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Mercury accumulates in the deep sea, but its ecological impact remains unclear. This study reveals distinct patterns of mercury-transforming processes in deep-sea sediments, uncovering potential novel taxa and pathways.

Chen et al. reveal that plastisphere viral communities possess habitat-dependent potential for modulating global methane cycling. In aquatic environments, these viruses significantly promote methane emissions, emphasizing the significance of viruses in plastic pollution risk assessments.

Antimicrobial resistance has evolved over decades due to widespread antimicrobial use, with resistance genes now circulating across humans, animals and the environment, creating complex cross-sector connectivity challenges. This Perspective advocates for genomics-based studies of AMR connectivity to enable coordinated global action and investment under the One Health framework.

The soils of urban greenspaces are strikingly rich. This study finds that the variety of microbial life there is linked to acidic conditions and that this diversity is more homogenous than found in farmland soils.

A combination of metagenomic data from experimental and natural warming with microbial culturing experiments shows that warming increases the potential of evolution of antibiotic resistance in soil bacteria.

Arsenic contamination of groundwater and soils threatens the health of tens of millions people worldwide. A series of laboratory experiments suggest that in Arabidopsis, inositol transporters are responsible for arsenite loading into the phloem, the key source of arsenic in seeds.

A survey of sediments from 18 estuaries over 4000 km of coastal China reveals diverse and abundant antibiotic resistance genes. Analyses of socio-economic factors suggest that the presence of antibiotic resistance genes correlates with human activity.

Nitrous oxide (N₂O) emissions are continuously increasing owing to human activities. This Review discusses the temporal and spatial variability of N₂O sources, N₂O production pathways, and the potential of biogeoengineering strategies in agricultural soils and terrestrial water bodies to mitigate emissions.

The effects of microplastics (MPs) on soil microbial communities and antimicrobial resistance genes are not well understood. Here, the authors used microcosm studies to show that MP diversity, and partially fungicide treatment and reduced plant diversity, correlate with higher levels of ARG and related genetic factors.

Zhang et al. propose the ecological status of the ocean by considering microbial diversity, structure, and biogeochemical potential. Ecological status of 32.44% surface ocean will change due to climate change in 2100, assuming no policy intervention.

The role of soil health in crop productivity and environmental sustainability is often overlooked. Using a 0.5° × 0.5° global dataset, this study shows that soil health accounts for 12% of yield variation and 22% of nitrogen use efficiency variation. Enhancing global soil health could increase yields by 7.8 Mt and cut nitrogen surplus by 8.1 Mt by 2050.

Pathogenic viruses and antibiotic-resistant bacteria thrive on plastic. The biohazard risks of this ‘plastisphere’ shouldn’t be overlooked in efforts to tackle the pollution crisis.

The evolutionary reasons for the variation in silicon concentrations across plant families remain unclear. This paper provides new evidence that silicon variation is closely linked to global and long-term climate change, suggesting temperature could have driven the evolution of plant silicification.

NH₄⁺-derived pathways, rather than NO₃^--derived pathway, are the dominant hyporheic N₂O sources in lower-order streams. These findings provide insights into better estimation of N₂O emissions in global models of riverine ecosystems and emphasize the importance of managing ammonium.

The roles of marine plastisphere in global nitrogen cycling are largely unknown. Here, the authors indicate that the plastisphere could act as a potential source of N2O production, which is mainly regulated by the biotic denitrification

In this study, the authors analyzed global metagenomic data from agricultural soils and show that organic fertilization co-selects for antibiotic and metal(loid) resistance genes in genomic elements, while metatranscriptomic data additionally provides evidence for co-regulation of these gene sets.

It is challenging to produce biomass FG continuously due to the lack of an integrated device. Here, we create an integrated automatic system with energy requirement-oriented allocation to achieve continuous biomass FG production with a much lower carbon footprint.

The biogeochemical roles of the plastisphere regulating N cycling are elusive. This study reveals the plastisphere as an emerging nitrifying niche, featured by distinct shifts in nitrifiers and potential substrate exchanges compared to seawater.

Applying economic complexity methods, this study maps global progress toward the SDGs, uncovering distinct development paths and disparities among 166 countries. It highlights overlooked areas in sustainable development, offering insights into how nations can better achieve the SDGs.

This study proposes that the optimal allocation of roof area for rooftop agriculture and photovoltaics is 61% of the flat rooftop area to the former and the rest for the latter. However, maintaining this productivity requires considerable water use and materials.

Phosphate-solubilizing bacteria (PSB) are crucial for enhancing phosphorus bioavailability and regulating phosphorus transformation processes. This study employed a function-oriented single-cell Raman approach to identify, quantify and sequence active PSB from complex soil matrices to explore the mechanisms of phosphorus solubilization for efficient phosphorus management.

The joint effects of chemical pollution and climate change on soil food webs remain underexplored. This Progress discusses the impacts of these stressors on soil food web structure along with a potential framework to mitigate the adverse effects on soil functions.

Using spatial statistics on a detailed land use map, the study highlights the impact of cropland fragmentation in China. Optimizing cropping structures to meet animal food demand or relocating fragmented croplands for large-scale farming can release the potential of the fragmented croplands for increased agricultural productivity and environmental protection.

Liu et al. demonstrate that human-driven soil contamination in natural areas mirrors that in nearby urban greenspaces globally, and highlight the potential influence that soil contaminants have on ecosystem functions.

Antibiotic resistance genes pose a serious threat to human health, yet the impact of phages on these genes’ transmission in bacterial communities is not well understood. In this study, the authors show that human activities accelerate the movement of phage-encoded antibiotic-resistance genes between habitats.

Analysing biogeographic patterns in soil viromes based on 1,824 soil metagenomes from sites around the world, the authors show that viral diversity rarely corresponds to overall microbial diversity, with soil texture and moisture being closely associated with viral diversity.

The coupling of anaerobic oxidation of methane and arsenate reduction is an important pathway of releasing arsenic from soils, according to incubation experiments of arsenate-contaminated wetland soils.

The combination of metagenome and virus-enriched virome sequencing provides comprehensive profiles of viral communities and their associated antibiotic resistance genes and reveals the factors driving changes in the plastisphere.

Pig-manure-derived nanosized microbiomes transiently elevated high-risk antibiotic resistance gene abundance and microdiversity, which is driven by manure-derived Acinetobacter and their associated phages, based on an analysis of an agricultural soil microcosm experiment.

Soil viral communities remain understudied. Here, Liao et al. retrieve a catalogue of around sixty thousand vOTUs through a systematic viromic pipeline, and uncover the response of soil viral communities to anthropogenic land use changes.

The increasing use of manufactured sand in China since 2010 has greatly reduced the proportion of natural sand in the country’s total sand supply, from 80% in 1995 to 21% in 2020, according to a material flow analysis of sand in China.

Microorganisms and minerals both contribute to organic carbon preservation and accumulation in soil. The soil microbial carbon pump describes the microbial processes, but a separate soil mineral carbon pump needs to be acknowledged and investigated.

Climate change and human activities are increasing the exposure of deltaic communities to natural hazards. This Review discusses lessons that the Asian mega-deltas can share to develop long-term resilience strategies.

In this Review, Rillig, Kim and Zhu review our current understanding of the soil plastisphere, including the members of the microbial community that are enriched, the possible mechanisms underpinning this selection and functional properties.

The health of the city depends on how well all the elements of this system are interconnected and operating in harmony. Here the authors introduced the concept of urbanome which is analogous to the human genome that can be used to characterise the form and functioning of cities.

Remediation of contaminated and disused brownfields enables urban development, but many remediation strategies have high environmental or social burdens. This Review examines sustainable technologies to remediate and redevelop these sites, highlighting strategies to maximize co-benefits.

An archaeon, ‘Candidatus Argoarchaeum ethanivorans’, which is involved in the oxidation of ethane observed in anoxic marine habitats, is identified and metabolically characterized.

Irrigation expansion is expected to meet increasing food demand and help agriculture adapt to climate change. This Review article synthesizes the various linkages between irrigation and climate, evaluating their impacts on each other and presenting innovative solutions for sustainable irrigation under climate change.

Crop microbiomes provide plants with beneficial functions including increased nutrient acquisition and stress tolerance, but the current capability of utilizing indigenous crop microbiomes is limited due to low efficiency of separating the targeted functional microbes. A newly proposed framework using single-cell-sorting Raman spectroscopy combined with a synthetic community approach has the potential to design and optimize a ‘beneficial biome’.