Life history strategies of soil bacterial communities across global terrestrial biomes

Reducing antibiotic resistance genes in soil: The role of organic materials in reductive soil disinfestation

Increasing attention has been given to the role of reductive soil disinfestation (RSD) on antibiotic resistance genes (ARGs) in soil. The selection of organic materials in RSD is crucial to the effectiveness of the RSD method. However, the effects of distinct organic materials on ARGs remains unclear. In this study, we selected straw and rapeseed meal as the organic materials in RSD and explored their effects on ARGs. The results showed that using straw significantly reduced the abundance of ARGs, high-risk ARGs, and mobile genetic elements (MGEs) by 31.5 %-65.8 %, while using rapeseed meal led to ARGs enrichment. Structural equation modeling (SEM) analysis identified MGEs and microbial communities as the primary drivers of ARGS changes under different organic materials. The abundance of MGEs was effectively controlled in straw treatments, reducing the potential for horizontal gene transfer of ARGs. Bacterial diversity was significantly lower in the straw treatments compared to the rapeseed meal treatments, potentially leading to a reduced abundance of ARGs host bacteria. Network co-occurrence analysis further revealed that Symbiobacteraceae and Bacillus were potential bacterial hosts of ARGs. In straw treatments, these genera' abundance decreased by 12 %-100 % compared to the control (CK) and rapeseed meal groups, further inhibiting the spread of ARGs. These findings demonstrate that RSD with straw as the organic material is more effective in mitigating ARGs compared to rapeseed meal, providing insights into controlling soil antibiotic resistance risks and utilizing agricultural waste resources.

Soil microbial responses to multiple global change factors as assessed by metagenomics

Anthropogenic activities impose multiple concurrent pressures on soils globally, but responses of soil microbes to multiple global change factors are poorly understood. Here, we apply 10 treatments (warming, drought, nitrogen deposition, salinity, heavy metal, microplastics, antibiotics, fungicides, herbicides and insecticides) individually and in combinations of 8 factors to soil samples, and monitor their bacterial and viral composition by metagenomic analysis. We recover 742 mostly unknown bacterial and 1865 viral Metagenome-Assembled Genomes (MAGs), and leverage them to describe microbial populations under different treatment conditions. The application of multiple factors selects for prokaryotic and viral communities different from any individual factor, favouring the proliferation of potentially pathogenic mycobacteria and novel phages, which apparently play a role in shaping prokaryote communities. We also build a 25 M gene catalog to show that multiple factors select for metabolically diverse, sessile and non-biofilm-forming bacteria with a high load of antibiotic resistance genes. Finally, we show that novel genes are relevant for understanding microbial response to global change. Our study indicates that multiple factors impose selective pressures on soil prokaryotes and viruses not observed at the individual factor level, and emphasizes the need of studying the effect of concurrent global change treatments.

Land Use Types Drive the Distinct Patterns of Bacterial and Fungal Communities in Soils from the Semi-arid Area

Land types and ways of utilization significantly influence soil microbial communities in arid and semi-arid regions, which are vital for nutrient cycling and ecosystem functionality. In this study, the soil bacterial and fungal communities of five land types, including natural grasslands, farmlands, artificial grasslands, uncultivated lands, and riverbeds in the semi-arid lower reaches of the Heihe River, China, were investigated. Farmlands exhibited the highest bacterial Chao1 richness and Shannon diversity, while uncultivated soils had the lowest bacterial Chao1 richness. Fungal diversity was highest in uncultivated soils compared to farmlands. Principal coordinate analysis (PCoA) showed distinct microbial community structures across land types, with Actinobacteria, Proteobacteria, Firmicutes, and Chloroflexi dominating bacterial communities, and Ascomycota and Basidiomycota dominating fungal communities. Life history strategies revealed distinct patterns between bacterial and fungal communities within farmland soils and artificial grassland soils. Microbial community assembly in natural grasslands was primarily deterministic, with limited stochastic influence, while farmlands exhibited mixed assembly processes. Co-occurrence network analysis showed more stable and cooperative microbial networks in natural grasslands, while farmland networks were more competitive and reliant on key species. These findings provide important insights into the role of land use in shaping microbial diversity and ecosystem function, offering guidance for sustainable land management in semi-arid oasis regions.

Trait-Based Life History Strategies Shape Bacterial Niche Breadth

The ecological niche represents a fundamental property of organisms, reflecting their diversity of utilized resources or environmental tolerances across space and time. Despite a wealth of studies revealing that not all bacteria being everywhere, the key traits that determine niche breadth have remained unclear. Here, bacterial niche breadth based on a large-scale soil survey across a wide range of environmental gradients at a national-scale is characterized, and evaluated their life-history traits utilizing over 2000 bacterial genomic datasets from the Genome Taxonomy Database (GTDB). A positive relationship between gene functional diversity and niche breadth is found, and identified a key set of bacterial traits associated with niche breadth, which are assigned to five life-history categories, encompassing growth, competition, stress tolerance, resource acquisition, and dispersal ability. The traits of these categories are captured by distinct clusters in the full dimensionality of trait space, suggesting that a broad-niche taxon may indeed possess multiple facets of life history strategies essential for survival in diverse environments. Bacterial taxa with wider niche breadth maximized a diversity of traits associated with different life history strategies, whereas specialists tended to harbor a smaller number of traits associated with fewer life history strategies. Together, this study offers new insights into developing a trait-based understanding of bacterial niche breadth from the perspective of life history theory.

Climate-driven succession in marine microbiome biodiversity and biogeochemical function

Seasonal and El Niño-Southern Oscillation (ENSO) warming result in similar ocean changes as predicted with climate change. Climate-driven environmental cycles have strong impacts on microbiome diversity, but impacts on microbiome function are poorly understood. Here we quantify changes in microbial genomic diversity and functioning over 11 years covering seasonal and ENSO cycles at a coastal site in the southern California Current. We observe seasonal oscillations between large-genome lineages during cold, nutrient rich conditions in winter and spring versus small-genome lineages, including Prochlorococcus and Pelagibacter, in summer and fall. Parallel interannual changes separate communities depending on ENSO condition. Biodiversity shifts translate into clear oscillations in microbiome functional potential. Ocean warming induced an ecosystem with less iron but more macronutrient stress genes, depressed organic carbon degradation potential and biomass, and elevated carbon-to-nutrient biomass ratios. The consistent microbial response observed across time-scales points towards large climate-driven changes in marine ecosystems and biogeochemical cycles.

Integrating 'cry for help' strategies for sustainable agriculture

Plants recruit specific soil microbes through a sophisticated 'cry for help' strategy to mitigate environmental stresses. Recent advances highlight the potential of leveraging this mechanism to develop microbe-based approaches for enhancing crop health, but challenges remain in refining the criteria and conceptual frameworks to effectively investigate and harness these plant-microbe interactions.

Disturbance and stability dynamics in microbial communities for environmental biotechnology applications

Microbial communities are corner stones of environmental biotechnology, driving essential processes such as waste degradation, pollutant removal, and nutrient cycling, all fundamental to industrial bioprocesses and sustainability. The structure and functions of these communities are influenced by environmental disturbances, which can arise from changes in operational conditions. Understanding disturbance-stability dynamics, including the roles of rare taxa and gene potential, is crucial for optimizing processes such as wastewater treatment, bioenergy production, and environmental bioremediation. This review highlights recent theoretical, technical, and experimental advances - including ecological theory, multiscale approaches, and the use of machine learning and artificial intelligence - to predict community responses to disturbances. Together, these insights offer a valuable outlook for developing scalable and robust biotechnology applications.

Prioritizing microbial functions over soil quality for enhanced multifunctionality in saline-sodic soil remediation

Paddy cultivation has become a widely adopted approach for saline-sodic wasteland reclamation, aiming to mitigate the food crisis and enhance soil quality. Nevertheless, the impact of long-term paddy cultivation on the interplay between soil quality, microbial metabolic functions, and soil ecosystem multifunctionality (EMF) remains unclear. Here, we evaluated soil physicochemical properties, the abundance of 132 biomarker functional genes, and soil EMF across a 78-year period of saline-sodic paddy cultivation. After 78 years of paddy cultivation, soil pH and electrical conductivity (EC) decreased by 43.38% and 93.02% compared to saline-sodic wasteland (WL), respectively. Moreover, principal component analysis was used to select a minimal dataset of soil indicators and to establish a soil quality index (SQI). Significant positive correlations were observed between SQI and rice yield, implying that soil quality was the main factor driving increases in saline-sodic farmland. The Mantel test indicates that soil microbial biomass, SQI, and the availability of nutrients exhibit a significant positive relationship with the abundance and expression of genes related to carbon (C), nitrogen (N), and phosphorus (P) cycling, encompassing crucial biogeochemical processes like hemicellulose degradation, C fixation, N degradation, and organic P mineralization. This indicates that changes in soil physicochemical properties significantly affect biogeochemical cycling in saline-sodic soils. Differences in the abundance of microbial P core functional genes explained 41.9% of variation in soil EMF, followed by key soil physicochemical indicators (EC, available potassium, microbial biomass nitrogen, etc.) selected through random forest analysis. Further, we identified a key threshold for changes in soil EMF during long-term saline-sodic paddy cultivation, with EMF increasing for the first 20 years of restoration before decreasing thereafter. Finally, partial least squares path modeling revealed the roles of microbial functional genes and SQI in driving soil EMF before and after the threshold. Soil EMF is primarily influenced by the significant negative effects of P functional genes prior to the threshold value, whereas beyond the threshold, it is mainly affected by the positive effects of C functional genes. These findings provide insights into the functional restoration and sustainable development of saline-sodic agricultural ecosystems.

Periodic flooding alters ecological processes and carbon metabolism efficiency of riparian soil microbial communities in the three Gorges Reservoir area, China

Soil microbial communities are the most active components in the riparian biota, and are critical in driving carbon cycling. The periodic flooding in riparian zones is a primary driving force in the changes of soil microbial community structures and function. However, whether such events can induce changes in microbial carbon metabolism efficiency has not been fully revealed, especially in large reservoirs that experience counter-seasonal water level fluctuations (WLFs). In this study, high-throughput sequencing and the 18O-H2O cultivation method were applied to investigate the soil microbial community and carbon metabolism in a tributary riparian zone in China's Three Gorges Reservoir, which has experienced large WLFs. Three elevations in the riparian zone (155, 165, and 170 m) were selected as treatments for different flooding intensities. As the frequency of flooding decreased, soil enzyme activity decreased first and then increased. In contrast, soil water content, fungal α-diversity, microbial co-occurrence network complexity, average variation degree, βNTI, and total cohesion decreased slowly. The assembly mechanism of microbial communities is primarily governed by homogeneous dispersion. This suggests that periodic flooding significantly alters microbial ecological processes. Additionally, we found that decreased extracellular enzyme activity increases microbial carbon use efficiency and decreases the metabolic quotient, promoting soil carbon storage. This study enhances our understanding of the response and mechanisms of soil microbial communities to periodic flooding. It provides a theoretical foundation for soil ecosystem management and conservation.

Forest Wildfire Increases the Seasonal Allocation of Soil Labile Carbon Fractions Due to the Transition from Microbial K- to r-Strategists

Promoting the formation and accumulation of soil carbon (C) is one of the natural solutions to address climate change, but frequent wildfires increase its uncertainty and challenge. This two-year study deciphered the driving pathways of seasonal and vertical patterns in a soil C pool following a wildfire from a microbial perspective. Results showed that total organic C concentration and stock postfire decreased by 29.9 and 17.5% on average compared with the unburned control, respectively, whereas the allocations of labile C increased by 25.1-45.7%. Fire-induced alterations in labile C fractions were complicated due to their significant seasonality and respective sensitivities. Nonetheless, we emphasized that microbial life-history traits were the decisive mediators of variations and that significant positive linkages existed between labile C and microbial r-selected communities. Fire stimulated lower bacterial and fungal copiotroph/oligotroph ratios and higher ribosomal ribonucleic acid operon copy number, shifting microbes from K- to r-strategists. From integrated soil C pool management indices, fire can be concluded to reduce C stability and accelerate C cycling, but whether the recaptured prevalence of K-strategist over time will modify C processes remains unknown. This study provided a stepping stone for future efforts in accurate C predictions and reasonable C management.

Codon bias, nucleotide selection, and genome size predict in situ bacterial growth rate and transcription in rewetted soil

In soils, the first rain after a prolonged dry period represents a major pulse event impacting soil microbial community function, yet we lack a full understanding of the genomic traits associated with the microbial response to rewetting. Genomic traits such as codon usage bias and genome size have been linked to bacterial growth in soils-however, often through measurements in culture. Here, we used metagenome-assembled genomes (MAGs) with 18O-water stable isotope probing and metatranscriptomics to track genomic traits associated with growth and transcription of soil microorganisms over one week following rewetting of a grassland soil. We found that codon bias in ribosomal protein genes was the strongest predictor of growth rate. We also found higher growth rates in bacteria with smaller genomes, suggesting that reduced genome size enables a faster response to pulses in soil bacteria. Faster transcriptional upregulation of ribosomal protein genes was associated with high codon bias and increased nucleotide skew. We found that several of these relationships existed within phyla, indicating that these associations between genomic traits and activity could be generalized characteristics of soil bacteria. Finally, we used publicly available metagenomes to assess the distribution of codon bias across a pH gradient and found that microbial communities in higher pH soils-which are often more water limited and pulse driven-have higher codon usage bias in their ribosomal protein genes. Together, these results provide evidence that genomic characteristics affect soil microbial activity during rewetting and pose a potential fitness advantage for soil bacteria where water and nutrient availability are episodic.

Increasing pesticide diversity impairs soil microbial functions

Pesticide application is essential for stabilizing agricultural production. However, the effects of increasing pesticide diversity on soil microbial functions remain unclear, particularly under varying nitrogen (N) fertilizer management practices. In this study, we investigated the stochasticity of soil microbes and multitrophic networks through amplicon sequencing, assessed soil community functions related to carbon (C), N, phosphorus (P), and sulfur (S) cycling, and characterized the dominant bacterial life history strategies via metagenomics along a gradient of increasing pesticide diversity under two N addition levels. Our findings show that higher pesticide diversity enriches the abundance of bacterial specialists and opportunists capable of degrading or resisting pesticides, reducing the proportion of bacterial generalists in the absence of N addition. These shifts can complicate multitrophic microbial networks. Under increased pesticide diversity, selective pressure may drive bacteria to streamline their average genome size to conserve energy while enhancing C, N, P, and S metabolic capacities, thus accelerating soil nutrient loss. In comparison, N addition was found to reduce bacterial niche differentiation at higher pesticide diversity, mitigating the impacts of network complexity and functional traits associated with pesticide diversity, ultimately alleviating soil nutrient loss. Our results reveal the contrasting impacts of pesticide diversity on microbial functions under different N input scenarios and emphasize that strategic N fertilizer management can mitigate the ecological effects of pesticide use in agricultural systems.

Growth of microbes in competitive lifestyles promotes increased ARGs in soil microbiota: insights based on genetic traits

BACKGROUND

The widespread selective pressure of antibiotics in the environment has led to the propagation of antibiotic resistance genes (ARGs). However, the mechanisms by which microbes balance population growth with the enrichment of ARGs remain poorly understood. To address this, we employed microcosm cultivation at different antibiotic (i.e., Oxytetracycline, OTC) stresses across the concentrations from the environmental to the clinical. Paired with shot-gun metagenomics analysis and quantification of bacterial growth, trait-based assessment of soil microbiota was applied to reveal the association between key ARG subtypes, representative bacterial taxa, and functional-gene features that drive the growth of ARGs.

RESULTS

Our results illuminate that resistome variation is closely associated with bacterial growth. A non-monotonic change in ARG abundance and richness was observed over a concentration gradient from none to 10 mg/l. Soil microbiota exposed to intermediate OTC concentrations (i.e., 0.1 and 0.5 mg/l) showed greater increases in the total abundance of ARGs. Community compositionally, the growth of representative taxa, i.e., Pseudomonadaceae was considered to boost the increase of ARGs. It has chromosomally carried kinds of multidrug resistance genes such as mexAB-oprM and mexCD-oprJ could mediate the intrinsic resistance to OTC. Streptomycetaceae has shown a better adaptive ability than other microbes at the clinical OTC concentrations. However, it contributed less to the ARGs growth as it represents a stress-tolerant lifestyle that grows slowly and carries fewer ARGs. In terms of community genetic features, the community aggregated traits analysis further indicates the enhancement in traits of resource acquisition and growth yield is driving the increase of ARGs abundance. Moreover, optimizations in energy production and conversion, alongside a streamlining of bypass metabolic pathways, further boost the growth of ARGs in sub-inhibitory antibiotic conditions.

CONCLUSION

The results of this study suggest that microbes with competitive lifestyles are selected under the stress of environmental sub-inhibitory concentrations of antibiotics and nutrient scarcity. They possess greater substrate utilization capacity and carry more ARGs, due to this they were faster growing and leading to a greater increase in the abundance of ARGs. This study has expanded the application of trait-based assessments in understanding the ecology of ARGs propagation. And the finding illustrated changes in soil resistome are accompanied by the lifestyle switching of the microbiome, which theoretically supports the ARGs control approach based on the principle of species competitive exclusion. Video Abstract.

Root exudates regulate soil antibiotic resistance genes via rhizosphere microbes under long-term fertilization

Organic fertilizer application promotes the prevalence of antibiotic resistance genes (ARGs), yet the factors driving temporal differences in ARG abundance under long-term organic fertilizer application remain unclear. This study investigated the temporal dynamics of ARG diversity and abundance in both bulk and rhizosphere soils over 17 years (2003-2019), and explored microbial evolution strategies, ARG hosts succession and the influence of root exudates on ARGs regulation. The results showed that the ARGs abundance in rhizosphere soil was lower than that in bulk soil under long-term fertilization, and ARGs abundance exhibited a decrease and then remained stable in rhizosphere soil over time. There was a strong association between host bacteria and dominant ARGs (p < 0.05). Structural equations demonstrated that bacterial community had a most pronounced influence on ARGs (p < 0.05), and metabolites exhibited an important mediation effect on bacterial community (p < 0.05), thereby impacting ARGs. The metabolome analysis evidenced that significant correlations were found between defensive root exudates and most ARGs abundance (p < 0.05), like, luteolin-7-glucoside was negatively correlated with tetA(58). These findings provide deeper insights into the dynamics of soil ARGs under long-term fertilization, and identify critical factors that influence ARGs colonization in soils, providing support for controlling the spread of ARGs in agriculture soils.

A Global Relationship Between Genome Size and Encoded Carbon Metabolic Strategies of Soil Bacteria

Microbial traits are critical for carbon sequestration and degradation in terrestrial ecosystems. Yet, our understanding of the relationship between carbon metabolic strategies and genomic traits like genome size remains limited. To address this knowledge gap, we conducted a global-scale meta-analysis of 2650 genomes, integrated whole-genome sequencing data, and performed a continental-scale metagenomic field study. We found that genome size was tightly associated with an increase in the ratio between genes encoding for polysaccharide decomposition and biomass synthesis that we defined as the carbon acquisition-to-biomass yield ratio (A/Y). We also show that horizontal gene transfer played a major evolutionary role in the expanded bacterial capacities in carbon acquisition. Our continental-scale field study further revealed a significantly negative relationship between the A/Y ratio and soil organic carbon stocks. Our work demonstrates a global relationship between genome size and the encoded carbon metabolic strategies of soil bacteria across terrestrial microbiomes.

Microbial life-history strategies and particulate organic carbon mediate formation of microbial necromass carbon and stabilization in response to biochar addition

Microbial necromass carbon (MNC) contributes significantly to the formation of soil organic carbon (SOC). However, the microbial carbon sequestration effect of biochar is often underestimated and influenced by nutrient availability. The mechanisms associated with the formation and stabilization of MNC remain unclear, especially under the combined application of biochar and nitrogen (N) fertilizer. Thus, in a long-term field experiment (11 years) based on biochar application, we utilized bacterial 16S rRNA gene sequencing, fungal ITS amplicon sequencing, metagenomics, and microbial biomarkers to examine the interactions between MNC accumulation and microbial metabolic strategies under combined treatment with biochar and N fertilizer. We aimed to identify the critical microbial modules and species involved, and to analyze the sites where MNC was immobilized from various components. Biochar application increased the MNC content by 13.9 %. Among the MNC components, fungal necromass contributed more to MNC, but bacteria were more readily enriched after biochar application. The microbial life-history strategies that affected MNC formation under the application of various amounts biochar were linked to the N application level. Under N added at 226.5 kg ha-1, communities such as Actinobacteria and Bacteroidetes with high-growth yield strategies were prevalent and contributed to MNC production. By contrast, under N added at 113.25 kg ha-1 with high biochar application, Proteobacteria with strong resource acquisition strategies were dominant and MNC accumulation was lower. The mineral-associated organic carbon pool was rapidly saturated with the addition of biochar, so the contribution of fungal necromass carbon may have been reduced by reutilization, thereby resulting in the more rapid preservation of bacterial necromass carbon in the particulate organic carbon pool. Overall, our findings indicate that microbial life history traits are crucial for linking microbial metabolic processes to the accumulation and stabilization of MNC, thereby highlighting the their importance for SOC accumulation in farmland soils, and the need to tailor appropriate biochar and N fertilizer application strategies for agricultural soils.

Soil viral-host interactions regulate microplastic-dependent carbon storage

Microplastic is globally regarded as an important factor impacting biogeochemical cycles, yet our understanding of such influences is limited by the uncertainties of intricate microbial processes. By multiomics analysis, coupled with soil chemodiversity characterization and microbial carbon use efficiency (CUE), we investigated how microbial responses to microplastics impacted soil carbon cycling in a long-term field experiment. We showed that biodegradable microplastics promoted soil organic carbon accrual by an average of 2.47%, while nondegradable microplastics inhibited it by 17.4%, as a consequence of the virus-bacteria coadaptations to the microplastics disturbance. In the relevant functional pathways, nondegradable microplastics significantly (P < 0.05) enhanced the abundance and transcriptional activity related to complex carbohydrate metabolism, whereas biodegradable microplastics significantly (P < 0.05) promoted functions involved in amino acid metabolism and glycolysis. Accordingly, viral lysis enhanced in nondegradable microplastics treatments to introduce more complex organic compounds to soil dissolved organic matters, thus benefiting the oligotrophs with high carbon metabolic capabilities in exploitation competition. In contrast, biodegradable microplastics enriched viral auxiliary metabolic genes of carbon metabolism through "piggyback-the-winner" strategy, conferring to dominant copiotrophs, enhanced substrate utilization capabilities. These virus-host interactions were also demonstrated in the corresponding soil plastisphere, which would alter microbial resource allocation and metabolism via CUE, affecting carbon storage consequently. Overall, our results underscore the importance of viral-host interactions in understanding the microplastics-dependent carbon storage in the soil ecosystem.

The biogeography of soil microbiome potential growth rates

Soil microbial growth, a vital biogeochemical process, governs both the accrual and loss of soil carbon. Here, we investigate the biogeography of soil microbiome potential growth rates and show that microbiomes in resource-rich (high organic matter and nutrients) and acid-neutral soils from cold and humid regions exhibit high potential growth. Conversely, in resource-poor, dry, hot, and hypersaline soils, soil microbiomes display lower potential growth rates, suggesting trade-offs between growth and resource acquisition or stress tolerance. In addition, the potential growth rates of soil microbiomes positively correlates with genome size and the number of ribosomal RNA operons but negatively correlates with optimum temperature, biomass carbon-to-phosphorus and nitrogen-to-phosphorus ratios. The spatial variation of microbial potential growth rates aligns with several macroecological theories. These findings not only enhance our understanding of microbial adaptation to diverse environments but also aid in realistically parameterizing microbial physiology in soil carbon cycling models.

Fertilization shapes microbial life strategies, carbon and nitrogen metabolic functions in Camellia oleifera soil

Mineral and organic fertilizers as well as microbial inoculations are crucial to maintain and to improve soil health and quality, ecosystem functions, and fruit yield in Camellia oleifera plantations. However, how these fertilizers shape the life strategies and functions of microbial communities in soil is unclear. Here, we conducted a one-year field experiment with three types of fertilizers: mineral (NPK), manure (Man), and microbial (MicrF), and analyzed soil properties, bacterial and fungal communities to assess microbial life strategies, functional traits and their determinants. The application of MicrF strongly increased the diversity of both soil bacterial (by 6.4%) and fungal communities (by 23%). Organic matter inputs from Man and MicrF had greater effects on the life strategies of bacteria than fungi: the dominant r-strategy bacteria (Proteobacteria, Bacteroidetes, and Actinobacteria) increased with Man and MicrF, but K-strategists (Acidobacteria) decreased. Conversely, the abundance of r-strategy fungi (Ascomycota) decreased, but that of K-fungi (Basidiomycota) increased. Predictions of the functions indicated that microbial fertilization accelerated the bacterial carbohydrates, carbon and nitrogen metabolism, while also increasing the prevalence of wood saprotrophic fungi. The changes in the taxonomic and functional characteristics of the microbial communities induced priming effects by co-metabolism, which were mainly regulated by contents of soil organic carbon, available phosphorus, and ammonium nitrogen, as well as carbon to nitrogen ratio. The application of MicrF is an effective approach to increase the diversity and multifunctionality of soil microbial communities in Camellia oleifera plantations, including organic matter decomposition, carbon and nitrogen metabolism. These findings provide valuable insights into the fertilizer regimes based on microbial ecological strategies and functional profiles in Camellia oleifera plantations.

DGCNN approach links metagenome-derived taxon and functional information providing insight into global soil organic carbon

Metagenomics can provide insight into the microbial taxa present in a sample and, through gene identification, the functional potential of the community. However, taxonomic and functional information are typically considered separately in downstream analyses. We develop interpretable machine learning (ML) approaches for modelling metagenomic data, combining the biological representation of species with their associated genetically encoded functions within models. We apply our methods to investigate soil organic carbon (SOC) stocks. First, we combine a diverse global set of soil microbiome samples with environmental data, improving the predictive performance of classic ML and providing new insights into the role of soil microbiomes in global carbon cycling. Our network analysis of predictive taxa identified by classical ML models provides context for their ecological significance, extending the focus beyond just the most predictive taxa to 'hidden' features within the model that might be considered less predictive using standard methods for explainability. We next develop unique graph representations for individual microbiomes, linking microbial taxa to their associated functions directly, enabling predictions of SOC via deep graph convolutional neural networks (DGCNNs). Interpretation of the DGCNNs distinguished between the importance of functions of key individual species, providing genome sequence differences, e.g., gene loss/acquisition, that associate with SOC. These approaches identify several members of the Verrucomicrobiaceae family and a range of genetically encoded functions, e.g., related to carbohydrate metabolism, as important for SOC stocks and effective global SOC predictors. These relatively understudied but widespread organisms could play an important role in SOC dynamics globally.

Emerging multiscale insights on microbial carbon use efficiency in the land carbon cycle

Microbial carbon use efficiency (CUE) affects the fate and storage of carbon in terrestrial ecosystems, but its global importance remains uncertain. Accurately modeling and predicting CUE on a global scale is challenging due to inconsistencies in measurement techniques and the complex interactions of climatic, edaphic, and biological factors across scales. The link between microbial CUE and soil organic carbon relies on the stabilization of microbial necromass within soil aggregates or its association with minerals, necessitating an integration of microbial and stabilization processes in modeling approaches. In this perspective, we propose a comprehensive framework that integrates diverse data sources, ranging from genomic information to traditional soil carbon assessments, to refine carbon cycle models by incorporating variations in CUE, thereby enhancing our understanding of the microbial contribution to carbon cycling.

Climate-driven succession in marine microbiome biodiversity and biogeochemical function

Seasonal and El Niño-Southern Oscillation (ENSO) warming result in similar ocean changes as predicted with climate change. Climate-driven environmental cycles have strong impacts on microbiome diversity, but impacts on microbiome function are poorly understood. We quantified changes in microbial genomic diversity and functioning over 11 years covering seasonal and ENSO cycles at a coastal site in the southern California Current. We observed seasonal oscillations between large genome lineages during cold, nutrient rich conditions in winter and spring versus small genome lineages, including Prochlorococcus and Pelagibacter , in summer and fall. Parallel interannual changes separated communities depending on ENSO condition. Biodiversity shifts translated into clear oscillations in microbiome functional potential. Ocean warming induced an ecosystem with less iron but more macronutrient stress genes, depressed organic carbon degradation potential and biomass, and elevated carbon-to-nutrient biomass ratios. The consistent microbial response observed across time-scales points towards large climate-driven changes in marine ecosystems and biogeochemical cycles.

Global patterns in the growth potential of soil bacterial communities

Despite the growing catalogue of studies detailing the taxonomic and functional composition of soil bacterial communities, the life history traits of those communities remain largely unknown. This study analyzes a global dataset of soil metagenomes to explore environmental drivers of growth potential, a fundamental aspect of bacterial life history. We find that growth potential, estimated from codon usage statistics, was highest in forested biomes and lowest in arid latitudes. This indicates that bacterial productivity generally reflects ecosystem productivity globally. Accordingly, the strongest environmental predictors of growth potential were productivity indicators, such as distance to the equator, and soil properties that vary along productivity gradients, such as pH and carbon to nitrogen ratios. We also observe that growth potential was negatively correlated with the relative abundances of genes involved in carbohydrate metabolism, demonstrating tradeoffs between growth and resource acquisition in soil bacteria. Overall, we identify macroecological patterns in bacterial growth potential and link growth rates to soil carbon cycling.

Variation in the response to antibiotics and life-history across the major Pseudomonas aeruginosa clone type (mPact) panel

Pseudomonas aeruginosa is a ubiquitous, opportunistic human pathogen. Since it often expresses multidrug resistance, new treatment options are urgently required. Such new treatments are usually assessed with one of the canonical laboratory strains, PAO1 or PA14. However, these two strains are unlikely representative of the strains infecting patients, because they have adapted to laboratory conditions and do not capture the enormous genomic diversity of the species. Here, we characterized the major P. aeruginosa clone type (mPact) panel. This panel consists of 20 strains, which reflect the species' genomic diversity, cover all major clone types, and have both patient and environmental origins. We found significant strain variation in distinct responses toward antibiotics and general growth characteristics. Only few of the measured traits are related, suggesting independent trait optimization across strains. High resistance levels were only identified for clinical mPact isolates and could be linked to known antimicrobial resistance (AMR) genes. One strain, H01, produced highly unstable AMR combined with reduced growth under drug-free conditions, indicating an evolutionary cost to resistance. The expression of microcolonies was common among strains, especially for strain H15, which also showed reduced growth, possibly indicating another type of evolutionary trade-off. By linking isolation source, growth, and virulence to life history traits, we further identified specific adaptive strategies for individual mPact strains toward either host processes or degradation pathways. Overall, the mPact panel provides a reasonably sized set of distinct strains, enabling in-depth analysis of new treatment designs or evolutionary dynamics in consideration of the species' genomic diversity.

IMPORTANCE

New treatment strategies are urgently needed for high-risk pathogens such as the opportunistic and often multidrug-resistant pathogen Pseudomonas aeruginosa. Here, we characterize the major P. aeruginosa clone type (mPact) panel. It consists of 20 strains with different origins that cover the major clone types of the species as well as its genomic diversity. This mPact panel shows significant variation in (i) resistance against distinct antibiotics, including several last resort antibiotics; (ii) related traits associated with the response to antibiotics; and (iii) general growth characteristics. We further developed a novel approach that integrates information on resistance, growth, virulence, and life-history characteristics, allowing us to demonstrate the presence of distinct adaptive strategies of the strains that focus either on host interaction or resource processing. In conclusion, the mPact panel provides a manageable number of representative strains for this important pathogen for further in-depth analyses of treatment options and evolutionary dynamics.

Microbial-mediated conversion of soil organic carbon co-regulates the evolution of antibiotic resistance

The influence of organic carbon on the proliferation of antibiotic resistance genes (ARGs) in the soil has been widely documented. However, it is unclear how soil organic carbon (SOC) interacts with the evolution of antibiotic resistance in bacteria. Here, we examined the variations in ARGs abundance during SOC mineralization and explored the microbiological mechanisms and key metabolic pathways involved in their coevolution. The results showed that the SOC mineralization rate was closely correlated with ARGs abundance (p < 0.05). High organic carbon (OC) mineralization was conducive to the occurrence of multidrug resistance genes. For example, multidrug_transporter and mexB increased 2.26 and 7.83 times from the initial level. The competitor (stress) evolutionary strategy model revealed that higher OC inputs drive environmental microorganisms to evolve from stress tolerant to high resistance and strong adaptation. Meta-genomic and transcriptomic analyses revealed that the conversion process of pyruvate to acetyl-CoA to acetate was the critical metabolic pathway for the co-regulation of antibiotic resistance. Gene deletion validation trials have demonstrated that the key functional genes (ackA and pta) involved in this process can modulate the development of vancomycin and multidrug resistance. This outcome provides a preliminary framework for microbial mechanisms that target the co-regulation of microbial OC conversion and the evolution of antibiotic resistance.

Beneficial rhizosphere bacteria provides active assistance in resisting Aphis gossypiis in Ageratina adenophora

Ageratina adenophora can enhance its invasive ability by using beneficial rhizosphere bacteria. Bacillus cereus is able to promote plant growth and provide a positive feedback effect to A. adenophora. However, the interaction between A. adenophora and B. cereus under the influence of native polyphagous insect feeding is still unclear. In this study, Eupatorium lindleyanum, a local species closely related to A. adenophora, was used as a control, aimed to compare the content of B. cereus in the roots of A. adenophora and rhizosphere soil after different densities of Aphis gossypii feeding, and then investigated the variations in the population of A. gossypii and soil characteristics after the addition of B. cereus. The result showed that B. cereus content in the rhizosphere soil and root of A. adenophora increased significantly under A. gossypii feeding compared with local plants, which also led to the change of α-diversity and β-diversity of the bacterial community, as well as the increase in nitrate nitrogen (NO3 -N) content. The addition of B.cereus in the soil could also inhibit the population growth of A. gossypii on A. adenophora and increase the content of ammonium nitrogen (NH4 +-N) in the soil. Our research demonstrated that B. cereus enhances the ability of A. adenophora to resist natural enemy by increasing soil ammonium nitrogen (NH4 +-N) and accumulating other beneficial bacteria, which means that rhizosphere microorganisms help invasive plants defend themselves against local natural enemies by regulating the soil environment.

The size and diversity of microbes determine carbon use efficiency in soil

Soil is home to a multitude of microorganisms from all three domains of life. These organisms and their interactions are crucial in driving the cycling of soil carbon. One key indicator of this process is Microbial Carbon Use Efficiency (CUE), which shows how microbes influence soil carbon storage through their biomass production. Although CUE varies among different microorganisms, there have been few studies that directly examine how biotic factors influence CUE. One such factor could be body size, which can impact microbial growth rates and interactions in soil, thereby influencing CUE. Despite this, evidence demonstrating a direct causal connection between microbial biodiversity and CUE is still scarce. To address these knowledge gaps, we conducted an experiment where we manipulated microbial body size and biodiversity through size-selective filtering. Our findings show that manipulating the structure of the microbial community can reduce CUE by approximately 65%. When we restricted the maximum body size of the microbial community, we observed a reduction in bacterial diversity and functional potential, which in turn lowered the community's CUE. Interestingly, when we included large body size micro-eukarya in the soil, it shifted the soil carbon cycling, increasing CUE by approximately 50% and the soil carbon to nitrogen ratio by about 25%. Our metrics of microbial diversity and community structure were able to explain 36%-50% of the variation in CUE. This highlights the importance of microbial traits, community structure and trophic interactions in mediating soil carbon cycling.

Changes in soil oxidase activity induced by microbial life history strategies mediate the soil heterotrophic respiration response to drought and nitrogen enrichment

Drought and nitrogen deposition are two major climate challenges, which can change the soil microbial community composition and ecological strategy and affect soil heterotrophic respiration (Rh). However, the combined effects of microbial community composition, microbial life strategies, and extracellular enzymes on the dynamics of Rh under drought and nitrogen deposition conditions remain unclear. Here, we experimented with an alpine swamp meadow to simulate drought (50% reduction in precipitation) and multilevel addition of nitrogen to determine the interactive effects of microbial community composition, microbial life strategy, and extracellular enzymes on Rh. The results showed that drought significantly reduced the seasonal mean Rh by 40.07%, and increased the Rh to soil respiration ratio by 22.04%. Drought significantly altered microbial community composition. The ratio of K- to r-selected bacteria (BK:r) and fungi (FK:r) increased by 20 and 91.43%, respectively. Drought increased hydrolase activities but decreased oxidase activities. However, adding N had no significant effect on microbial community composition, BK:r, FK:r, extracellular enzymes, or Rh. A structural equation model showed that the effects of drought and adding nitrogen via microbial community composition, microbial life strategy, and extracellular enzymes explained 84% of the variation in Rh. Oxidase activities decreased with BK:r, but increased with FK:r. Our findings show that drought decreased Rh primarily by inhibiting oxidase activities, which is induced by bacterial shifts from the r-strategy to the K-strategy. Our results highlight that the indirect regulation of drought on the carbon cycle through the dynamic of bacterial and fungal life history strategy should be considered for a better understanding of how terrestrial ecosystems respond to future climate change.

Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model

Soil microbiomes are highly diverse, and to improve their representation in biogeochemical models, microbial genome data can be leveraged to infer key functional traits. By integrating genome-inferred traits into a theory-based hierarchical framework, emergent behaviour arising from interactions of individual traits can be predicted. Here we combine theory-driven predictions of substrate uptake kinetics with a genome-informed trait-based dynamic energy budget model to predict emergent life-history traits and trade-offs in soil bacteria. When applied to a plant microbiome system, the model accurately predicted distinct substrate-acquisition strategies that aligned with observations, uncovering resource-dependent trade-offs between microbial growth rate and efficiency. For instance, inherently slower-growing microorganisms, favoured by organic acid exudation at later plant growth stages, exhibited enhanced carbon use efficiency (yield) without sacrificing growth rate (power). This insight has implications for retaining plant root-derived carbon in soils and highlights the power of data-driven, trait-based approaches for improving microbial representation in biogeochemical models.

Ecological relevance of flagellar motility in soil bacterial communities

Flagellar motility is a key bacterial trait as it allows bacteria to navigate their immediate surroundings. Not all bacteria are capable of flagellar motility, and the distribution of this trait, its ecological associations, and the life history strategies of flagellated taxa remain poorly characterized. We developed and validated a genome-based approach to infer the potential for flagellar motility across 12 bacterial phyla (26 192 unique genomes). The capacity for flagellar motility was associated with a higher prevalence of genes for carbohydrate metabolism and higher maximum potential growth rates, suggesting that flagellar motility is more prevalent in environments with higher carbon availability. To test this hypothesis, we applied a method to infer the prevalence of flagellar motility in whole bacterial communities from metagenomic data and quantified the prevalence of flagellar motility across four independent field studies that each captured putative gradients in soil carbon availability (148 metagenomes). We observed a positive relationship between the prevalence of bacterial flagellar motility and soil carbon availability in all datasets. Since soil carbon availability is often correlated with other factors that could influence the prevalence of flagellar motility, we validated these observations using metagenomic data from a soil incubation experiment where carbon availability was directly manipulated with glucose amendments. This confirmed that the prevalence of bacterial flagellar motility is consistently associated with soil carbon availability over other potential confounding factors. This work highlights the value of combining predictive genomic and metagenomic approaches to expand our understanding of microbial phenotypic traits and reveal their general environmental associations.

Wildfire impact on soil microbiome life history traits and roles in ecosystem carbon cycling

Wildfires, which are increasing in frequency and severity with climate change, reduce soil microbial biomass and alter microbial community composition and function. The soil microbiome plays a vital role in carbon (C) and nitrogen (N) cycling, but its complexity makes it challenging to predict post-wildfire soil microbial dynamics and resulting impacts on ecosystem biogeochemistry. The application of biogeochemically relevant conceptual trait-based frameworks to the soil microbiome can distill this complexity, enabling enhanced predictability of soil microbiome recovery following wildfire and subsequent impacts to biogeochemical cycles. Conceptual frameworks that have direct links to soil C and N cycling have been developed for the soil microbiome; the Y-A-S framework overviews soil microbiome life history strategies that have tradeoffs with one another and others have proposed frameworks specific to wildfire. Here, we aimed to delineate post-wildfire changes of bacterial traits in western US coniferous forests to inform how severe wildfire influences soil microbiome recovery and resultant biogeochemical cycling. We utilized a comprehensive metagenome-assembled genome catalog from post-wildfire soils representing 1 to 11 years following low- and high-severity burning to identify traits that enable the persistence of microbial taxa in burned soils and influence ecosystem C and N cycling. We found that high-severity wildfire initially selects for fast growers and, up to a decade post-fire, taxa that invest in genes for acquiring diverse resources from the external environment, which in combination could increase soil C losses. This work begins to disentangle how climate change-induced shifts in wildfire behavior might alter microbially mediated soil biogeochemical cycling.

Quantifying microbial DNA in metagenomes improves microbial trait estimation

Shotgun metagenomics is a powerful tool for studying the genomic traits of microbial community members, such as genome size, gene content, etc. While such traits can be used to better understand the ecology and evolution of microbial communities, the accuracy of their estimations can be critically influenced by both known and unknown factors. One factor that can bias trait estimations is the proportion of eukaryotic and viral DNA in a metagenome, as some bioinformatic tools assume that all DNA reads in a metagenome are bacterial or archaeal. Here, we add to a recent debate about the influence of eukaryotic DNA in the estimation of average genome size from a global soil sample dataset using a new bioinformatic tool. Contrary to what was assumed, our reanalysis of this dataset revealed that soil samples can contain a substantial proportion of non-microbial DNA, which severely inflated the original estimates of average genome size. Correcting for this bias significantly improves the statistical support for the negative relationship between average bacterial genome size and soil pH. These results highlight that metagenomes can contain large quantities of non-microbial DNA and that new methods that correct for this can improve microbial trait estimation.

Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient

Bacterial gene repertoires reflect adaptive strategies, contribute to ecosystem functioning and are limited by genome size. However, gene functional diversity does not necessarily correlate with taxonomic diversity because average genome size may vary by community. Here, we analyse gene functional diversity (by shotgun metagenomics) and taxonomic diversity (by 16S rRNA gene amplicon sequencing) to investigate soil bacterial communities along a natural pH gradient in 12 tropical, subtropical, and temperate forests. We find that bacterial average genome size and gene functional diversity decrease, whereas taxonomic diversity increases, as soil pH rises from acid to neutral; as a result, bacterial taxonomic and functional diversity are negatively correlated. The gene repertoire of acid-adapted oligotrophs is enriched in functions of signal transduction, cell motility, secretion system, and degradation of complex compounds, while that of neutral pH-adapted copiotrophs is enriched in functions of energy metabolism and membrane transport. Our results indicate that a mismatch between taxonomic and functional diversity can arise when environmental factors (such as pH) select for adaptive strategies that affect genome size distributions.