Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change

Microbial Biotic Associations Dominated Adaptability Differences of Dioecious Poplar Under Salt Stress

How different stress responses by male and female plants are influenced by interactions with rhizosphere microbes remains unclear. In this study, we employed poplar as a dioecious model plant and quantified biotic associations between microorganisms to explore the relationship between microbial associations and plant adaptation. We propose a health index (HI) to comprehensively characterize the physiological characteristics and adaptive capacity of plants under stress. It was found that male poplars demonstrated higher salt stress tolerance than females, and root-secreted citric acid was significantly higher in the rhizospheres of male poplars. Positive biotic association among bacteria increased poplar HI significantly under salt stress, while fungal and cross-domain biotic association (bacteria-fungi) did not. We further identified a keystone bacterial taxon regulating bacterial biotic association, ASV_22706, which was itself regulated by citric acid and significantly positively correlated with host HI. The abundance of keystone fungal taxa was positively correlated with HI of male poplars and negatively correlated with HI of female poplars. Compared with female poplars, male poplars enriched more prebiotics and probiotics under stress. This work primarily reveals the relationship between adaptation differences and microbial interactions in dioecious plants, which suggests a microbial approach to improve plant adaptability to stress conditions.

Pangenomes suggest ecological-evolutionary responses to experimental soil warming

Below-ground carbon transformations that contribute to healthy soils represent a natural climate change mitigation, but newly acquired traits adaptive to climate stress may alter microbial feedback mechanisms. To better define microbial evolutionary responses to long-term climate warming, we study microorganisms from an ongoing in situ soil warming experiment where, for over three decades, temperate forest soils are continuously heated at 5°C above ambient. We hypothesize that across generations of chronic warming, genomic signatures within diverse bacterial lineages reflect adaptations related to growth and carbon utilization. From our bacterial culture collection isolated from experimental heated and control plots, we sequenced genomes representing dominant taxa sensitive to warming, including lineages of Actinobacteria, Alphaproteobacteria, and Betaproteobacteria. We investigated genomic attributes and functional gene content to identify signatures of adaptation. Comparative pangenomics revealed accessory gene clusters related to central metabolism, competition, and carbon substrate degradation, with few functional annotations explicitly associated with long-term warming. Trends in functional gene patterns suggest genomes from heated plots were relatively enriched in central carbohydrate and nitrogen metabolism pathways, while genomes from control plots were relatively enriched in amino acid and fatty acid metabolism pathways. We observed that genomes from heated plots had less codon bias, suggesting potential adaptive traits related to growth or growth efficiency. Codon usage bias varied for organisms with similar 16S rrn operon copy number, suggesting that these organisms experience different selective pressures on growth efficiency. Our work suggests the emergence of lineage-specific trends as well as common ecological-evolutionary microbial responses to climate change.IMPORTANCEAnthropogenic climate change threatens soil ecosystem health in part by altering below-ground carbon cycling carried out by microbes. Microbial evolutionary responses are often overshadowed by community-level ecological responses, but adaptive responses represent potential changes in traits and functional potential that may alter ecosystem function. We predict that microbes are adapting to climate change stressors like soil warming. To test this, we analyzed the genomes of bacteria from a soil warming experiment where soil plots have been experimentally heated 5°C above ambient for over 30 years. While genomic attributes were unchanged by long-term warming, we observed trends in functional gene content related to carbon and nitrogen usage and genomic indicators of growth efficiency. These responses may represent new parameters in how soil ecosystems feedback to the climate system.

Unveiling the latitudinal dependency of global patterns in soil prokaryotic gene content

Prokaryotic genomic traits offer insights into their functional roles, evolutionary processes, and ecological interactions, but global patterns in soil microbial genomes remain poorly understood. In this study, we examined 6436 metagenome-assembled genomes (MAGs) from global soil environments to explore the driving factors of prokaryotic gene content. Through random forest analysis, we found that, among numerous potential influencing factors such as climate, soil physicochemical properties, and human activities, geographic latitude was the primary factor affecting prokaryotic gene content. Our results showed a marked decrease in gene content from the tropics to the poles, with polar MAGs containing 10.4 % and 13.3 % fewer genes than those in tropical and temperate zones, respectively. This decline correlates with shifts in key metabolic processes, such as nitrogen fixation and energy conversion. Furthermore, we assessed interspecies metabolic interactions using Metabolic Resource Overlap (MRO) and Metabolic Interaction Potential (MIP) metrics. Our analysis revealed significantly lower MRO in high-latitude microbial communities, yet comparable MIP values to those in lower latitudes, indicating that reduced competition may contribute to genomic streamlining. These findings highlight the significant influence of latitude and interspecies interactions on microbial genomic characteristics, advancing our comprehension of microbial ecological adaptations.

Partial substitution of rice straw with biochar alters soil microbial biomass phosphorus and turnover by regulating carbon:phosphorus stoichiometry

Microbial biomass phosphorus (MBP) and its turnover play a crucial role in crop phosphorus (P) nutrition. However, the response of MBP to organic amendments, especially under the combined application of biochar and straw in Oxisols remains poorly understood. This study investigated the effects of substituting rice straw with different biochar proportions (0 %, 10 %, 30 %, and 50 %) on soil CO2 emissions, microbial biomass carbon (MBC) and MBP content, their turnover parameters and carbon:phosphorus (C:P) stoichiometry during a 60-day incubation. The results showed that 10 % biochar substitution did not alter MBP content but decreased MBP flux and turnover rate, consequently prolonging turnover time. In contrast, higher biochar substitution rates (30 % and 50 %) increased MBP content by 7.37 % and 5.71 %, respectively, and gradually recovered MBP turnover. Notably, these higher biochar ratios also significantly decreased dissolved C:P and microbial C:P ratios, exacerbating C:P stoichiometric imbalance. The partial least squares path model (PLS-PM) indicated the MBC:MBP ratio as the primary driver of microbial P immobilization and turnover, demonstrating a positive correlation with CO2 emission rates. These results imply that strategic substitution of straw with biochar can increase potential soil P supply by enlarging MBP pools and accelerating MBP turnover, thereby improving crop P utilization efficiency.

pH-dependent genotypic and phenotypic variability in Oleidesulfovibrio alaskensis G20

Sulfate-reducing bacteria (SRB) exhibit versatile metabolic adaptability with significant flexibility influenced by pH fluctuations, which play a critical role in biogeochemical cycles. In this study, we used a model SRB, Oleidesulfovibrio alaskensis G20, to determine the temporal effects of pH variations (pH 6, 7, and 8) on both growth dynamics and metabolic gene expressions. The specific growth rate at pH 6 (0.014 h-1) closely matched that at pH 7 (0.016 h-1), while pH 8 exhibited a lower growth rate (0.010 h-1). Lactate consumption peaked at pH 7 (0.35 mM lactate.h-1) and declined at pH 8 (0.09 mM lactate.h-1). Significant hydrogen production was evident under both acidic and alkaline conditions. Gene expression studies revealed that ATPases function as proton pumps, while hydrogenases mediate reversible proton-to-hydrogen conversion. Sulfate and energy metabolism act as electron acceptors and donors, while amino acid synthesis regulates basic and acidic amino acids to mitigate pH stress. Downregulation of FtsZ at pH 6 suggests impaired division, correlating with slightly longer lengths (~2 µm), while upregulation of divisome proteins at pH 8 suggests efficient division processes, aligning with shorter lengths (~1.8 µm). This study will facilitate the employment of O. alaskensis G20 in extreme pH environments, enhancing its effectiveness in optimizing bioremediation and anaerobic digestion processes.

IMPORTANCE

Sulfate-reducing bacteria (SRB) play essential roles in global sulfur and carbon cycling and are critical for bioremediation and anaerobic digestion processes. However, detailed studies on the genotypic and phenotypic responses of SRB under varying pH conditions are limited. This study addresses this gap by examining the pH-dependent genetic and metabolic adaptations of Oleidesulfovibrio alaskensis G20, revealing key mechanisms regulating hydrogenase and ATPase activities, cell division, and extracellular polymeric substance formation. These findings provide new insights into how SRB maintains pH homeostasis, showcasing their ability to survive and function in both acidic and alkaline environments. Furthermore, this study reveals critical genetic and phenotypic characteristics that will directly aid to engineer industrial effluent management systems, bioremediation, and dissolved heavy metal recovery. By elucidating the dynamic response of O. alaskensis G20 to varied pH environments, the research provides a foundation for enhancing the resilience and performance of SRB-based systems, paving the way for improved environmental and industrial applications.

Microbial life-history strategies and genomic traits between pristine and cropland soils

Microbial life-history strategies [inferred from ribosomal RNA operon (rrn) gene copy numbers] and associated genomic traits and metabolism potentials in soil significantly influence ecosystem properties and functions globally. Yet, the differences in microbial strategies and traits between disturbed (cropland) and pristine soils, along with their dominant driving factors, remain underexplored. Our large-scale survey of 153 sites, including 84 croplands and 69 pristine soils, combined with long-term field experiments demonstrates that cropland soils support microbial communities with more candidate r-strategies characterized by higher rrn copy numbers and genomic traits conducive to rapid resource utilization. Conversely, pristine soils tend to host communities aligned with more candidate K-strategies marked by high resource use potentials. Elevated nitrogen (N) and phosphorus (P) levels in cropland soils emerge as key factors promoting these candidate r-strategies, overshadowing the influence of organic carbon content, soil structure, or climatic conditions. Results from four long-term field experiments also corroborate that sustained N and P inputs significantly elevate rrn copy numbers, favoring these candidate r-strategists. Our findings highlight that land use and fertilization practices critically shape microbial life-history strategies, with nutrient availability being a decisive factor in increasing the r-strategists in cropland soils.IMPORTANCEMicrobial life-history strategies and genomic traits are key determinants shaping the response of populations to environmental impacts. In this paper, 84 cropland and 69 pristine soil samples were studied, and microorganisms in two ecosystems were categorized into two types of ecological groups using the classical copiotroph-oligotroph dichotomy, promoting a general understanding of the ecological roles of microorganisms. This study is the first to investigate the microbial life-history strategies under different land uses across five climatic zones in China. The results showed that the microbes in cropland soils are more copiotrophic than pristine soils. It also demonstrates that elevated levels of nitrogen and phosphorus in cropland soils are the key factors promoting these r-strategies. This observation emphasizes the critical role of nutrient management in shaping microbial community dynamics and ecosystem functioning and lays the foundation for predicting the response of microbial community composition under resource perturbation.

Long-term NPK fertilization enhances microbial carbon use efficiency in Andosols by alleviating P limitation and shifting microbial strategies

Microbial carbon use efficiency (CUE) is an essential indicator of soil organic carbon (SOC) dynamics. The high yield (Y)-resource acquisition (A)-stress tolerance (S) life strategy framework was used to assess microbial adaptation and its impact on CUE in response to soil environment and nutrient availability. Topsoil (0-15 cm) was collected from a 36-year experimental field of Andosol in Japan with six fertilizer treatments: no application, inorganic PK, NK, NPK, compost, and NPK with compost (NPKCM) to elucidate the effects of nutrient availability and environmental changes caused by fertilization on CUE. Soil chemical properties, microbial biomass and community structure, and extracellular enzyme activities (EEAs) were measured. Microbial nutrient limitation and CUE were assessed using enzyme stoichiometry (CUEst), and structural equation modeling (SEM) tested the conjecture that microbial nutrient limitation, mainly P-limitation, reduces CUEst through changes in bacterial community structures and EEAs. Results showed higher CUEst in NPK-treated soils (NPK: 0.37, NPKCM: 0.32) compared to P-deficient soils (Ctrl: 0.19, NK: 0.22). Increased P availability and reduced DOC:AP and IN:AP ratios in NPK-treated soils favored a shift of dominant bacterial strategies from A-strategists (including Alphaproteobacteria, Vicinamibacterales, and AD3) to Y-strategists (including Bacteroidota, Verrucomicrobiota, Blastocatellales, Bryobacterales, and Ktedonobacterales). SEM revealed that increased soil C and P availability alleviated microbial P limitation, enhancing CUEst directly and via reducing C-acquiring EEAs and altering microbial strategies. Overall, NPK fertilization may be an optimal strategy for enhancing SOC sequestration by improving microbial CUE in Andosols, emphasizing the trade-off between nutrient acquisition and energy conservation.

A trait spectrum linking nitrogen acquisition and carbon use of ectomycorrhizal fungi

Trait spectra have been used in various branches of ecology to explain and predict patterns of species distributions. Several categorical and continuous traits have been proposed as relevant for ectomycorrhizal fungi, but a spectrum that unifies co-varying traits remains to be established and tested. Here, we propose a nitrogen acquisition and carbon use trait spectrum for ectomycorrhizal fungi in nitrogen-limited forests, which encompasses several morphological, physiological, and metabolic traits. Using a simple stoichiometric model, the trait spectrum is linked to the concept of apparent carbon use efficiency and resolves the contradiction that species with high supply of host carbon can maintain nitrogen transfer despite building large mycelial biomass. We suggest that ectomycorrhizal fungal species are distributed along this spectrum, with lifestyles ranging from 'absorbers' with a niche in high productive forests with high availability of soluble nitrogen to 'miners' with the ability to exploit organic matter in forests with low nitrogen availability. Further, we propose ways to test the outlined trait spectrum empirically.

Precipitation changes reshape desert soil microbial community assembly and potential functions

Understanding the responses of desert microbial communities to escalating precipitation changes is a significant knowledge gap in predicting future soil health and ecological function. Through a five-year precipitation manipulation experiment, we investigated the contrasting eco-evolutionary processes of desert bacteria and fungi that manifested in changes to the assembly and potential functions of the soil microbiome. Elevated precipitation increased the alpha diversity and network complexity of bacteria and fungi, proportion of non-dominant phyla, and abundance of carbon- and nitrogen-fixing bacteria and saprophytic, symbiotic, and pathogenic fungi. Conversely, decreased precipitation reduced the alpha diversity and network complexity of bacteria and fungi while increasing the proportion of non-dominant phyla, stability of the network, and abundance of functional genes related to carbon and nitrogen degradation, nitrification, and ammonification. This suggests that soil microbes may attenuate the negative effects of reduced precipitation by streamlining communities, enhancing carbon and nitrogen acquisition, and promoting nitrogen cycling. Furthermore, we revealed that soil properties and vegetation attributes explained approximately 27.86%-37.75% and 17.76%-22.84% of the variation in bacterial and fungal communities, respectively. Finally, we demonstrated that precipitation-driven soil nutrient content and vegetation attributes are the potentially critical factors in shaping the soil microbial assembly and functions. These findings provide a foundation for understanding the response of desert soil microbes to escalating climate change.

Revisiting the classical biodiversity-ecosystem functioning and stability relationships in microbial microcosms

The question of how biodiversity influences ecosystem functioning and stability has been a central focus in ecological research. Yet, this question remains unresolved, primarily because of the widely divergent definitions of functioning, stability, and diversity. Consequently, forecasts of ecosystem services will remain speculative until we can establish more precise and comprehensive definitions for these concepts than previously. Here, we investigated how the maximum specific growth rate, productivity, mortality rate, and species interaction in microbial communities vary with a diversity gradient ranging from 1 to 16 species under control conditions, starvation, or saline stress. We found that diversity played a critical role in maintaining community growth and stability under control conditions, with higher diversity associated with increased maximum specific growth rate and decreased mortality rate. However, higher diversity was associated with an increased mortality rate under starvation, while diversity did not affect the mortality rate under saline stress. Diversity stabilized microbial productivity only under control conditions, defying the "diversity begets stability" hypothesis under stress. Beneficial interactions among species were prevalent in most samples, but species interaction increased mortality rates under starvation. Our findings suggest that while biodiversity is crucial for preserving ecosystem functioning and stability, the presence of multiple definitions and contextual dependence on environmental conditions argues against any general relationship between diversity and ecosystem functioning/stability. Furthermore, we provide new insights into the longstanding debate surrounding the "diversity begets stability" hypothesis and the "diversity destabilizes ecosystem" hypothesis in that diversity begets stability under control conditions but destabilizes ecosystems under severe stress.

Rare taxa in the core microbiome

Rare taxa are an important constituent of the microbiome and play a crucial role in maintaining biodiversity and ecosystem dynamics. However, little is known about rare taxa within the core microbiome (i.e., core rare taxa), nor do we understand the factors that drive their distribution and occupancy in ecosystems. In this opinion article, we define and explore the role of core rare taxa and the ecological and genetic drivers of their persistence. We also discuss 'innate' and 'adaptive' resilience in relation to core rare taxa and their drivers. Finally, we emphasize the need to develop appropriate metrics to quantify core rare taxa and their functions, as this can have significant implications for biodiversity conservation and microbiome engineering in the long run.

Impacts of biodegradable microplastics on rhizosphere bacterial communities of Arabidopsis thaliana: Insights into root hair-dependent colonization

Biodegradable microplastics (MPs) affect plant health by altering rhizosphere microbial communities. Root hairs create a unique niche for diverse microbes, but the effects of biodegradable MPs on root hair-dependent bacterial colonization are unclear, particularly the direct relationship between microbes in the rhizosphere and bulk soil. Here, the effects of polybutylene adipate terephthalate (PBAT) MPs on root hair-dependent bacterial colonization and diversity in the rhizosphere were revealed using an absolute quantitative method and in-situ zymography with two genotypes of Arabidopsis thaliana (long root hair, wild-type, WT and short root hair, rop2-1 mutant, ROP). The results showed that rhizosphere enzyme activity hotspots, bacterial diversity, and colonization increased from ROP to WT plants. PBAT MPs reduced root hair-dependent bacterial colonization and β-glucosidase hotspots by 17.1 % and 9.8 %, respectively. Despite increasing bacterial absolute abundance in both rhizosphere and bulk soil, PBAT MPs diminished bacterial community modularity and shifted bacterial life strategies from K- to r-strategy via elevated rRNA (rrn) copy numbers and copiotroph/oligotroph ratio. This study indicated that PBAT MPs decreased root hair-dependent bacterial colonization and diversity in the rhizosphere by altering the microbial life history strategies and increasing copiotrophic abundance. This study explained the effects of PBAT MPs on rhizosphere bacterial colonization and diversity from the perspective of root hairs.

Opposite effects of N on warming-induced changes in bacterial and fungal diversity

The diversity of bacteria and fungi is linked to distinct ecosystem functions, and divergent responses to global changes in these two kingdoms affect the relative contributions of the kingdoms to the soil carbon and nutrient cycles. Climate warming and nitrogen (N) enrichment, which are projected to increase concurrently through modelling efforts, are considered the main drivers of biodiversity loss. However, it is unclear how bacterial and fungal diversity respond differently to the simultaneous occurrence of climate warming and nitrogen enrichment, and the underlying mechanisms involved remain unknown. Using a 9-yr warming and N enrichment experiment in an alpine permafrost area of the Tibetan Plateau, we demonstrated the contrasting response of bacterial and fungal diversity to combined warming and N enrichment, showing a reduction in bacterial richness (8.8%) and an increase in fungal diversity (33.6%). Furthermore, the negative effects of warming on fungal richness were reversed by N enrichment, and the negative effects of nitrogen enrichment on bacteria were amplified by warming. Our results also demonstrated that both biotic interactions, such as bacterial-fungal antagonism, and abiotic factors, primarily the soil C/N ratio and pH, play crucial roles in shaping microbial biodiversity. Our findings suggest that fungal diversity is expected to greatly increase in a warmer and more nitrogen-enriched world, potentially leading to the enhancement of ecosystem functions driven by fungi.

Traits determine dispersal and colonization abilities of microbes

Many microbes disperse through the air, yet the phenotypic traits that enhance or constrain aerial dispersal or allow successful colonization of new habitats are poorly understood. We used a metabarcoding bacterial and eukaryotic data set to explore the trait structures of the aquatic, terrestrial, and airborne microbial communities near the Salton Sea, California, as well as those colonizing a series of experimental aquatic mesocosms. We assigned taxonomic identities to amplicon sequence variants (ASVs) and matched them to functional trait values through published papers and databases that infer phenotypic and/or metabolic traits information from taxonomy. We asked what traits distinguish successful microbial dispersers and/or colonizers from terrestrial and aquatic source communities. Our study found broad differences in taxonomic and trait composition between dispersers and colonizers compared to the source soil and water communities. Dispersers were characterized by larger cell diameters, colony formation, and fermentation abilities, while colonizers tended to be phototrophs that form mucilage and have siliceous coverings. Shorter population doubling times, spore-, and/or cyst-forming organisms were more abundant among the dispersers and colonizers than the sources. These results show that the capacity for aerial dispersal and colonization varies among microbial functional groups and taxa and is related to traits that affect other functions like resource acquisition, predator avoidance, and reproduction. The ability to disperse and colonize new habitats may therefore distinguish microbial guilds based on tradeoffs among alternate ecological strategies.IMPORTANCEMicrobes have long been thought to disperse rapidly across biogeographic barriers; however, whether dispersal or colonization vary among taxa or groups or is related to cellular traits remains unknown. We use a novel approach to understand how microorganisms disperse and establish themselves in different environments by looking at their traits (physiology, morphology, life history, and behavior characteristics). By collecting samples from habitats including water, soil, and the air and colonizing experimental tanks, we found dispersal and invasion vary among microorganisms. Some taxa and functional groups are found more often in the air or colonizing aquatic environments, while others that are commonly found in the soil or water rarely disperse or invade new habitat. Interestingly, the traits that help microorganisms survive and thrive also play a role in their ability to disperse and colonize. These findings have significant implications for understanding microorganisms' success and adaptation to new environments.

Environmental matrix and moisture influence soil microbial phenotypes in a simplified porous media incubation

Soil moisture and porosity regulate microbial metabolism by influencing factors, such as system chemistry, substrate availability, and soil connectivity. However, accurately representing the soil environment and establishing a tractable microbial community that limits confounding variables is difficult. Here, we use a reduced-complexity microbial consortium grown in a glass bead porous media amended with chitin to test the effects of moisture and a structural matrix on microbial phenotypes. Leveraging metagenomes, metatranscriptomes, metaproteomes, and metabolomes, we saw that our porous media system significantly altered microbial phenotypes compared with the liquid incubations, denoting the importance of incorporating pores and surfaces for understanding microbial phenotypes in soils. These phenotypic shifts were mainly driven by differences in expression of Streptomyces and Ensifer, which included a significant decrease in overall chitin degradation between porous media and liquid. Our findings suggest that the success of Ensifer in porous media is likely related to its ability to repurpose carbon via the glyoxylate shunt amidst a lack of chitin degradation byproducts while potentially using polyhydroxyalkanoate granules as a C source. We also identified traits expressed by Ensifer and others, including motility, stress resistance, and carbon conservation, that likely influence the metabolic profiles observed across treatments. Together, these results demonstrate that porous media incubations promote structure-induced microbial phenotypes and are likely a better proxy for soil conditions than liquid culture systems. Furthermore, they emphasize that microbial phenotypes encompass not only the multi-enzyme pathways involved in metabolism but also include the complex interactions with the environment and other community members.IMPORTANCESoil moisture and porosity are critical in shaping microbial metabolism. However, accurately representing the soil environment in tractable laboratory experiments remains a challenging frontier. Through our reduced complexity microbial consortium experiment in porous media, we reveal that predicting microbial metabolism from gene-based pathways alone often falls short of capturing the intricate phenotypes driven by cellular interactions. Our findings highlight that porosity and moisture significantly affect chitin decomposition, with environmental matrix (i.e., glass beads) shifting community metabolism towards stress tolerance, reduced resource acquisition, and increased carbon conservation, ultimately invoking unique microbial strategies not evident in liquid cultures. Moreover, we find evidence that changes in moisture relate to community shifts regarding motility, transporters, and biofilm formation, which likely influence chitin degradation. Ultimately, our incubations showcase how reduced complexity communities can be informative of microbial metabolism and present a useful alternative to liquid cultures for studying soil microbial phenotypes.

Thermal Compensatory Response of Soil Heterotrophic Respiration Following Wildfire

Frequent wildfires pose a serious threat to carbon (C) dynamics of forest ecosystems under a warming climate. Yet, how wildfires alter the temperature sensitivity (Q10) of soil heterotrophic respiration (Rh) as a critical parameter determining the C efflux from burned landscapes remains unknown. We conducted a field survey and two confirmatory experiments in two fire-prone regions of China at <1, 3, 6, and 12 months after wildfires (n = 160 soil samples). We found that wildfire generally reduced the Q10 for soil organic and mineral horizons within the first year after wildfire mainly due to substrate depletion, which was confirmed by a uniform inoculation experiment. Mineral protection of organic matter in the mineral horizon rich in iron/aluminum (hydr)oxides and a near-neutral pH in organic horizons of postfire soils further suppressed the Q10. Decreased Q10 persisted in organic horizons even after removing substrate limitation, reflecting the dominance of a thermally adapted, r-strategist microbial community in postfire soils. Moreover, fire-induced low C quality increased Q10, which supported the C quality-temperature hypothesis, but a C-limited condition restricted this stimulatory effect. This study illustrates that a thermal compensatory response of Rh will help maintain C stocks in forest ecosystems after wildfires in a warming world.

Legacies of temperature fluctuations promote stability in marine biofilm communities

The increasing frequency and intensity of extreme climate events are driving significant biodiversity shifts across ecosystems. Yet, the extent to which these climate legacies will shape the response of ecosystems to future perturbations remains poorly understood. Here, we tracked taxon and trait dynamics of rocky intertidal biofilm communities under contrasting regimes of warming (fixed vs. fluctuating) and assessed how they influenced stability dimensions in response to temperature extremes. Fixed warming enhanced the resistance of biofilm by promoting the functional redundancy of stress-tolerance traits. In contrast, fluctuating warming boosted recovery rate through the selection of fast-growing taxa at the expense of functional redundancy. This selection intensified a trade-off between stress tolerance and growth further limiting the ability of biofilm to cope with temperature extremes. Anticipating the challenges posed by future extreme events, our findings offer a forward-looking perspective on the stability of microbial communities in the face of ongoing climatic change.

Melatonin application enhances the remediation of cadmium-contaminated soils by Cinnamomum camphora

Cinnamomum camphora (C. camphora) is a tolerant plant with high potential for cadmium (Cd) uptake and resistance. However, it is still unclear how melatonin application regulates Cd absorption and detoxification in C. camphora, and whether the soil quality is improved after remediation. In this study, melatonin was applied at the concentration of 20 mg·kg-1 soil to the Cd-contaminated soil planted with C. camphora. We aimed to investigate the effect of exogenous melatonin on Cd phytoextraction and detoxification in C. camphora by assessing physiological and biochemical responses. We found that melatonin application improved Cd content in C. camphora (p < 0.05), with a pronounced increase by 150 % in both stem phloem and leaves. Under Cd stress, melatonin application resulted in a Cd bioconcentration factor that was over 2-times higher, and Cd translocation factors from root to stem and from stem to vein which were increased to the level of 1.0. Exogenous melatonin also enhanced plant growth and photosynthesis under the 180-day Cd stress. In addition, melatonin promoted C. camphora to modify its antioxidant defense systems in response to various temporal stages of Cd stress. At the early stage, melatonin decreased malondialdehyde by >20 % and increased both proline and glutathione reduction by over 30 %. At the late stage, melatonin increased glutathione and soluble sugar by 46.0 % and 10.7 %, respectively. Peroxidase activity was stimulated by melatonin throughout the growth period (p < 0.05). In the remediated soil, melatonin application decreased soil respiration by 12.5 % and inhabited activities of urease, catalase, and dehydrogenase, indicating improved soil quality. Overall, our findings suggest that melatonin application can enhance Cd phytoextraction and detoxification in C. camphora from contaminated soils, providing new insights into applicable strategies for Cd phytoremediation.

Biogeographic patterns of viral communities, ARG profiles and virus-ARG associations in adjacent paddy and upland soils across black soil region

Biogeographic distribution of prokaryotic and eukaryotic communities has been extensively studied. Yet, our knowledge of viral biogeographic patterns, the corresponding driving factors and the virus-resistome associations is still limited. Here, using metagenomic analysis, we explored the viral communities and profiles of antibiotic resistance genes (ARGs) in 30 fields of paddy (rice soils, RS) and upland soils (corn soils, CS) at a regional scale across black soil region of Northeast China. Our finding revealed that viral communities displayed significant distance-decay relationships, and environmental variables largely dominated viral community patterns in agricultural soils. Compared to RS, viral community in CS harbored significantly higher viral α-diversity and distinct β-diversity, and exhibited a higher turnover along with environmental gradients and spatial distance. However, no clear latitudinal diversity gradient (LDG) pattern was observed in viral diversity over large-scale sampling for RS and CS, and heterogeneous distribution of soil viruses was well maintained over large-scale sampling. Soil pH was the important influential factor driving viral community, and the high soil nutrient levels negatively affected viral diversity. Uroviricota, Nucleocytoviricota and Artverviricota were the main viral phyla in agricultural soils, and virus-host linkages spanned 17 prokaryotic phyla, including Actinobacteriota and Proteobacteria. Besides, 2578 ARG subtypes were retrieved and conferred resistance to 27 types of antibiotics, in which multidrug was the predominant ARG type in Mollisols. Procrustes analysis showed the significant contribution of viral community to ARG profiles, which was more obvious in CS compared to RS. We identified 9.61 % and 11.4 % of soil viruses carried at least one ARG can infect multi-host in RS and CS. Furthermore, 43 and 77 complete viral metagenome-assembled genome (vMAG) were reconstructed in RS and CS, respectively. Notably, the lysogenic phages in RS contained 29.7 % of ARGs, a higher proportion than the 12.5 % found in CS. Overall, our study underscored the prevalent distribution of viral communities and ARG profiles at a large spatial scale, and the distinct ecological strategies of virus-ARG associations in adjacent paddy and upland soils.

An integrated fast-slow plant and nematode economics spectrum predicts soil organic carbon dynamics during natural restoration

Aboveground and belowground attributes of terrestrial ecosystems interact to shape carbon (C) cycling. However, plants and soil organisms are usually studied separately, leading to a knowledge gap regarding their coordinated contributions to ecosystem C cycling. We explored whether integrated consideration of plant and nematode traits better explained soil organic C (SOC) dynamics than plant or nematode traits considered separately. Our study system was a space-for-time natural restoration chronosequence following agricultural abandonment in a subtropical region, with pioneer, early, mid and climax stages. We identified an integrated fast-slow trait spectrum encompassing plants and nematodes, demonstrating coordinated shifts from fast strategies in the pioneer stage to slow strategies in the climax stage, corresponding to enhanced SOC dynamics. Joint consideration of plant and nematode traits explained more variation in SOC than by either group alone. Structural equation modeling revealed that the integrated fast-slow trait spectrum influenced SOC through its regulation of microbial traits, including microbial C use efficiency and microbial biomass. Our findings confirm the pivotal role of plant-nematode trait coordination in modulating ecosystem C cycling and highlight the value of incorporating belowground traits into biogeochemical cycling under global change scenarios.

Impacts of trophic interactions on carbon accrual in soils

The transformation and stabilization of soil organic carbon (SOC) are important processes of global carbon (C) cycling, with implications for climate change. Much attention has been given to microbial anabolic processes driving SOC accrual. These are referred to as the soil microbial carbon pump (MCP), which emphasizes the contribution of microbial metabolism and necromass to the stable soil C pool. However, we still lack a fundamental understanding of how trophic interactions between soil fauna and microbiota modulate microbial necromass production and, consequently, SOC formation. Here, we provide an ecological perspective on the impacts of trophic interactions on modulating necromass formation and C accrual in soils. We discuss the mechanisms of trophic interactions in the context of food web ecology, with a focus on trophic control of microbial population densities and their influences on soil microbiota assembly. We foresee that integrating trophic interactions into the soil MCP framework can provide a more comprehensive basis for guiding future research efforts to elucidate the mechanisms modulating microbial necromass and SOC formation in terrestrial ecosystems. This perspective offers an ecological foundation for leveraging the use of biological interventions to enhance SOC accrual, providing valuable insights for sustainable C management strategies.

Differential impacts of nitrogen addition on soil dissolved organic carbon in humid and non-humid regions: A global meta-analysis

Soil dissolved organic carbon (DOC) is the most active carbon pool, providing essential carbon and energy to soil microorganisms while playing a crucial role in carbon sequestration, transport, and stabilization in soils. Nitrogen (N) addition, a key factor influencing terrestrial carbon cycling, can significantly alter soil DOC dynamics. However, the global patterns and underlying drivers of DOC responses to N addition, particularly across regions with varying aridity indices, remain unclear. This study analyzed 1132 paired observations from 103 independent studies to quantify the response pattern of DOC to N addition in humid (554 observations) and non-humid (574 observations) regions and identify the factors driving these effects. The findings revealed an asymmetrical effect of N addition on soil DOC between humid and non-humid regions, rather than on microbial biomass carbon (MBC) or soil organic carbon (SOC). Specifically, N addition significantly decreased soil DOC (-2.49%) in humid regions, while it increased DOC (7.30%) in non-humid regions. The effect size of soil DOC decreased linearly with the ratio of MBC to SOC in humid regions but increased linearly in non-humid regions. In humid regions, soil DOC response was positively correlated with initial MBC and inversely correlated with initial soil pH, whereas the opposite trend was observed in non-humid regions. Seasonal precipitation variability was identified as a significant driver of soil DOC response, independent of temperature, soil properties, and N addition rates. Moreover, initial SOC content was the primary driving factor for soil DOC response in humid regions, while the N addition rates were the primary driver in non-humid regions. These findings have important implications for enhancing soil carbon pool management, improving global carbon models, and addressing climate change, particularly under varying climatic conditions.

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.

Impacts of plant root traits and microbial functional attributes on soil respiration components in the desert-oasis ecotone

Dividing soil respiration (Rs) into autotrophic respiration (Ra) and heterotrophic respiration (Rh) represents a pivotal step in deciphering how Rs responds to environmental perturbations. Nevertheless, in arid ecosystems beset by environmental stress, the partitioning of Rs and the underlying mechanisms through which microbial and root traits govern the distinct components remain poorly understood. This study was strategically designed to investigate Rs and its components (Ra and Rh), soil properties, and root traits within the desert-oasis ecotone (encompassing the river bank, transitional zone, and desert margin) of northwest China. Employing metagenomics, we quantitatively characterized microbial taxonomic attributes (i.e., taxonomic composition) and functional attributes (specifically, functional genes implicated in microbial carbon metabolism). Field measurements during the growing season of 2019 unveiled a pronounced decline in soil respiration rates along the environmental gradient from the river bank to the desert margin. The mean soil respiration rate was recorded as 1.82 ± 0.41 μmol m-2 s-1 at the river bank, 0.49 ± 0.15 μmol m-2 s-1 in the transitional zone, and a meager 0.45 ± 0.12 μmol m-2 s-1 in the desert margin. Concomitantly, the Ra and Rh components exhibited a similar trend throughout the study period, with Rh emerging as the dominant driver of Rs. Utilizing random forest modeling, we unearthed significant associations between microbial taxonomic and functional features and Rs components. Notably, both Ra and Rh displayed robust positive correlations with the abundance of phosphatidylinositol glycan A, a key player in microbial carbon metabolism. Partial least squares path modeling further elucidated that soil properties and microbial functions exerted direct and positive influences on both Ra and Rh, whereas taxonomic features failed to register a significant impact. When considering the combined effects of biotic and abiotic factors, microbial functional attributes emerged as the linchpin in dictating Rs composition. Collectively, these findings suggest that a trait-based approach holds great promise in more effectively revealing the response mechanisms of Rs composition to environmental changes, thereby offering novel vistas for future investigations into carbon cycling in terrestrial soils.

Overall biomass yield on multiple nutrient sources

Microorganisms primarily utilize nutrients to generate biomass and replicate. When a single nutrient source is available, the produced biomass typically increases linearly with the initial amount of that nutrient. This linear trend can be accurately predicted by "black box models", which conceptualize growth as a single chemical reaction, treating nutrients as substrates and biomass as a product. However, natural environments usually present multiple nutrient sources, prompting us to extend the black box framework to incorporate catabolism, anabolism, and biosynthesis of biomass precursors. This modification allows for the quantification of co-utilization effects among multiple nutrients on microbial biomass production. The extended model differentiates between different types of nutrients: non-degradable nutrients, which can only serve as a biomass precursor, and degradable nutrients, which can also be used as an energy source. We experimentally demonstrated using Escherichia coli that, in contrast to initial model predictions, different nutrients affect each other's utilization in a mutually dependent manner; i.e., for some combinations, the produced biomass was no longer proportional to the initial amounts of nutrients present. To account for these mutual effects within a black box framework, we phenomenologically introduced an interaction between the metabolic processes involved in utilizing the nutrient sources. This phenomenological model qualitatively captures the experimental observations and, unexpectedly, predicts that the total produced biomass is influenced not only by the combination of nutrient sources but also by their relative initial amounts - a prediction we subsequently validated experimentally. Moreover, the model identifies which metabolic processes - catabolism, anabolism, or precursor biosynthesis-is affected in each specific nutrient combination, offering insights into microbial metabolic coordination.

Xizang meadow degradation alters resource exchange ratio, network complexity, and biomass allocation tradeoff of arbuscular mycorrhizal symbiosis

The response of arbuscular mycorrhizal (AM) symbiosis to environmental fluctuations involves resource exchange between host plants and fungal partners, associations between different AM fungal taxa, and biomass allocation between AM fungal spore and hyphal structures; yet a systematic understanding of these responses to meadow degradation remains relatively unknown, particularly in Xizang alpine meadow. Here, we approached this knowledge gap by labeling dual isotopes of air 13CO2 and soil 15NH4Cl, computing ecological networks of AM fungal communities, and quantifying AM fungal biomass allocation among spores, intra- and extraradical hyphae. We found that the exchange ratio of photosynthate and nitrogen between plants and AM fungi increased with the increasing severity of meadow degradation, indicating greater dependence of host plants on this symbiosis for resource acquisition. Additionally, using 18S rRNA gene metabarcoding, we found that AM fungal co-occurrence networks were more complex in more degraded meadows, supporting the stress gradient hypothesis. Meadow degradation also increased AM fungal biomass allocation toward traits associated with intra- and extraradical hyphae at the expense of spores. Our findings suggest that an integrated consideration of resource exchange, ecological networks, and biomass allocation may be important for the restoration of degraded ecosystems.

Microecological shifts govern the fostering of soil and crop pathogens in agro-ecosystems under different fertilization regimes

Pathogenic bacteria in agroecosystems have been of great concern because of their threat to crop and human health. This study aimed to understand how the microecological environment created by different fertilization regimes affects the fate of soil and crop pathogenic microorganisms. The situation of soil and crop pathogenic bacteria in different ecosystems was explored by setting up seven different fertilization treatments. Network modularization and cohesion index analyses demonstrated that microbial networks were least stable in the 100% chemical fertilizer treatment. Regarding microbial community evolution, as the percentage of chemical fertilizer application increased, microbial evolution gradually shifted from the K-strategy to the r-strategy, implying that environmental microorganisms following chemical fertilizer application increase were primarily developed to enhance survival and reproduction, which in turn increased the occurrence of pathogenic bacteria. Compared to soils treated with 100% organic fertilizer (T1), the relative abundance of the pathogenic bacteria Gemmatimonas, Gaiella, and Gemmatirosa in soils treated with 100% chemical fertilizer (T6) increased by 74.09%, 18.01%, and 61.18%, respectively. Additionally, 100% chemical fertilizer application showed the highest diversity of soil pathogens and an enhanced microbial "Matthew effect" in roots. Structural equation modeling revealed that variations in soil microbial communities and pathogenic bacteria had a marked influence on the occurrence of crop pathogens. This study provides microecological evidence for the prevalence of pathogenic bacteria under different fertilization conditions and provides important theoretical and practical insights for optimal agroecosystem management.

Challenges in alpine meadow recovery: The minor effect of grass restoration on microbial resource limitation

Microorganisms play a vital role in restoring soil multifunctionality and rejuvenating degraded meadows. The availability of microbial resources, such as carbon, nitrogen, and phosphorus, often hinders this process. However, there is limited information on whether grass restoration can alleviate microbial resource limitations in damaged slopes of high-altitude regions. This study focused on alpine bare land impacted by engineering activities, with the goal of using grass seeds to improve soil resource availability and multifunctionality. High-throughput sequencing and enzyme stoichiometry (vector analyses) were employed to analyze microbial community composition and assess resource limitations. Our findings suggested that soil carbon, nitrogen, and phosphorus contents were low, ranging from 7.67 to 12.6 g kg-1for carbon, 0.61 to 0.98 g kg-1,for nitrogen, and 0.65 to 0.78 g kg-1for phosphorus. Nevertheless, the standardized scores for high yield and resource acquisition strategies remained at 0.26 and 1.36 in the four groups, which were lower than those of the stress tolerance strategy. Microorganisms primarily employed the stress tolerance strategy, focusing on repairing injured cells rather than promoting cell growth, which suggests that microbial growth and metabolism were only marginally enhanced. Because of this strategy's limited impact on enhancing microbial community diversity and fostering a co-occurrence network, the resultant levels remained comparable to those observed in degraded meadows. In this case, microbial resource limitations persisted, with phosphorus remaining a constraint. Consequently, grass restoration alone offered limited relief for microbial resource limitations in alpine meadows, underscoring the challenges of solely relying on grass seeds to recover damaged alpine ecosystems.

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.

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.

Long-term climate establishes functional legacies by altering microbial traits

Long-term climate history can influence rates of soil carbon cycling but the microbial traits underlying these legacy effects are not well understood. Legacies may result if historical climate differences alter the traits of soil microbial communities, particularly those associated with carbon cycling and stress tolerance. However, it is also possible that contemporary conditions can overcome the influence of historical climate, particularly under extreme conditions. Using shotgun metagenomics, we assessed the composition of soil microbial functional genes across a mean annual precipitation gradient that previously showed evidence of strong climate legacies in soil carbon flux and extracellular enzyme activity. Sampling coincided with recovery from a regional, multi-year severe drought, allowing us to document how the strength of climate legacies varied with contemporary conditions. We found increased investment in genes associated with resource cycling with historically higher precipitation across the gradient, particularly in traits related to resource transport and complex carbon degradation. This legacy effect was strongest in seasons with the lowest soil moisture, suggesting that contemporary conditions-particularly, resource stress under water limitation-influences the strength of legacy effects. In contrast, investment in stress tolerance did not vary with historical precipitation, likely due to frequent periodic drought throughout the gradient. Differences in the relative abundance of functional genes explained over half of variation in microbial functional capacity-potential enzyme activity-more so than historical precipitation or current moisture conditions. Together, these results suggest that long-term climate can alter the functional potential of soil microbial communities, leading to legacies in carbon cycling.

Metabolic labour division trade-offs in denitrifying microbiomes

Division of metabolic labour is a defining trait of natural and engineered microbiomes. Denitrification-the stepwise reduction of nitrate and nitrite to nitrogenous gases-is inherently modular, catalysed either by a single microorganism (termed complete denitrifier) or by consortia of partial denitrifiers. Despite the pivotal role of denitrification in biogeochemical cycles and environmental biotechnologies, the ecological factors selecting for complete versus partial denitrifiers remain poorly understood. In this perspective, we critically review over 1500 published metagenome-assembled genomes of denitrifiers from diverse and globally relevant ecosystems. Our findings highlight the widespread occurrence of labour division and the dominance of partial denitrifiers in complex ecosystems, contrasting with the prevalence of complete denitrifiers only in simple laboratory cultures. We challenge current labour division theories centred around catabolic pathways, and discuss their limits in explaining the observed niche partitioning. Instead, we propose that labour division benefits partial denitrifiers by minimising resource allocation to denitrification, enabling broader metabolic adaptability to oligotrophic and dynamic environments. Conversely, stable, nutrient-rich laboratory cultures seem to favour complete denitrifiers, which maximise energy generation through denitrification. To resolve the ecological significance of metabolic trade-offs in denitrifying microbiomes, we advocate for mechanistic studies that integrate mixed-culture enrichments mimicking natural environments, multi-meta-omics, and targeted physiological characterisations. These undertakings will greatly advance our understanding of global nitrogen turnover and nitrogenous greenhouse gases emissions.

Dynamics of bacterial growth, and life-history tradeoffs, explain differences in soil carbon cycling due to land-use

Soil contains a considerable fraction of Earth's organic carbon. Bacterial growth and mortality drive the microbial carbon pump, influencing carbon use efficiency and necromass production, key determinants for organic carbon persistence in soils. However, bacterial growth dynamics in soil are poorly characterized. We used an internal standard approach to normalize 16S ribosomal RNA gene sequencing data allowing us to quantify growth dynamics for 30 days following plant litter input to soil. We show that clustering taxa into three groups optimized variation of bacterial growth parameters in situ. These three clusters differed significantly with respect to their lag time, growth rate, growth duration, and change in abundance due to growth (ΔNg) and mortality (ΔNd), matching predictions of Grime's CSR life-history framework. In addition, we show a striking relationship between ΔNg and ΔNd, which reveals that growth in soil is tightly coupled to death. This result suggests a fitness paradox whereby some bacteria can optimize fitness in soil by minimizing mortality rather than maximizing growth. We hypothesized that land-use constrains microbial growth dynamics by favoring different life-history strategies and that these constraints control carbon mineralization. We show that life-history groups vary in prevalence with respect to land-use, and that bacterial growth dynamics correlated with carbon mineralization rate and net growth efficiency. Meadow soil supported more bacterial growth, greater mortality, and higher growth efficiency than agricultural soils, pointing toward more efficient conversion of plant litter into microbial necromass, which should promote long-term C stabilization.

Sowing success: ecological insights into seedling microbial colonisation for robust plant microbiota engineering

Manipulating the seedling microbiota through seed or soil inoculations has the potential to improve plant health. Mixed in-field results have been attributed to a lack of consideration for ecological processes taking place during seedling microbiota assembly. In this opinion article, we (i) assess the contribution of ecological processes at play during seedling microbiota assembly (e.g., propagule pressure and priority effects); (ii) investigate how life history theory can help us identify microbial traits involved in successful seedling colonisation; and (iii) suggest how different plant microbiota engineering methods could benefit from a greater understanding of seedling microbiota assembly processes. Finally, we propose several research hypotheses and identify outstanding questions for the plant microbiota engineering community.

Soil moisture determines effects of climates and soil properties on nitrogen cycling: Examination of arid and humid soils

While soil moisture has a significant effect on nitrogen (N) cycling, how it influences the dependence of this important biological process on environmental factors is unknown. Specifically, it is unclear how the relationships of net N mineralization (Nm) and soil moisture vary with soil properties and climates. In turn, how the relationships of Nm vs. soil properties and climates vary with soil moisture is also unknown. Therefore, soil samples from the 26 sites were collected within two climatic regions (i.e., arid and humid) across China. Then a four-week microcosmic incubation experiment was conducted at five soil moisture levels (20, 40, 60, 80, and 100% field water holding capacity (FWHC)) at 25 °C to measure the dynamics of Nm. The results showed that increasing soil moisture significantly increased Nm (+212%) and the N mineralization rate constant (k) (+0.26%), and that the effects of soil moisture were greater in humid soils (+250%) than arid soils (+178%). The slopes of the relationship between Nm vs. soil moisture increased with soil organic carbon (SOC) (+50.6%) and total N (TN) (+65.3%) concentrations, and decreased with pH (-43.0%) and clay content (-0.09%), especially in arid regions. Additionally, Nm was significantly correlated with soil properties and mean annual precipitation (MAP), and the slopes of most of these relationships increased with soil moisture in arid soils (+59.2-3805%), but decreased in humid soils (-1.96-140%). The results indicated that increasing soil moisture strengthened the dependence of Nm on soil properties and climates in arid soils, and that increasing soil pH and clay content reduced, but SOC and TN concentrations enhanced the dependence of Nm on soil moisture. Therefore, with changes in rainfall distribution patterns and an increase in extreme rainfall events, there is enormous potential for Nm in agricultural soils in arid regions, which is regulated by soil moisture and properties. On the contrary, in humid regions, the decoupling of the effects of soil moisture and soil properties on N mineralization could be due to microbial adaptation. Moreover, the coupled effects of soil environment and properties on N cycling in different climatic regions merit great consideration in experimental research as well as in biogeochemical model development and prediction.

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.

Data-driven discovery of the interplay between genetic and environmental factors in bacterial growth

A complex interplay of genetic and environmental factors influences bacterial growth. Understanding these interactions is crucial for insights into complex living systems. This study employs a data-driven approach to uncover the principles governing bacterial growth changes due to genetic and environmental variation. A pilot survey is conducted across 115 Escherichia coli strains and 135 synthetic media comprising 45 chemicals, generating 13,944 growth profiles. Machine learning analyzes this dataset to predict the chemicals' priorities for bacterial growth. The primary gene-chemical networks are structured hierarchically, with glucose playing a pivotal role. Offset in bacterial growth changes is frequently observed across 1,445,840 combinations of strains and media, with its magnitude correlating to individual alterations in strains or media. This counterbalance in the gene-chemical interplay is supposed to be a general feature beneficial for bacterial population growth.

The life strategy of bacteria rather than fungi shifts in karst tiankeng island-like systems

Karst tiankeng is a typical terrestrial habitat island-like system, known as an oasis in a degraded karst landscape. However, we know little about the composition, structure, and life strategies of soil microbial communities in the karst tiankeng ecosystem. In this study, we use amplicon sequencing to investigate the soil bacteria and fungi of 26 karst tiankeng in two typical karst tiankeng groups. The results showed that the composition and structure of bacterial and fungal communities were significantly different at two dimensions (among and within the karst tiankeng group). Bacteria showed more sensitivity to variation in the karst tiankeng area and isolation than fungi. With the increase of karst tiankeng area and isolation, the bacterial life strategies shift from K-strategist to r-strategist, likely due to the changes in soil properties (total phosphorus, Ca, and soil water content). Abundant and rare taxa play different roles in karst tiankeng ecosystems; abundant taxa serve a key role in nutrient cycles and life strategy shifts by occupying the key status in networks. Considering the key role of soil microbes in ecosystems, more attention must be paid to the impact of habitat loss on soil microbial life strategies, particularly in the ecological impact of life strategies change of abundant and rare taxa.

IMPORTANCE

These findings highlight that habitat loss or fragmentation induces a shift in microbial life strategies and improves our understanding of the composition and biogeography of karst ecosystem microorganisms.

Enhanced bioremediation of bensulfuron-methyl contaminated soil by Hansschlegelia zhihuaiae S113: Metabolic pathways and bacterial community structure

Bensulfuron-methyl (BSM), a widely used herbicide, can persist in soil and damag sensitive crops. Microbial degradation, supplemented with exogenous additives, provides an effective strategy to enhance BSM breakdown. Hansschlegelia zhihuaiae S113 has been shown to efficiently degrade this sulfonylurea herbicide. However, depending solely on a single strain for degradation proves inefficient and unlikely to achieve ideal remediation in practical applications. This study assessed the impact of various carbon sources on the degradation efficiency of S113 in BSM-polluted soil. Among these, glucose was the most effective, achieving a 98.7 % degradation rate after 9 d of inoculation. In addition, seven intermediates were detected during BSM degradation in soil through the cleavage of the phenyl ring ester bond, the pyrimidine rings, and urea bridge peptide bond, among other pathways. 2-amino-4,6-dimethoxy pyrimidine (ADMP), and 2-(aminosulfonylmethyl)-methyl benzoate(MSMB) were the primary intermediates. These metabolites were less toxic to maize, sorghum, and bacteria than the BSM. Community structure analysis indicated that variations in exogenous carbon sources and environmental pollutants significantly improved the ecological functions of soil microbial communities, enhancing pollutant degradation. Addition of carbon sources notably affected soil microbial community structure, modifying metabolic activities and interaction patterns. Specifically, glucose substantially increased the richness and diversity of soil bacterial communities. These findings offer valuable insights for field remediation practices and contributed to the development of more robust soil pollution management strategies.

Intimate microbe-water-mineral interactions mediate alkalization in the pyroxene-rich iron ore mines in Panxi area, Southwest China

In contrast to acid mine drainage, the microbial assembly and (bio)geochemical processes in alkaline mine conditions remain under-investigated. Here, microbe-water-mineral interactions were systematically investigated in two representative iron mines with alkaline conditions in the Panxi mining area, Southwest China. Compared to reference riverine samples less interfered by mining activities, the iron ore samples, composed of vanadium-titanium magnetite and pyroxene-rich bedrocks, exhibited elevated levels of Fe, HCl-extractable Fe(II), total sulfur, nitrate and sulfate, but lower total carbon (TC). Meanwhile, the mine drainage showed significantly higher sulfate, but lower TC concentrations than the riverine samples. Intriguingly, the Serpentinimonas spp., typically reported in serpentinites, prevailed in the microbial communities from the mine samples exhibiting higher pH. This suggests that the alkaline environments in Panxi mines result from serpentinization-like reactions. Enrichment of Thiobacillus spp. was observed in the mine-dwelling microbial communities, positively correlated with total sulfur, sulfate, nitrate, and Fe(II). Genome-resolved metagenomics suggested a chemoautotrophic lifestyle for the Thiobacillus species (e.g., carbon fixation, sulfur oxidation, and oxygen respiration), which may generate H+ and mitigate alkalization. This study provides valuable insights into progressive development of alkaline mine ecosystems and offers guidance for developing appropriate engineering strategies to restore the abandoned alkaline mines.

Temperature structuring of microbial communities on a global scale

Temperature is a fundamental physical constraint regulating key aspects of microbial life. Protein binding, membrane fluidity, central dogma processes, and metabolism are all tightly controlled by temperature, such that growth rate profiles across taxa and environments follow the same general curve. An open question in microbial ecology is how the effects of temperature on individual traits scale up to determine community structure and function at planetary scales. Here, we review recent theoretical and experimental efforts to connect physiological responses to the outcome of species interactions, the assembly of microbial communities, and their function as temperature changes. We identify open questions in the field and define a roadmap for future studies.

Soil microbiomes show consistent and predictable responses to extreme events

Increasing extreme climatic events threaten the functioning of terrestrial ecosystems1,2. Because soil microbes govern key biogeochemical processes, understanding their response to climate extremes is crucial in predicting the consequences for ecosystem functioning3,4. Here we subjected soils from 30 grasslands across Europe to four contrasting extreme climatic events under common controlled conditions (drought, flood, freezing and heat), and compared the response of soil microbial communities and their functioning with those of undisturbed soils. Soil microbiomes exhibited a small, but highly consistent and phylogenetically conserved, response under the imposed extreme events. Heat treatment most strongly impacted soil microbiomes, enhancing dormancy and sporulation genes and decreasing metabolic versatility. Microbiome response to heat in particular could be predicted by local climatic conditions and soil properties, with soils that do not normally experience the extreme conditions being imposed being most vulnerable. Our results suggest that soil microbiomes from different climates share unified responses to extreme climatic events, but that predicting the extent of community change may require knowledge of the local microbiome. These findings advance our understanding of soil microbial responses to extreme events, and provide a first step for making general predictions about the impact of extreme climatic events on soil functioning.

Effects of stand age and soil microbial communities on soil respiration throughout the growth cycle of poplar plantations in northeastern China

Introduction

Many studies have identified stand age and soil microbial communities as key factors influencing soil respiration (Rs). However, the effects of stand age on Rs and soil microbial communities throughout the growth cycle of poplar (Populus euramevicana cv.'I-214') plantations remain unclear.

Methods

In this study, we adopted a spatial approach instead of a temporal one to investigate Rs and soil microbial communities in poplar plantations of 15 different ages (1-15  years old).

Results

The results showed that Rs exhibited clear seasonal dynamics, with the highest rates observed in the first year of stand age (1-year-old). As stand age increased, Rs showed a significant decreasing trend. We further identified r-selected microbial communities (copiotrophic species) as key biological factors influencing the decline in Rs with increasing stand age. Other abiotic factors, such as soil temperature (ST), pH, soil organic carbon (SOC), nitrate nitrogen (NO3 --N), and the C/N ratio of plant litter (Litter C/N), were also significantly correlated with Rs. Increased stand age promoted fungal community diversity but suppressed bacterial community diversity. Bacterial and fungal communities differed significantly in abundance, composition, and function, with the Litter C/N ratio being a key variable affected by microbial community changes.

Conclusion

This study provides crucial empirical evidence on how stand age affects Rs, highlighting the connection between microbial community assemblages, their trophic strategies, and Rs over the growth cycle of poplar plantations.

Microbial trait multifunctionality drives soil organic matter formation potential

Soil microbes are a major source of organic residues that accumulate as soil organic matter, the largest terrestrial reservoir of carbon on Earth. As such, there is growing interest in determining the microbial traits that drive soil organic matter formation and stabilization; however, whether certain microbial traits consistently predict soil organic matter accumulation across different functional pools (e.g., total vs. stable soil organic matter) is unresolved. To address these uncertainties, we incubated individual species of fungi in soil organic matter-free model soils, allowing us to directly relate the physiological, morphological, and biochemical traits of fungi to their soil organic matter formation potentials. We find that the formation of different soil organic matter functional pools is associated with distinct fungal traits, and that 'multifunctional' species with intermediate investment across this key grouping of traits (namely, carbon use efficiency, growth rate, turnover rate, and biomass protein and phenol contents) promote soil organic matter formation, functional complexity, and stability. Our results highlight the limitations of categorical trait-based frameworks that describe binary trade-offs between microbial traits, instead emphasizing the importance of synergies among microbial traits for the formation of functionally complex soil organic matter.

Quinolone-mediated metabolic cross-feeding develops aluminium tolerance in soil microbial consortia

Aluminium (Al)-tolerant beneficial bacteria confer resistance to Al toxicity to crops in widely distributed acidic soils. However, the mechanism by which microbial consortia maintain Al tolerance under acid and Al toxicity stress remains unknown. Here, we demonstrate that a soil bacterial consortium composed of Rhodococcus erythropolis and Pseudomonas aeruginosa exhibit greater Al tolerance than either bacterium alone. P. aeruginosa releases the quorum sensing molecule 2-heptyl-1H-quinolin-4-one (HHQ), which is efficiently degraded by R. erythropolis. This degradation reduces population density limitations and further enhances the metabolic activity of P. aeruginosa under Al stress. Moreover, R. erythropolis converts HHQ into tryptophan, promoting the synthesis of peptidoglycan, a key component for cell wall stability, thereby improving the Al tolerance of R. erythropolis. This study reveals a metabolic cross-feeding mechanism that maintains microbial Al tolerance, offering insights for designing synthetic microbial consortia to sustain food security and sustainable agriculture in acidic soil regions.

Mangrove wetland recovery enhances soil carbon sequestration capacity of soil aggregates and microbial network stability in southeastern China

Mangrove wetlands are highly productive ecosystems in tropical and subtropical coastal zones, play crucial roles in water purification, biodiversity maintenance, and carbon sequestration. Recent years have seen the implementation of pond return initiatives, which have facilitated the gradual recovery of mangrove areas in China. However, the implications of these initiatives for soil aggregate stability, microbial community structure, and network interactions remain unclear. This study assesses the impacts of converting ponds to mangroves-both in natural and artificially restored settings-on soil aggregate stability and microbial networks at typical mangrove restoration sites along China's southeastern coast. Our observations confirmed our hypothesis that pond-to-mangrove conversions resulted in an increase in the proportion of large aggregates (>0.25 mm), improved soil aggregate structural stability, and increased carbon sequestration. However, mangrove recovery led to a decrease in the abundance and diversity of soil fungi communities. In terms of co-occurrence networks, naturally restored mangrove wetlands exhibited more nodes and edges. The naturally recovered mangrove wetlands demonstrated a higher level of community symbiosis compared to those that were manually restored. Conversely, bacterial networks showed a different pattern, with significant shifts in key taxa related to carbon sequestration functions. For instance, the proportion of bacterial Desulfobacterota and fungi Basidiomycota in natural recovery mangrove increased by 15.03 % and 7.82 %, respectively, compared with that in aquaculture ponds. Soil fungi and bacteria communities, as well as carbon sequestration by aggregates, were all positively correlated with soil total carbon content (P < 0.05). Both bacterial and fungal communities contributed to soil aggregate stability. Our study highlights the complex relationships between soil microbial communities, aggregate stability, and the carbon cycle before and after land-use changes. These findings underscore the potential benefits of restoring mangrove wetlands, as such efforts can enhance carbon storage capacity and significantly contribute to climate change mitigation.

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.

Chemodiversity of dissolved organic matter and its association with the bacterial community at a zinc smelting slag site after 10 years of direct revegetation

Dissolved organic matter (DOM) plays a critical role in driving the development of biogeochemical functions in revegetated metal smelting slag sites, laying a fundamental basis for their sustainable rehabilitation. However, the DOM composition at the molecular level and its interaction with the microbial community in such sites undergoing long-term direct revegetation remain poorly understood. This study investigated the chemodiversity of DOM and its association with the bacterial community in the rhizosphere and non-rhizosphere slags of four plant species (Arundo donax, Broussonetia papyrifera, Cryptomeria fortunei, and Robinia pseudoacacia) planted at a zinc smelting slag site for 10 years. The results indicated that the relative abundance of lipids decreased from 18 % to 5 %, while the relative abundance of tannins and lignins/CRAM-like substances increased from 4 % to 10 % and from 44 % to 64 % in the revegetated slags, respectively. The chemical stability of the organic matter in the rhizosphere slag increased due to the retention of recalcitrant DOM components, such as lignins, aromatics, and tannins. As the diversity and relative abundance of the bacterial community increased, particularly within the Proteobacteria, there was better utilization of recalcitrant components (e.g., lignins/CRAM-like compounds), but this utilization was not invariable. In addition, potential preference associations between specific bacterial OTUs and DOM molecules were observed, possibly stimulated by heavy metal bioavailability. Network analysis revealed complex connectivity and strong interactions between the bacterial community and DOM molecules. These specific interactions between DOM molecules and the bacterial community enable adaptation to the harsh conditions of the slag environment. Overall, these findings provide novel insights into the transformation of DOM chemodiversity at the molecular level at a zinc smelting slag sites undergoing long-term revegetation. This knowledge could serve as a crucial foundation for developing direct revegetation strategies for the sustainable rehabilitation of metal smelting slag sites.