-seepage controlled catchment, NH4 appeared to be the dominant form of N with surface water concentrations in the range of 2–6 mg N L−1, which stems from production in an organic-rich subsurface. The concentrations of NH4 in the surface water were governed by the mixing process in autumn and winter and were reduced down to 0.1 mg N L−1 during the algal growing season in spring. The depletion of dissolved NH4 in spring suggests uptake by primary producers, consistent with high concentrations of chlorophyll a, O2, and suspended solids during this period. Total P and turbidity were high during winter (range 0.5–2.5 mg P L−1 and 200–1800 FNU, respectively, where FNU represents Formazin Nephelometric Unit) due to the release of P and reduced iron from anoxic sediment to the water column, where Fe2+ was rapidly oxidized and precipitated as iron oxides which contributed to turbidity. In the other seasons, P is retained in the sediment by sorption to precipitated iron oxides. Nitrogen is exported from the polder to the receiving waters throughout the whole year, mostly in the form of NH4 but in the form of organic N in spring. P leaves the polder mainly during winter, primarily associated with Fe(OH)3 colloids and as dissolved P. Based on this new understanding of the dynamics of N and P in this low-lying urban catchment, we suggested management strategies that may effectively control and reduce eutrophication in urban polders and receiving downstream waters.

Anaerobic methanotrophic (ANME) archaea have recently been reported to be capable of using insoluble extracellular electron acceptors via extracellular electron transfer (EET). In this study, we investigated EET by a microbial community dominated by “Candidatus Methanoperedens” archaea at the anode of a bioelectrochemical system (BES) poised at 0 V vs. standard hydrogen electrode (SHE), in this way measuring current as a direct proxy of EET by this community. After inoculation of the BES, the maximum current density was 274 mA m–2 (stable current up to 39 mA m–2). Concomitant conversion of 13CH4 into 13CO2 demonstrated that current production was methane-dependent, with 38% of the current attributed directly to methane supply. Based on the current production and methane uptake in a closed system, the Coulombic efficiency was about 17%. Polarization curves demonstrated that the current was limited by microbial activity at potentials above 0 V. The metatranscriptome of the inoculum was mined for the expression of c-type cytochromes potentially used for EET, which led to the identification of several multiheme c-type cytochrome-encoding genes among the most abundant transcripts in “Ca. Methanoperedens.” Our study provides strong indications of EET in ANME archaea and describes a system in which ANME-mediated EET can be investigated under laboratory conditions, which provides new research opportunities for mechanistic studies and possibly the generation of axenic ANME cultures.

Microbial communities are key drivers of carbon, sulfur, and nitrogen cycling in coastal ecosystems, where they are subjected to dynamic shifts in substrate availability and exposure to toxic compounds. However, how these shifts affect microbial interactions and function is poorly understood. Unraveling such microbial community responses is key to understand their environmental distribution and resilience under current and future disturbances. Here, we used metagenomics and metatranscriptomics to investigate microbial community structure and transcriptional responses to prolonged ammonium deprivation, and sulfide and nitric oxide toxicity stresses in a controlled bioreactor system mimicking coastal sediment conditions. Ca. Nitrobium versatile, identified in this study as a sulfide-oxidizing denitrifier, became a rare community member upon ammonium removal. The ANaerobic Methanotroph (ANME) Ca. Methanoperedens nitroreducens showed remarkable resilience to both experimental conditions, dominating transcriptional activity of dissimilatory nitrate reduction to ammonium (DNRA). During the ammonium removal experiment, increased DNRA was unable to sustain anaerobic ammonium oxidation (anammox) activity. After ammonium was reintroduced, a novel anaerobic bacterial methanotroph species that we have named Ca. Methylomirabilis tolerans outcompeted Ca. Methylomirabilis lanthanidiphila, while the anammox Ca. Kuenenia stuttgartiensis outcompeted Ca. Scalindua rubra. At the end of the sulfide and nitric oxide experiment, a gammaproteobacterium affiliated to the family Thiohalobacteraceae was enriched and dominated transcriptional activity of sulfide:quinone oxidoreductases. Our results indicate that some community members could be more resilient to the tested experimental conditions than others, and that some community functions such as methane and sulfur oxidation coupled to denitrification can remain stable despite large shifts in microbial community structure. Further studies on complex bioreactor enrichments are required to elucidate coastal ecosystem responses to future disturbances.

In recent years, the externalization of electrons as part of respiratory metabolic processes has been discovered in many different bacteria and some archaea. Microbial extracellular electron transfer (EET) plays an important role in many anoxic natural or engineered ecosystems. In this study, an anaerobic methane-converting microbial community was investigated with regard to its potential to perform EET. At this point, it is not well-known if or how EET confers a competitive advantage to certain species in methane-converting communities. EET was investigated in a two-chamber electrochemical system, sparged with methane and with an applied potential of +400 mV versus standard hydrogen electrode. A biofilm developed on the working electrode and stable low-density current was produced, confirming that EET indeed did occur. The appearance and presence of redox centers at −140 to −160 mV and at −230 mV in the biofilm was confirmed by cyclic voltammetry scans. Metagenomic analysis and fluorescence in situ hybridization of the biofilm showed that the anaerobic methanotroph ‘Candidatus Methanoperedens BLZ2’ was a significant member of the biofilm community, but its relative abundance did not increase compared to the inoculum. On the contrary, the relative abundance of other members of the microbial community significantly increased (up to 720-fold, 7.2% of mapped reads), placing these microorganisms among the dominant species in the bioanode community. This group included Zoogloea sp., Dechloromonas sp., two members of the Bacteroidetes phylum, and the spirochete Leptonema sp. Genes encoding proteins putatively involved in EET were identified in Zoogloea sp., Dechloromonas sp. and one member of the Bacteroidetes phylum. We suggest that instead of methane, alternative carbon sources such as acetate were the substrate for EET. Hence, EET in a methane-driven chemolithoautotrophic microbial community seems a complex process in which interactions within the microbial community are driving extracellular electron transfer to the electrode.

The impacts of ecotourism on biodiversity are poorly understood and the outcome of this type of research is often contradictory. On the one hand ecotourism could impact the occurrence, survival or behavior of species, on the other hand ecotourism is often mentioned as providing a "human shield" by deterring negative practices like gold mining, logging and hunting. Brownsberg Nature Park is easily the most visited protected area of Suriname, with a high number of ecotourists visiting from abroad. A four-year study on the impact of ecotourism on medium-large terrestrial mammals was carried out between 2013 and 2016 using 16 camera trap stations. The area has a clear gradient of tourism pressure, with the pressure decreasing further away from the lodging facilities. Evidently, the impacts of human presence on the mammal communities were more significant in the busiest areas. Most species avoided areas with many hikers or switched to a more nocturnal activity pattern. In these areas the impact was not reflected in species numbers, however it was causing a significant decrease in the diversity of mammals. On the other hand, vehicles had little impact on species avoidance or diversity, but did increase nocturnality, even more than hikers. A few species seemed to be "attracted" by hikers and/or traffic. Giant armadillos (Priodontes maximus) and spotted pacas (Cuniculus paca) used the pools in the road created by traffic. Ocelots (Leopardus pardalis), margays (Leopardus wiedii) and red-rumped agoutis (Dasyprocta leporina) seemed to favor human disturbance probably because of predator release. Some of the most impacted species were the jaguar (Panthera onca), puma (Puma concolor) and lowland tapir (Tapirus terrestris), all three species with significant contribution to ecosystem balance. Management measures should focus on lowering the number of hikers in popular places and limiting the number of vehicles in recreational areas.

Imaging mass cytometry (IMC) is able to quantify the expression of dozens of markers at sub-cellular resolution on a single tissue section by combining a novel laser ablation system with mass cytometry. As such, it allows us to gain spatial information and antigen quantification in situ, and can be applied to both snap-frozen and formalin-fixed, paraffin-embedded (FFPE) tissue sections. Herein, we have developed and optimized the immunodetection conditions for a 34-antibody panel for use on human snap-frozen tissue sections. For this, we tested the performance of 80 antibodies. Moreover, we compared tissue drying times, fixation procedures and antibody incubation conditions. We observed that variations in the drying times of tissue sections had little impact on the quality of the images. Fixation with methanol for 5 min at −20°C or 1% paraformaldehyde (PFA) for 5 min at room temperature followed by methanol for 5 min at −20°C were superior to fixation with acetone or PFA only. Finally, we observed that antibody incubation overnight at 4°C yielded more consistent results as compared to staining at room temperature for 5 h. Finally, we used the optimized method for staining of human fetal and adult intestinal tissue samples. We present the tissue architecture and spatial distribution of the stromal cells and immune cells in these samples visualizing blood vessels, the epithelium and lamina propria based on the expression of α-smooth muscle actin (α-SMA), E-Cadherin and Vimentin, while simultaneously revealing the colocalization of T cells, innate lymphoid cells (ILCs), and various myeloid cell subsets in the lamina propria of the human fetal intestine. We expect that this work can aid the scientific community who wish to improve IMC data quality.

The Amsterdam area, a highly manipulated delta area formed by polders and reclaimed lakes, struggles with high nutrient levels in its surface water system. The polders receive spatially and temporally variable amounts of water and nutrients via surface runoff, groundwater seepage, sewer leakage, and via water inlets from upstream polders. Diffuse anthropogenic sources, such as manure and fertiliser use and atmospheric deposition, add to the water quality problems in the polders. The major nutrient sources and pathways have not yet been clarified due to the complex hydrological system in lowland catchments with both urban and agricultural areas. In this study, the spatial variability of the groundwater seepage impact was identified by exploiting the dense groundwater and surface water monitoring networks in Amsterdam and its surrounding polders. A total of 25 variables (concentrations of total nitrogen (TN), total phosphorus (TP), NH4, NO3, HCO3, SO4, Ca, and Cl in surface water and groundwater, N and P agricultural inputs, seepage rate, elevation, land-use, and soil type) for 144 polders were analysed statistically and interpreted in relation to sources, transport mechanisms, and pathways. The results imply that groundwater is a large source of nutrients in the greater Amsterdam mixed urban–agricultural catchments. The groundwater nutrient concentrations exceeded the surface water environmental quality standards (EQSs) in 93 % of the polders for TP and in 91 % for TN. Groundwater outflow into the polders thus adds to nutrient levels in the surface water. High correlations (R2 up to 0.88) between solutes in groundwater and surface water, together with the close similarities in their spatial patterns, confirmed the large impact of groundwater on surface water chemistry, especially in the polders that have high seepage rates. Our analysis indicates that the elevated nutrient and bicarbonate concentrations in the groundwater seepage originate from the decomposition of organic matter in subsurface sediments coupled to sulfate reduction and possibly methanogenesis. The large loads of nutrient-rich groundwater seepage into the deepest polders indirectly affect surface water quality in the surrounding area, because excess water from the deep polders is pumped out and used to supply water to the surrounding infiltrating polders in dry periods. The study shows the importance of the connection between groundwater and surface water nutrient chemistry in the greater Amsterdam area. We expect that taking account of groundwater–surface water interaction is also important in other subsiding and urbanising deltas around the world, where water is managed intensively in order to enable agricultural productivity and achieve water-sustainable cities.

The capital of The Netherlands, Amsterdam, is home to more than 800,000 people. Developments in water safety, water quality, and robust water infrastructure transitioned Amsterdam into an attractive, economically healthy, and safe city that scores highly in the field of water management. However, investments need to be continued to meet future challenges. Many other cities in the world have just started their transition to become water-wise. For those cities, it is important to assess current water management and governance practices, in order to set their priorities and to gain knowledge from the experiences of more advanced cities such as Amsterdam. We investigate how Amsterdam’s water management and governance developed historically and how these lessons can be used to further improve water management in Amsterdam and other cities. This retrospective analysis starts at 1672 and applies the City Blueprint Approach as a baseline water management assessment. It shows that developments in water infrastructure and water management have often been reactive in response to various crises. International knowledge exchange, implementation of integrated water resources management, and long-term planning improved the city considerably. We conclude that experiences from the past can be used to meet present and future challenges in many cities across the globe.

Fine organic suspended sediments (refractory detritus) play an important role in the underwater light attenuation of large shallow lakes with a peat origin and a eutrophication history. Wind driven resuspension of this material, its flocculation in the water column and the settlement of the formed flocs are the main processes governing the dynamics of this material. For restoration of the macrophyte community in such lakes, reduction of this refractory detritus to improve underwater light climate is the key process when eutrophication reduction measures alone are not effective enough. The shallow Lake Loosdrecht (The Netherlands) was used as case study to illustrate the effects of artificially created deepenings on suspended matter concentrations and the consequences for the underwater light climate. Suspended sediment balances were created for the current situation and the situation with deepenings. Field measurements were taken to quantify various processes and results of the calculations from the suspended sediment balances were used to quantify the effects on light climate and potential habitat for macrophytes. These calculations show that creating deepenings (three sections with a total surface area of 120 ha and a depth of 12 m on a 10% section of the lake) decreases the concentration of organic detritus by 25% and decreases attenuation coefficients from 2.5 m-1 to 2.2 m-1. P-load reductions affecting chlorophyll-a levels lead to a change of attenuation coefficients from 2.5 m-1 to 2.0 m-1. The combination of deepenings with P-load reduction measures gives the most optimal result and leads to a predicted attenuation coefficient of 1.6 m-1. These improvements of the underwater light climate are a first step to the recovery of the submerged macrophyte community.

In Suriname, mercury (Hg) use has recently increased because of gold mining, which has put fish-reliant communities (e.g., Indigenous and Tribal) at risk of enhanced Hg exposure through the riverine fish these communities consume. To quantify how the magnitude of these risks change according to location and time, we measured total mercury (HgT) in fish at sites downstream and upstream of an artisanal and small-scale gold mining (ASGM) operation in 2004–2005 and in 2017–2018. We tested whether fish HgT burdens over dynamic ranges were increased. Surprisingly, our findings did not support broadly increased fish Hg burden over time or that proximity to ASGM was diagnostic to fish HgT-burden. Subsequently, we elected to test the HgT stable isotope ratios on a set of freshly collected 2020 fish to determine whether differences in Hg source and delivery pathways might cofound results. We found that remote unmined sites were more susceptible to gaseous elemental Hg deposition pathways, leading to enhanced risk of contamination, whereas ASGM proximate sites were not. These results highlight that elemental mercury releases from ASGM practices may have significant impact on fish-reliant communities that are far removed from ASGM point source contamination. [Display omitted] • Fish mercury burdens did not noticeably increase over a 20-year delay span. • Fish mercury burdens were inconsistent with typical size-burden relationships. • Fish were increased in mercury relative to global trends even in remote areas. • Proximity to mercury-use gold mining was a poor predictor for fish mercury. • Remote intact ecosystems were more mercury sensitive than disturbed ecosystems. [ABSTRACT FROM AUTHOR]

We investigated long-term changes in the fish fauna of Brokopondo Reservoir, Suriname, the first large reservoir (1560 km²) that was created in tropical rainforest. Before closure of the dam in 1964, the fish fauna of Suriname River had 172 species, high diversity and high evenness. The riverine fauna was dominated by small-sized species, but no single species was dominant in numbers. Large catfishes were dominant in biomass. Species were evenly distributed over riverine habitats: rapids, tributaries and main channel. Four years after closure of the dam, only 62 fish species were collected from Brokopondo Reservoir, but the composition of the fish fauna was still changing. The reservoir fauna in 1978 was very similar to the reservoir fauna in 2005, indicating that a stable equilibrium had been reached 14 years after closure of the dam. The reservoir fauna had 41 species, low diversity and low evenness. Most species of Suriname River and its tributaries with strict habitat requirements did not survive in Brokopondo Reservoir. Fish community structure was different among four habitats of Brokopondo Reservoir. The open-water habitat (10 species) was dominated by the piscivores Serrasalmus rhombeus, Acestrorhynchus microlepis and Cichla ocellaris and their prey Bryconops melanurus and two Hemiodus species. B. melanurus fed on zooplankton, Culicinae pupae and terrestrial invertebrates. Hemiodus fed on fine flocculent detritus, demonstrating that the detritus-based food chain was still important in late stages of reservoir development. Serrasalmus rhombeus also fed on peccaries that drowned when swimming across the large reservoir in rough weather. The shore community (27 species) was dominated by seven cichlids, but early stages and juveniles of the open-water species S. rhombeus and B. melanurus also occurred in the shore habitat. Fish biomass in the shore habitat was 66.5±59.9 kg ha-1. The cichlid Geophagus surinamensis and the characid B. melanurus had a lower biomass in Brokopondo Reservoir than in Suriname River. Serrasalmus rhombeus showed reduced body length in Brokopondo Reservoir as compared to riverine populations.