Free-living nitrogen fixation is an important pathway for nitrogen inputs into soil and litter ecosystems. Here we compared free-living nitrogen fixation in forest soils and litter layers between limestone and clastic rock. We found that free-living nitrogen fixation activity is largest in litter followed by limestone soils and lowest in clastic rock soils. Compared to clastic rock soils, limestone soils had higher pH, exchangeable calcium, and greater abundances of diazotrophs and phoD-harboring bacteria, along with increased microbial network complexity and stability. Network analysis identified phoD-harboring bacteria as having strong associations with diazotrophs and arbuscular mycorrhizal fungi, indicating their key role in phosphorus supply for soil free-living nitrogen fixation. In contrast, litter free-living nitrogen fixation activity remained consistent across lithologies due to similar microbial populations. These results suggest that higher soil pH and calcium in limestone promote free-living nitrogen fixation activity by fostering beneficial microbial associations, an effect absent in litter.

Soil pollution is a defining feature of the Anthropocene. Industrial emissions, intensive agriculture, and waste mismanagement have loaded soils with heavy metals, legacy organics, microplastics, and other novel entities at levels that threaten biodiversity, food security, and human health. Meanwhile, climate change and land-use intensification alter soil temperature and moisture, creating complex multi-stressor conditions that conventional controlled single-variable tests rarely capture. 1) We argue that soil food webs spanning microbes, microfauna, mesofauna, and macrofauna constitute core living infrastructure for remediation and ecological risk assessment. 2) Building on recent advances, we synthesize evidence that cross-trophic interactions regulate the fate of organic pollutants, metals, and emerging contaminants, and that chemical stressors together with climate-driven shifts in temperature and moisture can reshape food-web structure, energy channels, and stability. 3) We outline how food web metrics and bioindicators can be operationalized to guide remediation design and ecological risk assessment. We propose that diverse, functionally redundant, and well-connected food webs provide resilience that buffers contaminant pulses while sustaining nutrient cycling. Realizing this potential requires trait-based multitrophic research aided by omics, synthetic biology, network analysis, and big data modeling to embed food web principles into nature-based remediation and governance.

Converting cropland to planted forests improves soil organic carbon (SOC) and total nitrogen (TN) storage while contributing to climate change mitigation, primarily through the regulation of belowground organisms and mineral protection such as calcium (Ca). However, the mechanistic pathways linking exchangeable Ca2+, soil micro-food web interactions, and nutrient accumulation under warming remain unclear. Here, we investigated their potential roles in driving the accumulation of mineral-associated organic matter (MAOM), SOC, and TN in planted forests compared with croplands under warming conditions. Planted forests exhibited higher MAOM, SOC, and TN than cropland and had stronger coupling between carbon and nitrogen. Warming increased MAOM, SOC, and TN in planted forests but reduced SOC in cropland. Compared to cropland, planted forests displayed elevated levels of soil exchangeable Ca2+, microbial necromass carbon and nitrogen, stronger Ca-microbial and multi-trophic associations. Warming further amplified positive Ca-microbial (e.g., bacteria and fungi) and cross-trophic associations (e.g., nematode-bacteria, nematode-fungi, nematode-protist, and omnivore-predator-bacteria/fungi) in planted forests by increasing plant productivity, litter biomass, and soil exchangeable Ca2+, whereas cropland showed limited responsiveness to temperature changes. In planted forests, soil exchangeable Ca2+ was positively correlated with Ca-microbial and cross-trophic associations, microbial necromass carbon and nitrogen, and the contents of MAOM, SOC, and TN. These relationships were absent in cropland. Notably, cross-trophic associations rather than microbial abundance or diversity, with significant modulation by soil exchangeable Ca2+, had the strongest positive relationship with MAOM, SOC, and TN accumulation in planted forests. Collectively, our findings lead to the hypothesis that warming promotes SOC and TN storage in planted forests by jointly strengthening exchangeable Ca2+, Ca-microbial and cross-trophic interactions. These results highlight the potential importance of multi-trophic interactions and Ca-mediated processes in stabilizing microbial necromass and fostering carbon and nitrogen preservation during vegetation restoration in response to warming.

Heavy metals are increasingly recognized as major drivers of antibiotic resistance gene (ARG) dissemination in soil ecosystems. However, the role of phages in heavy metal-driven ARG dissemination and the underlying mechanisms remain poorly understood. Here, through integrative metagenomic, viromics, and metabolomic analyses of paddy soils across China, we reveal that soil phages promote ARG dissemination under heavy metal stress, likely through two potential mechanisms. First, phage-encoded auxiliary metabolic genes (AMGs) reprogram host metabolism to enhance bacterial survival and adaptation, thereby facilitating the cotransfer of adjacent ARGs and indirectly promoting horizontal dissemination. Second, phage-encoded heavy metal detoxification genes (HDGs) directly mediate metal detoxification, driving the cotransfer of neighboring ARG fragments and inducing lipid peroxidation-associated increases in membrane permeability, which collectively enhance ARG mobilization. We further identify a significant enrichment of lysogenic phages coharboring ARGs with AMGs or HDGs (AMG-ARG and HDG-ARG fragments), underscoring their contribution to ARG dissemination. Phage transplantation experiments confirm that elevated heavy metal stress triggers lysogenic phage-mediated ARG transduction to bacterial hosts. Cumulatively, our experiments highlight the pivotal role of phages in mediating ARG transfer under heavy metal pressure and underscore the necessity of incorporating phage dynamics into ARG risk assessments.

Biological nitrogen fixation is a cornerstone of terrestrial nitrogen cycling, traditionally attributed to bacterial nitrogenase activity. However, the potential contribution of rhizospheric viruses remains largely unexplored. Here, we reveal the global distribution of nitrogen-fixing genes, with widespread detection of nifA, nifL, nifU, and nifH in both bacteria and viruses, and identify nifU as a viral auxiliary metabolic gene (AMG). Analysis of viral communities in rhizosphere and bulk soils cultivated with cowpea showed that viral nifU expression was significantly upregulated in rhizosphere soils. Using 15N₂ stable-isotope tracing and virus transplantation experiments, we demonstrate that virus-encoded nitrogen-fixing AMGs, horizontally transferred from bacteria such as Azospirillum thermophilum (70-99% homology), increased nitrogenase activity from 1.79 to 3.14 nmol C2H4 g-1 dry soil h-1. This enhancement was accompanied by shifts in bacterial community composition, with the relative abundance of the nitrogen-fixing genus Azotobacter reaching 90.8%. These results uncover a previously hidden role of rhizospheric viruses in promoting bacterial nitrogen fixation, suggesting that viral-mediated gene transfer could be leveraged to enhance nitrogen cycling in soils and inform sustainable soil management strategies.

Pharmaceutical pollution is an emerging environmental concern that can disrupt microbial communities and ecological processes, while climate warming adds further stress with broad ecological consequences. Soil invertebrates such as collembolans harbor gut microbiomes essential for host health and ecosystem stability, yet the responses of these communities—particularly viral communities—to combined pharmaceutical and warming pressures remain unclear. Here, we used controlled microcosm experiments with Folsomia candida to investigate how pharmaceutical diversity and fluctuating warming jointly shape gut microbiomes through bacteria–virus interactions. Pharmaceutical diversity significantly reduced the alpha diversity of gut viral communities in F. candida, an effect not observed in surrounding soils. Diurnal warming increased the proportion of lysogenic phages and enhanced auxiliary metabolic genes (AMGs) such as ACADM and nrdA. Functional validation in Escherichia coli BL21 confirmed that these genes mitigate oxidative stress and improve host thermal tolerance. In contrast, diverse pharmaceuticals increased the proportion of lytic phages, likely driving nutrient turnover through a “kill-the-winner” dynamic that stimulated bacterial taxa involved in pharmaceutical degradation. Moreover, warming amplified the disruption of gut bacterial communities caused by pharmaceutical diversity and strengthened bacteria–virus co-occurrence networks. Our findings reveal that gut viruses act as pivotal regulators of microbial adaptation under concurrent chemical and climate stressors. By mediating host resilience and microbial dynamics, the gut virome provides mechanistic insights into ecosystem stability, and may also serve as an early indicator of combined pharmaceutical and warming stress in soil invertebrate systems, underscoring the need to integrate viral–microbial interactions into One Health framework for environmental risk assessment.

Soil denitrification plays a crucial role in regulating soil nitrogen availability during vegetation restoration. However, there is limited evidence revealing the mechanisms involving the abundance, diversity, composition, and interactions of denitrifying microorganisms in driving soil denitrification remain unclear, particularly in vegetation restoration scenarios within karst ecosystems. This study investigated the association between soil denitrification rates and microbial traits across three vegetation restoration strategies in karst areas: forage grass, plantation forest, and a combination of plantation forest and forage grass. Compared to cropland, all strategies increased denitrification rates by 45%-170%, with the highest rates observed in the combination of plantation forest and forage grass, accompanied by reduced nitrate levels. The abundance of nirK- and nirS-harboring denitrifiers was higher in plantation forest and the combination of plantation forest and forage grass relative to cropland soils, and plantation forest soils also exhibiting higher nirS richness. Co-occurrence network analysis indicated enhanced microbial interactions in vegetation restoration, particularly for nirK- harboring microorganisms across all strategies and for nirS in the combination of plantation forest and forage grass, evidenced by enhanced topological features such as node and edge counts. Notably, while nirK abundance and nirS richness significantly contributed to denitrification rate variations, their network complexity was identified as the dominant predictor. Thus, vegetation restoration, particularly the combination of plantation forest and forage grass, accelerates soil denitrification rates primarily by fostering interspecies interactions among denitrifying microorganisms, alongside increases in the abundance and richness of denitrifying communities. These findings offer valuable insights for optimizing vegetation restoration strategies to improve soil nitrogen cycling through targeted management of denitrifying microorganisms and their interactions.

Cholera is a severe diarrheal disease caused by toxigenic Vibrio cholerae, whose virulence depends on lysogenic infection by CTXφ bacteriophages encoding the cholera toxin genes (ctxA and ctxB) and associated accessory genes (ace and zot). However, the global distribution and transmission dynamics of phage-encoded cholera toxin genes across environments remain poorly understood. To address this, we performed a large-scale bioinformatic analysis of publicly available whole genomes. We show that both phages and bacteria carrying toxin genes are globally distributed across human-associated, freshwater, fish, and mammalian habitats, with Vibrio and Aeromonas being the dominant bacterial taxa and Inoviridae is the most prevalent phage family. Phage-mediated horizontal gene transfer (HGT) of toxin genes occurred in both Vibrio and non-Vibrio species, with the highest transfer between Inoviridae and V. cholerae occuring predominantly among bacteria from the same habitat. Temporal analysis revealed an increase in candidate HGT events after 2000, peaking at 377845 events during 2010-2019. HGT events negatively correlated with the presence of CRISPR-Cas system and toxin-repression genes (hns, hapR, and tsrA) in host bacteria. Experimental validation indicated that H-NS and HapR inhibit phage infection by repressing phage release. Together, our results suggest that CRISPR-Cas phage defense system and toxin-repression mechanisms could constrain the spread of toxin-carrying phages, with potential implications for the occurrence and severity of cholera outbreaks worldwide.

Biochar amendment reshapes microbial community dynamics in vermicomposting, but the mechanism of how phages respond to this anthropogenic intervention and regulate the dissemination of antibiotic resistance genes (ARGs) remains unclear. In this study, we used metagenomics, viromics, and laboratory validation to explore how nano-biochar affects phage-host interactions and ARGs dissemination in vermicomposting. Our results revealed distinct niche-specific phage life strategies. In vermicompost, lytic phages dominated and used a "kill-the-winner" strategy to suppress antibiotic-resistant bacteria (ARB). In contrast, lysogenic phages prevailed in the earthworm gut, adopting a "piggyback-the-winner" strategy that promoted ARGs transduction through mutualistic host interactions. Nano-biochar induced the conversion of lysogenic to lytic phages in the earthworm gut, while concurrently reducing the abundance of lysogenic phages and their encoded auxiliary metabolic genes carried by ARB. This shift disrupted phage-host mutualism and inhibited ARGs transmission via a "phage shunting" mechanism. In vitro validation with batch culture experiments further confirmed that lysogenic phages increased transduction of ARGs in the earthworm gut, while nano-biochar reduced the spread of ARGs by enhancing lysis infectivity. Our study constructs a mechanistic framework linking nano-biochar induced shifts in phage lifestyles that suppress ARG spread, offering insights into phage-host coadaptation and resistance mitigation strategies in organic waste treatment ecosystems.

Introduction and methodsVegetation disturbance intensity serves as a critical determinant of changes in soil nutrients and microbial communities. Karst ecosystems are highly fragile, and vegetation degradation has contributed to severe desertification in these regions. However, the specific effects of vegetation disturbance intensity on soil nutrient availability, microbial diversity, and community composition remain poorly understood in karst areas. To address this knowledge gap, this study investigates how varying levels of vegetation disturbance influence soil properties, as well as the diversity, composition, and interactions of bacterial, fungal, and protist communities in a karst ecosystem. The study included four vegetation disturbance intensities: natural vegetation restoration (control) and slight, moderate, and extreme disturbance.ResultsThe findings reveal that higher disturbance intensity significantly alters soil nutrient levels, which in turn affects microbial diversity, abundance, community composition, and interspecies interactions. Specifically, increasing vegetation disturbance intensity led to significant declines in soil available nutrients, including nitrate nitrogen (NO₃−), available phosphorus (AP), and available potassium (AK). Both slight and moderate disturbances reduced bacterial richness and Shannon diversity, whereas extreme disturbance decreased fungal Shannon diversity compared to the control. Bacterial abundance under moderate and extreme disturbances was significantly lower than that in the control, whereas fungal abundance was significantly higher under extreme disturbance. Although vegetation disturbance reduced soil available nutrients, co-occurrence network analysis revealed greater network complexity under moderate and extreme disturbances, with bacterial-bacterial interactions predominating, alongside enhanced bacterial-fungal and bacterial-protistan interactions. Actinobacteria, Ascomycota, and Chlorophyta emerged as keystone taxa. Pearson correlation analysis identified NO3−, pH, and soil moisture as primary drivers of microbial abundance and diversity, indicating that higher disturbance intensities reduce bacterial abundance and fungal diversity by limiting soil nutrient availability and moisture. Additionally, community compositions of bacteria, fungi, and protists were significantly correlated with AP and AK.DiscussionThese findings suggest that short-term vegetation recovery following prolonged moderate and extreme disturbances promotes microbial adaptation to nutrient- and moisture-limited conditions through increased microbial interactions, compensating for losses in abundance and diversity. This study provides valuable insights for ecosystem management and soil restoration in degraded karst landscapes.

Saline-alkali soils cover millions of hectares worldwide, severely limiting agricultural productivity. Although various remediation strategies have been applied, the adaptive responses of microbial communities to these interventions remain poorly understood. This study investigated microbial community responses to saline-alkali stress under different remediation treatments, focusing on diversity patterns, community assembly mechanisms, network interactions and functional roles. A randomised block experiment was conducted with three treatments: untreated saline-alkaline (SA) soils, paddy-upland rotation (PUR) and organic fertiliser (OF) amendment. Both PUR and OF treatments increased the relative abundances of Bacteroidota, Acidobacteriota and Firmicutes, indicating enrichment of beneficial taxa. Specialists exhibited higher connectivity with other microbial species than generalists, emphasising their role in stabilising indigenous microbiota and enhancing resistance to saline-alkali stress. Community assembly was dominated by deterministic processes for specialists in SA and PUR soils, while stochastic processes prevailed in other contexts across both generalists and specialists. These results reveal distinct but complementary roles of microbial generalists and specialists in soil adaptation and highlight the mechanisms by which amendments shape microbial community structure and function. Our findings provide mechanistic insights into microbial contributions to saline-alkali soil remediation, informing strategies for sustainable soil restoration.

As global change intensifies, understanding the eco-evolutionary trade-offs among soil viral communities and the maintenance of their functional traits across environmental gradients is crucial for predicting soil health and ecological functions. Yet how viral communities respond to environmental change remain poorly understood. Using metavirome sequencing along an elevation gradient, which serves as an ideal proxy for environmental variations, we reveal the extensive diversity of viruses and expand the information on soil viruses in Africa. Compared to climate pressures associated with increasing elevation, nutritional constraints driven by higher elevation were more closely associated with significant differentiation in viral populations, mainly driven by an increase in both lytic viruses and functional diversity. These findings were consistently supported by field microcosm experiments on the same mountainsides and the global data sets from other mountain regions. With increasing elevation, phages undergo greater diversifying selection, encoded more bacterial life history strategy genes associated with stress tolerance and ruderals/opportunist, and had a higher proportion of unannotated functions, potentially playing a role in host carbon assimilation in nutrient-poor environments. These findings provide insights into the biogeography and ecological roles of viruses and serve as a foundation for understanding the response of soil viruses to global change.

ABSTRACT The compost microbiome is important in regulating soil carbon sequestration. However, there is limited information concerning phage communities and phage-encoded auxiliary metabolic genes (AMGs) in compost-applied soils. We combined metagenomics and meta-viromes to explore the potential role of bacterial and phage communities in carbon sequestration in the compost microbiome. The experiment comprised swine manure compost (SW) and vermicompost (VE) applied to the soil along with a control treatment (CK). The bacterial community richness decreased after swine manure application and increased after vermicomposting compared to the control treatment. The phage community in the vermicompost-applied soil was dominated (63.1%) by temperate phages. In comparison, the communities of the swine manure compost-applied soil (92.7%) and control treatments (75.4%) were dominated by virulent phages. Phage-encoded carbon sequestration AMGs were detected in all three treatments, with significant enrichment in the vermicompost-applied soil. The average carbon sequestration potential (the coverage ratio of phage AMGs:total genes) of phage AMGs ( aceF , GT 11, and GT 6) in the vermicompost-applied soil (65.18%) was greater than in the swine manure-applied (0) and control soils (50.21%). The results highlight the role of phage-encoded AMGs in improving soil carbon sequestration in vermicompost-applied soil. The findings provide new avenues for increasing soil carbon sequestration. IMPORTANCE The phage-bacteria interactions have a significant impact on the global carbon cycle. Soil microbial carbon sequestration is a process in combination withcarbon sequestration genes and growth activity. This is the first study aimed at understanding the carbon sequestration potential of phage communities in vermicompost. The results of this study provide variations in carbon sequestration genes in vermicompost microbial communities, and some novel phage auxiliary metabolic genes were revealed to assist bacterial communities to increase soil carbon sequestration potential. Our results highlight the importance of phages in soil carbon sequestration from the perspective of phage-bacterial community interactions.

Earthworms are keystone animals stimulating litter decomposition and nutrient cycling. However, earthworms comprise diverse species which live in different soil layers and consume different types of food. Microorganisms in the gut of earthworms are likely to contribute significantly to their ability to digest organic matter, but this may vary among earthworm species. Here, we analyse the effect of food (litter) quality on gut microbiota and their changes during the gut passage (from foregut to hindgut) of earthworms of different ecological groups. The endogeic (soil living) species Aporrectodea caliginosa and the anecic (litter feeding) species Lumbricus terrestris were fed with high- (rape leaves) and low-quality litter (wheat straw) in a microcosm experiment for 18 weeks. Irrespective of earthworm species, alpha diversity of bacterial and fungal communities changed little during the gut passage, with the composition and diversity of microbial communities in the gut generally resembling those in soil more than in litter. In addition, the low-quality litter supported higher alpha diversity and more complex communities than high-quality litter. Further, gut microbial communities of the anecic L. terrestris changed less during gut passage than those of the endogeic A. caliginosa, especially when fed low-quality litter. Our findings indicate that earthworm gut microbial communities are predominantly shaped by the soil they ingest, but are modulated by the quality of litter they feed on and earthworm ecological group. Overall, the results suggest that earthworms primarily influence soil microbiota by mixing and spreading microorganisms from different microhabitats through bioturbation rather than by digesting microorganisms.

Plastispheres, novel niches in the Anthropocene, harbor microbial communities with unique functional signatures. As the most abundant biological entity on Earth, viruses are key regulators of microbial community composition and metabolism. However, little is known about viral communities and their functions in the plastisphere. Here, we investigate the composition and functional profile of plastisphere viral communities through microcosm experiments combined with global plastisphere metagenomics data. We find that the plastisphere recruits a distinct viral community with 86.9% novel viral operational taxonomic units compared to control substrates. The plastisphere viral community modulates host methane metabolism through auxiliary metabolic genes and distinctive interactions with hosts. These auxiliary metabolic genes for methane cycling are prevalent in global plastisphere viral communities. Notably, the plastisphere microbiome adopts the life history strategy of copiotrophs in the nutrient-poor water environment, making the water plastisphere a potential hot spot for methane emission compared to the soil plastisphere. Our phage transplantation experiments reveal that lysogenic viruses significantly contribute to enhancing the methanogenic capacity of microorganisms and promoting methane emission of the water plastisphere. Overall, we decipher the role of viruses in the plastisphere and reinforce the necessity of incorporating viral contributions when assessing the effects of plastisphere communities on global biogeochemical cycles.

Phage-mediated horizontal transfer of virulence genes can enhance the transmission and pathogenicity of Salmonella enterica (S. enterica), a process potentially regulated by its regulatory mechanisms. In this study, we explored the global dynamics of phage-mediated horizontal transfer in S. enterica and investigated the role of its regulatory mechanisms in transduction. A total of 5178 viral sequences encoding 12 S. enterica virulence genes were retrieved from the Integrated Microbial Genomes and Virome (IMG/VR) database, alongside 466,136 S. enterica genomes from EnteroBase. Virulence genes, including iacP (acyl carrier protein), mgtB (P-type Mg2+ transporter), misL (autotransporter porin), and fliC (flagellar filament protein), were widely distributed in phages and S. enterica across North America, Europe, and Asia. Phylogenetic analysis revealed close genetic affinity between phage- and bacterial-encoded virulence genes, suggesting shared ancestry and historical horizontal gene transfer events. The global regulator carbon storage regulator A (csrA) was highly conserved and ubiquitous in S. enterica. Overexpression of csrA inhibited prophage cyclization and release by upregulating the prophage cI repressor during horizontal gene transfer. Overall, these findings enhance our understanding of phage-mediated horizontal transfer of virulence genes, explore new areas of bacterial regulators that inhibit gene exchange and evolution by affecting phage life cycles, and offer a novel approach to controlling the transmission of phage-mediated S. enterica virulence genes.

Although soil quality and gut probiotics have been extensively accepted as critical for human health, the combined effects of soil and fecal bacteria on public health remain underexplored. This study collected soil and human fecal samples from three towns with high, medium, and low proportion of longevous populations in a well-known longevity region in Yangtze River Delta, China. Beneficial elements were detected in all soils, including selenium (0.01-0.05 mg kg-1), germanium (1.07-1.44 mg kg-1), boron (0.42-1.49 mg kg-1), zinc (1.07-1.70 mg kg-1) and manganese (38.78-43.52 mg kg-1). These elements were more abundant in high-proportion region (HP) compared to medium (MP) and low (LP) proportion region (p < 0.05). Similar dominant bacteria were detected in all soils and feces, including Proteobacteria (29.93 %), Acidobacteriota (16.23 %), and Bacillus (2.25 %). Notably, positive correlations were detected between beneficial metal contents and soil bacterial abundance (p < 0.05), suggesting a role in promoting bacterial growth. Moreover, beneficial element metabolic genes, such as zupT (encoding high-affinity zinc transporter for active zinc ion transport) and mntA (encoding manganese ion transporter protein) were significantly enriched in HP soil and fecal bacteria (p < 0.05). Additionally, Source Tracker analysis indicated that 41.13 % of fecal bacteria in HP area originated from HP soil bacteria. Structural equation model indicated that soil beneficial elements significantly enhanced the relative abundance of probiotic associated genes in the dominant fecal bacteria (path coefficients of 0.869 and 0.905, respectively; p < 0.05). Together, soil-borne beneficial elements promote intestinal bacterial functionality, contributing to human health and longevity.

Bacteriophages (phages) influence biogeochemical cycling in soil ecosystems by mediating bacterial metabolism. However, the participation of phages in soil's overall ecological functions (multifunctionality) remains unclear. Hence, this study investigated the potential for phages and bacterial communities to shape the multifunctionality of compost-applied soils. The findings revealed that cow compost and vermicompost applications enhanced the soil's multifunctionality; consequently, the highest multifunctionality was observed in the soil with vermicompost application (p < 0.05). The composition and diversity of bacteria and phages, as well as the abundance of functional genes of bacteria and phages related to carbon, nitrogen, phosphorus and sulphur metabolism, were dramatically altered following the application of both compost types. Moreover, the impact of phage diversity on soil multifunctionality is crucial for multi-threshold calculations. Structural equation modelling indicated that the effects of bacterial diversity on soil multifunctionality following compost application were paramount, with a path coefficient of 0.88 (p < 0.01). The rise in phage diversity and the enrichment of functional genes indirectly led to a dramatic increase in the soil's ecological multifunctionality by affecting the host bacteria's metabolic processes. These results offer a novel avenue to improve soil's functions and environmental services by transforming the phage community composition and functions of soils.

Microplastics (MPs) pose significant environmental challenges owing to their widespread occurrence and diverse origins, raising concerns about potential ecosystem degradation. The co-occurrence of invasive alien species and MPs in agroecosystems exacerbates threats to soil and plant health. However, research on the potential of biochar from invasive alien plant species, such as Solidago canadensis, for remediating MP contamination in the soil, particularly polyethylene (PE) and polylactic acid (PLA), is limited. We demonstrated that S. canadensis-derived biochar significantly improved soil quality, including increased microbial biomass, elevated inorganic nitrogen levels, and enhanced enzyme activity in soils contaminated with PE and PLA. Modified S. canadensis biochar (SBM) was superior to unmodified S. canadensis biochar and control treatments without biochar (NOB) in mitigating MP toxicity. Furthermore, SBM successfully restored carbon use efficiency (CUE) by increasing the dissolved organic nitrogen and microbial biomass carbon, thereby mitigating CUE limitations. Principal component and correlation analyses of soil properties, enzyme activities, and microbial biomass in biocharamended treatments revealed distinct patterns compared to the NOB treatment. In conclusion, this study highlighted the potential of biochar, especially SBM, to mitigate the adverse effects of PE and PLA microplastic contamination while preserving beneficial soil properties. These findings underscore the importance of invasive alien plant-based biochar amendments for promoting soil health in the presence of MP pollution.

The amelioration and reclamation of saline-alkali lands are crucial for maintaining arable land and coastal agricultural production. However, the impact and the drivers of saline-alkali land utilization on soil bacterial diversity and function are not clear. In this study, soils with long-term amelioration and original saline-alkali soils in the coastal area of the Yellow Sea were collected, and their physicochemical properties and the diversity of their bacterial community were determined. Our results showed that amelioration significantly alleviated the salinity stress from 21.6 to 0.49 g kg-1 and increased the bacterial diversity of richness index from 6065 to 7257, Shannon index from 9.6 to 10.5. Our study also found that amelioration significantly enriched the ecological niche of soil bacteria, increasing the NST index by 56.6%. Meanwhile, diverse collections of characteristic species responded to soil nutrient and stress conditions at different stages of amelioration, accompanied by a shift and enrichment of core functional species. Similarly, it was observed that soil amelioration significantly increased the functional diversity and abundance of soil bacteria. The functional pathways of sulphur and the phosphorus cycling of bacteria were significantly affected by amelioration, while more research is required to verify the mechanism. Our findings suggest that amelioration improved the potential productivity, and could be beneficial for the stability and sustainability of soil ecosystems by stimulating the activity of the bacterial community.