Lijun Hou

The concurrent intensification of hypoxia and acidification poses a growing threat to estuarine-coastal ecosystems globally, yet their interactive impacts on nitrification, a key process in the nitrogen (N) cycle and a substantial source of nitrous oxide (N ₂ O), remain poorly understood. This knowledge gap hinders reliable projections of future N cycling and climate feedbacks in these critical ecosystems. Here, we demonstrate that along the estuarine-coastal continuum, the co-occurrence of hypoxia and acidification suppresses nitrification rates but stimulates nitrification-derived N ₂ O emissions—although their combined effect is lesser than the sum of their individual effects. Metatranscriptomic analysis provided molecular evidence for these isotopically traced responses and uncovered critical microbial coping strategies through transcriptional adjustments in metabolic pathways for energy conservation and stress tolerance. This previously overlooked interaction disrupts microbial N cycling with potential impacts on N ₂ O emissions and climate feedbacks, highlighting the necessity to revise predictive models by incorporating such multistressor dynamics.

Reducing anthropogenic nitrous oxide emissions from agricultural lands is critical to combating climate change. Nitrification inhibitors and synthetic microbial consortia have already demonstrated potential in decreasing soil nitrification-derived nitrous oxide emissions. However, targeted interventions addressing denitrification sources while balancing agricultural sustainability remain challenging. Here, we identify triazole compounds as cytochrome P450 inhibitors capable of reducing soil denitrification-derived nitrous oxide emissions by 85-100% in laboratory settings. Extending our findings to in-situ paddy fields, we observe that triazoles (at 0.05% of fertilizer nitrogen) reduce nitrous oxide emissions by 33-54%. These potential inhibitors specifically target the NAD(P)H and nitric oxide binding sites of P450Nor, strongly inhibiting fungal nitrous oxide emissions. Occupancy of the heme-iron(III) site within the P450Nor active pocket enhances this selectivity, which is critical for effective inhibition. Given the projected increase in agricultural nitrous oxide emissions, our findings offer insights into the development of denitrification inhibitors and highlight triazole as a promising solution for nitrous oxide mitigation in agricultural ecosystems.

Antimony (Sb) has emerged as a global environmental concern due to its increasing anthropogenic release and its potential toxicity. This review synthesizes the global Sb biogeochemical cycle, quantifying both natural fluxes and profound anthropogenic perturbations. Natural Sb cycling is driven by rock weathering, atmospheric emissions (2.1 Gg·yr ⁻¹ ), natural deposition, terrestrial vegetation turnover (∼5.64 Gg·yr ⁻¹ ), and riverine export to oceans (37.4 ± 7.8 Gg·yr ⁻¹ ). In the ocean, hydrothermal vents add ∼3.5 ± 2.4 Gg·yr ⁻¹ , while outputs occur via sediment burial and oceanic lithosphere subduction. Human activities now dominate the cycle, contributing ∼72% of total atmospheric inputs, and the total Sb emission (7.6 Gg·yr ⁻¹ ) increased by 260% compared with the natural emission alone. Mining is the largest disturbance, releasing ∼48.68 Gg·yr ⁻¹ into rivers and accumulating ∼66.8 Gg·yr ⁻¹ in surrounding soils. Urban wastewater discharges and atmospheric deposition via runoff further contribute to aquatic systems. An estimated total marine input of ∼43.5 Gg·yr ⁻¹ slightly exceeds outputs (∼40.5 Gg·yr ⁻¹ ), indicating a human‐induced imbalance in the global Sb cycle. Significant uncertainties remain due to scarce emission factors and regional variability, highlighting the need for more precise data to inform sustainable resource management and pollution control strategies.

Coastal blue-carbon burial is vulnerable to climate change, yet marine hydrodynamic effects remain poorly quantified. Here we estimate hydrodynamic effects on carbon accumulation rate (CAR), by integrating global observations across mangroves, marshes and seagrasses with multiple drivers. Across all ecosystems, hydrodynamics explains 11.8–16.2% of CAR variability, whereas within individual ecosystems it explains 14.5–31.4%, 13.2–13.9% and 14.7–17.7% in mangroves, marshes and seagrasses, respectively. Limited tidal ranges leave low-CAR, inundation-tolerant seagrasses more common, whereas larger tidal ranges support broader intertidal habitats for high-CAR mangroves and marshes. Wave forcing shows contrasting relationships with CAR: positive in mangroves and seagrasses, potentially linked to organic matter inputs, but negative in marshes, likely reflecting lateral export. As sea-level rise accelerates and storms intensify, carbon-release risks may become heterogeneous, with marshes most vulnerable and mangroves and seagrasses more conditional and regionally uncertain. These findings provide a hydrodynamic framework for predicting future carbon dynamics.

Climate-induced permafrost thaw unlocks large stores of organic carbon that are mineralized and emitted as carbon dioxide (CO₂) from rivers to the atmosphere¹. Concurrently, warming and permafrost thaw can increase mineral weathering rates, thus affecting the release and sequestration of inorganic carbon^2-4. Yet how these biological and geological carbon cycles interact and jointly affect CO₂ dynamics (emission compared with drawdown) in permafrost rivers remains unknown⁵. Here we combine CO₂ emissions, organic and inorganic solute concentrations, dual carbon isotopes (δ¹³C-Δ¹⁴C) and geochemical modelling to infer how permafrost thaw may affect river biogeochemistry over decades to centuries across the Qinghai-Tibet Plateau. Leveraging a gradient of thermal permafrost degradation, we find that river CO₂ emissions decline, whereas solute fluxes from rock weathering increase with decreasing permafrost cover. Across this region, net CO₂ drawdown fluxes from rock weathering are about 35% of river CO₂ emissions, varying from around 15% in catchments with continuous permafrost to more than 100% in catchments with discontinuous or isolated permafrost. Thus, carbon fluxes from chemical weathering may become increasingly important with ongoing permafrost thaw, potentially even outpacing river CO₂ emissions. Our findings disentangle the interplay between biological and geological carbon fluxes that are important for the cryosphere and the global carbon cycle.

The genus Nitrospira, which includes canonical nitrite-oxidizing bacteria (NOB) and species capable of complete ammonia oxidation (comammox), plays an important role in the global biogeochemical nitrogen cycle. Typically, lineage IV Nitrospira predominate in marine environments, and other lineages are thought to be less abundant and remain poorly characterized in oceanic systems. Here, we recovered five novel metagenome-assembled genomes (MAGs) affiliated with Nitrospira lineage II–IV from deep-sea sediments. Notably, two of these MAGs represent members of lineage III and comammox Nitrospira, respectively, suggesting the presence of previously uncharacterized lineages in the deep sea. Phylogenetic and gene locus analyses indicated that deep-sea lineage III and comammox Nitrospira form distinct evolutionary clades that diverge from their terrestrial and coastal relatives, and we therefore designate these two marine-derived groups as “lineage III clade B” and “comammox clade A4”, respectively. Comparative read recruitment analyses revealed that these lineages exhibit potential pan-oceanic distribution in deep-sea sediments and waters, albeit at very low abundances. Furthermore, the identification of genes encoding amtB-type ammonium transporters (amtB), the ABC-type glycerol-3-phosphate transport system (ugpABCE), a multi-subunit Na+/H+ antiporter (mnh), and betaine transporters (BetT, opuABC) suggests that these newly discovered Nitrospira species possess adaptive capabilities to thrive in oligotrophic and saline marine environments. These findings provide novel insights into the occurrence, metabolic features, and adaptation strategies of lineage III and comammox Nitrospira, expand our understanding of Nitrospira diversity in the deep sea, and offer valuable perspectives on the evolutionary history of various Nitrospira lineages.

Complete ammonia oxidizers (comammox), oxidizing ammonia to nitrate directly, have been found to exist widely in multiple environments, but their distribution patterns are still under-explored in Antarctic environments. For the first time, the sediments were collected from West Antarctic lakes to investigate distribution patterns and community structure for comammox, ammonia oxidizing archaea (AOA) and bacteria (AOB), and nitrite-oxidizing bacteria (NOB), as well as the associations between ammonia oxidizers and antibiotic resistance genes (ARGs). Comammox clade B and AOB were dominant ammonia oxidizers, with the abundances of (1.62 ± 0.10) × 10² – (5.21 ± 0.74) × 10⁶ and (0.17 ± 0.05) × 10⁵ – (4.79 ± 0.65) × 10⁵ copies g^− 1 sediment, respectively. Comammox clade B, instead of clade A, occurred in all sediments, exhibiting higher abundances than AOB and AOA in most of the sediments. The abundances for comammox clade B demonstrated significant positive correlation (p < 0.01) with NH₄⁺-N levels, but negative correlation (p < 0.05) with C: N ratios. The coexistence of ammonia oxidizers in lake sediments was jointly structured by niche differentiation and environmental variables, and pH, modulated by penguin guano input, was found to be the most crucial factor in shaping their community structure. Co-occurrence network analyses revealed strong synergistic interactions between comammox and AOB, AOA, NOB, which played a critical role in nitrification processes. Our results further confirmed that comammox could act as important hosts for ARGs, hence stimulated their transmission and proliferation in the sediments. This study presented novel insights into the distribution patterns for ammonia oxidizers, their niche differentiation and the associations with ARGs in natural lake sediments of West Antarctica.

As a key component of stable soil organic matter, microbial necromass carbon (MNC) serves as a pivotal contributor to long‐term carbon sequestration in coastal blue carbon ecosystems. Despite its recognized importance, the ecosystem‐specific characteristics and accumulation mechanisms of MNC remain poorly understood across various coastal wetlands. In the present study, surface soils contained higher MNC contents than subsurface soils across mangroves, salt marshes, and bare flats. Additionally, distinct accumulations of MNC were found across the three types of wetlands. Mangrove wetlands exhibited a significantly higher MNC contents, especially bacterial necromass carbon (BNC) contents, compared with salt marsh and bare flat wetlands. Nitrogen availability, especially total nitrogen (TN), microbial biomass nitrogen (MBN), and the ratio of microbial biomass carbon to MBN, emerged as key drivers of necromass formation, emphasizing the importance of nutrient regulation. Furthermore, BNC accumulation in mangrove soils may be improved by iron‐mediated stabilization. Interestingly, BNC exhibited the opposite trend from fungal necromass carbon (FNC), which contributed less to soil organic carbon (SOC) in mangroves than in salt marshes and bare flats. The overall proportions of MNC in the SOC pool are similar across all wetland types despite these disparate contributions, most likely as a result of a dilution effect resulting from the accumulation of refractory, plant‐derived organic carbon in mangroves. Elucidating these dynamics is crucial for advancing our understanding of wetland carbon restoration of these ecosystems to enhance their carbon sequestration potential.

Forests are recognized as the largest natural source of nitrous oxide (N2O) emissions on land, with deforestation drastically reducing the cover and biodiversity of native forests worldwide. Yet, how losses in forest biodiversity affect soil N2O fluxes remains poorly understood. Here, we combined a global tree diversity–forest soil N2O data set, including 201 paired comparable observations from global forests, with a three-year field survey of in-situ flux data gathered from a long-term plant diversity field experiment. Our analyses reveal that tree diversity has a significant negative effect on soil N2O emissions, primarily driven by a decrease in N2O production associated with denitrification. More specifically, we showed that reductions in N2O emissions with tree diversity can be attributed to a decrease in the availability of soil inorganic nitrogen. Predictive modeling further shows that compared to forests with a single tree species, forests with two tree species can reduce global forest N2O emissions by 10.39%, while those with 24 tree species achieve the maximum mitigation effect, reducing emissions by 56.30%. Taken together, our work highlights the contribution of tree diversity for mitigating N2O emissions, highlighting the importance of accounting for biodiversity when reforesting old forests and supporting new afforestation processes.

Research on the morphology, physiology and genomics of Asgard archaea has provided valuable insights into the evolutionary history of eukaryotes^1,2,3. A previous study suggested that eukaryotes are nested within Heimdallarchaeia⁴, but their exact phylogenetic placement within Asgard archaea remains controversial^4,5. This debate complicates understanding of the metabolic features and timescales of early eukaryotic ancestors. Here we generated 223 metagenome-assembled nearly complete genomes of Asgard archaea that have not previously been documented. We identify 16 new lineages at the genus level or higher, which substantially expands the known phylogenetic diversity of Asgard archaea. Through sophisticated phylogenomic analysis of this expanded genomic dataset involving several marker sets we infer that eukaryotes evolved before the diversification of all sampled Heimdallarchaeia, rather than branching with Hodarchaeales within the Heimdallarchaeia. This difference in the placement of eukaryotes is probably caused by the previously underappreciated chimeric nature of Njordarchaeales genomes, which we find are composed of sequences of both Asgard and TACK archaea (Asgard’s sister phylum). Using ancestral reconstruction and molecular dating, we infer that the last Asgard archaea and eukaryote common ancestor emerged before the Great Oxidation Event and was probably an anaerobic H₂-dependent acetogen. Our findings support the hydrogen hypothesis of eukaryogenesis, which posits that eukaryotes arose from the fusion of a H₂-consuming archaeal host and a H₂-producing protomitochondrion.