Chemoautotrophs within Campylobacterota, especially Sulfurovum and Sulfurimonas, are abundant in the seawater-sediment interface of the Formosa cold seep in the South China Sea. However, the in situ activity and function of Campylobacterota are unknown. In this study, the geochemical role of Campylobacterota in the Formosa cold seep was investigated with multiple means. Two members of Sulfurovum and Sulfurimonas were isolated for the first time from deep-sea cold seep. These isolates are new chemoautotrophic species that can use molecular hydrogen as an energy source and CO2 as a sole carbon source. Comparative genomics identified an important hydrogen-oxidizing cluster in Sulfurovum and Sulfurimonas. Metatranscriptomic analysis detected high expression of hydrogen-oxidizing gene in the RS, suggesting that H2 was likely an energy source in the cold seep. Genomic analysis indicated that the Sulfurovum and Sulfurimonas isolates possess a truncated sulfur-oxidizing system, and metatranscriptomic analysis revealed that Sulfurovum and Sulfurimonas with this genotype were active in the surface of RS and likely contributed to thiosulfate production. Furthermore, geochemical and in situ analyses revealed sharply decreased nitrate concentration in the sediment-water interface due to microbial consumption. Consistently, the denitrification genes of Sulfurimonas and Sulfurovum were highly expressed, suggesting an important contribution of these bacteria to nitrogen cycling. Overall, this study demonstrated that Campylobacterota played a significant role in the cycling of nitrogen and sulfur in a deep-sea cold seep. IMPORTANCE Chemoautotrophs within Campylobacterota, in particular Sulfurovum and Sulfurimonas, are ubiquitous in deep-sea cold seeps and hydrothermal vents. However, to date, no Sulfurovum or Sulfurimonas has been isolated from cold seeps, and the ecological roles of these bacteria in cold seeps remain to be investigated. In this study, we obtained two isolates of Sulfurovum and Sulfurimonas from Formosa cold seep, South China Sea. Comparative genomics, metatranscriptomics, geochemical analysis, and in situ experimental study indicated collectively that Campylobacterota played a significant part in nitrogen and sulfur cycling in cold seep and was the cause of thiosulfate accumulation and sharp reduction of nitrate level in the sediment-water interface. The findings of this study promoted our understanding of the in situ function and ecological role of deep-sea Campylobacterota.

The different types of land-use and soil lithology in urban and peri-urban areas of modern cities compose a complex mosaic of soil ecosystems. It is largely unknown how these differences result in changes in bacterial community composition and structure as well as in functional guilds involved in N cycling. To investigate the bacterial composition and the proportion of denitrifiers in agricultural, forested, schoolyard and industrial areas, 24 samples were collected from urban and peri-urban sites of Lefkosia. Bacterial diversity and the proportion of denitrifiers were assessed by NGS and qPCR, respectively. Proteobacteria, Actinobacteria, Bacteriodetes, Chloroflexi, Acidobacteria and Planctomycetes were identified as the most dominant phyla across all sites, while agricultural sites exhibited the highest bacterial diversity. Heavy metals such as Co, Pb, V and Al were identified as key factors shaping bacterial composition in industrial and schoolyard sites, while the bacterial assemblages in agricultural and forested sites were associated with Ca. Variance partitioning analysis showed that 10.2% of the bacterial community variation was explained by land use management, 5.1% by chemical elements due to soil lithology, and 1.4% by sampling location. The proportion of denitrifiers varied with land use management. In industrial and schoolyard sites, the abundance of the nosZII bacterial community increased while nirK abundance declined. Our data showed that land use and lithology have a moderate impact on the bacterial assemblages in urban and peri-urban areas of Lefkosia. As the nosZII bacterial community is important to the N2O sink capacity of soils, it would be interesting to elucidate the factors contributing to the proliferation of the nosZII clade in these soils.

As urban areas expand around the world, there are growing efforts to restore and protect natural and agricultural systems for the multitude of ecosystem services they provide to urban communities. This study presents a researcher-farmer collaboration in a highly urbanized area of O\'ahu focused on understanding the historical and current challenges and opportunities faced by a culturally and socially valued spring-dependent urban farm, Sumida Farm, which produces the majority of the state of Hawai\'i\'s watercress. We conducted a long-term trend analysis (25 years) of factors identified by the farmers to be important historical drivers of crop yield, including groundwater pumping, pest outbreaks, temperature, Oceanic Niño Index, and precipitation. We combined this analysis with a year of intensive spring water sampling on the farm to evaluate nutrient and contaminant composition and flow to understand water-related stressors, as well as evaluate the potential of the farm to provide nutrient retention services. We found negative correlations between historical crop yields and increases in the Oceanic Niño Index, temperature thresholds, and pest outbreaks. Despite the surrounding urbanization, we found on-farm water quality to be very high, and microbial analyses revealed an abundance of denitrifiers (nirS gene) suggesting that the farm provides a nutrient retention service to downstream systems. Finally, we found that socio-cultural values including heritage value, aesthetic value, and educational value are increasingly important for the Sumida family and surrounding community. These socio-cultural benefits alongside highly valued local food production and nutrient retention services are essential for continued community and political support. Collectively, our study demonstrates that challenges facing urban agricultural systems shift through time, and that recognition of the beyond crop-yield benefits of these systems to urban communities is essential to their long-term survival.

Mycobacterium tuberculosis (Mtb) has an old history as a human pathogen and still kills over one million people every year. One key feature of this bacterium is its dormancy: a phenomenon responsible for major changes in its metabolism and replication that have been associated with the need for a lengthy therapy for Mtb. This process is regulated by key heme-based sensors, particularly DosT and DevS (DosS), among other co-regulators, and also linked to nitrogen utilization (nitrate/nitrite) and stringent responses. In face of the current threat of tuberculosis, there is an urgent need to develop new therapeutic agents capable of targeting the dormant state, associated with the need for a lengthy therapy. Interestingly, many of those key proteins are indeed metallo-containing or metallo-dependent biomolecules, opening exciting bioinorganic opportunities. Here, we critically reviewed a series of small molecules targeting key proteins involved in these processes, including DosT/DevS/DevR, RegX3, MprA, MtrA, NarL, PknB, Rel, PPK, nitrate and nitrite reductases, GlnA1, aiming for new opportunities and alternative therapies. In the battle against Mycobacterium tuberculosis, new drug targets must be searched, in particular  those involved in dormancy. A series of exciting cases for drug development involving metallo-containing or metallo-dependent biomolecules are reviewed, opening great opportunities for the bioinorganic chemistry community.

Existing methods that apply the planetary boundary for the nitrogen cycle in life cycle assessment are spatially generic and use an indicator with limited environmental relevance. Here, we develop a spatially resolved method that can quantify the impact of nitrogen emissions to air, soil, freshwater or coastal water on \"safe operating space\" (SOS) for natural soil, freshwater and coastal water. The method can be used to identify potential \"planetary boundary hotspots\" in the life cycle of products and to inform appropriate interventions. The method is based on a coupling of existing environmental models and the identification of threshold and reference values in natural soil, freshwater and coastal water. The method is demonstrated for a case study on nitrogen emissions from open-field tomato production in 27 farming areas based on data for 199 farms in the year 2014. Nitrogen emissions were modelled from farm-level data on fertilizer application, fuel consumption and climate- and soil conditions. Two sharing principles, \"status quo\" and \"gross value added\", were tested for the assignment of SOS to 1 t of tomatoes. The coupling of models and identification of threshold and reference values resulted in spatially resolved characterization factors applicable to any nitrogen emission and estimations of SOS for each environmental compartment. In the case study, tomato production was found to range from not transgressing to transgressing its assigned SOS in each of the 27 farming areas, depending on the receiving compartment and sharing principle. A high nitrogen use efficiency scenario had the potential to reverse transgressions of assigned SOS for up to three farming locations. Despite of several sources of uncertainty, the developed method may be used in decision-support by stakeholders, ranging from individual producers to global governance institutions. To avoid sub-optimization, it should be applied with methods covering the other planetary boundaries.

Urban centres acquire and accumulate many materials from their hinterland, among these are nutrient elements such as nitrogen (N). The popular North American vision of a peri-urban setting is one where urban food production, composting and re-cycling are assumed to limit urban accumulation of nutrients. This study quantifies this assumption using the Lower Fraser Valley (LFV) of British Columbia as an example, ideal because it is surrounded by mountains, ocean and an international border which collectively delimit the peri-urban boundaries. Nitrogen influxes are dominated by livestock feed imports to support dairy and poultry production (18000 tonnes N), followed by human food imports (9210 tonnes N), as well as 5410 tonnes N as fertilizer and 4690 tonnes N in atmospheric deposition. There is a transfer of 6700 tonnes N from agricultural to urban ecosystems displacing food imports, but food production contributes to the N footprint of the LFV. Nitrogen effluxes are dominated by sewage disposal (10400 tonnes N), solid waste disposal (7020 tonnes N) and atmospheric emissions (9460 tonnes N). The total influx is 15 kg N per person, the net influx is 3.1 kg N per person. Per unit land area, these are a total influx of 24 kg N/ha and a net influx of 4.7 kg N/ha. The atmospheric emissions are 4.7 kg N per person and 7.2 kg/ha. The N in soil is mobile and it is assumed soil N is at a steady state concentration, thus the surplus N is lost from the soil, probably by leaching and runoff. The Fraser River is estimated to acquire and transport 5230 tonnes N from the region into the ocean each year, in addition to 10300 tonnes N from sewage outfall. This is coupled with effluxes of phosphorus (estimated previously), and the result probably has an impact on the coastal waters. There is little reuse of imported N and current waste management practices including composting and combustion do little to improve N efficiency.

Groundwater is extensively used in Jakarta to compensate for the limited public water supply network. Recent observations show a rise in nitrate (NO3(-)) levels in the shallow aquifer, thus pointing at a potential risk for public health. The detected levels are still below national and international regulatory limits for drinking water but a strategy is necessary to contain the growing problem. We combine 3years of available data in the Ciliwung River, the major river flowing through Jakarta, with a distributed river-aquifer interaction model to characterise the impact of urbanisation on the N-cycle of both surface and groundwater systems. Results show that the N-cycle in the river-aquifer system is heterogeneous in space, seasonal dependent (i.e. flow regime) and strongly affected by urban pollution. Results suggest also that although the main sources of N related groundwater pollution are leaking septic tanks, the aquifer interaction with the Ciliwung River may locally have a strong effect on the concentrations. In the general context of pollution control in urban areas, this study demonstrates how advanced process-based models can be efficiently used in combination with field measurements to bring new insights into complex contamination problems. These are essential for more effective and integrated management of water quality in river-aquifer systems.

Soil microbial biomass (SMB) and bacterial community structure, which are critical to global ecosystem and fundamental ecological processes, are sensitive to anthropogenic activities and environmental conditions. In this study, we examined the possible effects of closed-off management (an ecological natural restoration measures, ban on anthropogenic activity, widely employed for many important wetlands) on SMB, soil bacterial community structure and functional marker genes of nitrogen cycling in Dongting Lake wetland. Soil samples were collected from management area (MA) and contrast area (CA: human activities, such as hunting, fishing and draining, are permitted) in November 2013 and April 2014. Soil properties, microbial biomass carbon (MBC), and bacterial community structure were investigated. Comparison of the values of MA and CA showed that SMB and bacterial community diversity of the MA had a significant increase after 7 years closed-off management. The mean value of Shannon-Weiner diversity index of MA and CA respectively were 2.85 and 2.07. The gene copy numbers of 16S rRNA and nosZ of MA were significant higher than those of CA. the gene copy numbers of ammonia-oxidizing archaea (AOA) and nirK of MA were significant lower than those of CA. However, there was no significant change in the gene copy numbers of ammonia-oxidizing bacteria (AOB) and nirS.