Life and death in the soil microbiome: how ecological processes influence biogeochemistry

High potential in synergizing the reduction of dissolved organic carbon concentration and carbon dioxide emissions for submerged-vegetation-covered river networks

Various technologies and projects have been explored and developed for the synergetic control of environmental pollution and carbon emissions in aquatic ecosystems. Planting submerged vegetation in shallow waters was also expected to achieve this purpose. However, the magnitude and mechanism of carbon dioxide (CO2) emission affected by submerged vegetation is not clear enough in complex aquatic ecosystems. This study investigated the influences of submerged plants on CO2 emission, ecosystem metabolism features, and microbial community traits based on observations in river networks on the Changjiang River Delta. The results showed that CO2 emission from planted waters accounted for 73% of unplanted waters. Meanwhile, planted waters had higher dissolved organic carbon removal capacity in overlying water and higher potential of carbon sequestration in sediment at the same time. These distinctions between the two habitats were attributed to (1) improved CO2 and bicarbonate consumption in water columns via enhancing photosynthesis and (2) inhibited CO2 production by reconstructing the benthic microbial community. Additional eco-advantages were found in planted sediments, such as a high potential of methane oxidation and xenobiotics biodegradation and a low risk of becoming black and odorous. In brief, submerged vegetation is beneficial in promoting pollution removal and carbon retention synchronously. This study advances our understanding of the feedback between aquatic metabolism and CO2 emission.

Impact of elevated CO2 on soil microbiota: A meta-analytical review of carbon and nitrogen metabolism

In the face of 21st-century challenges driven by population growth and resource depletion, understanding the intricacies of climate change is crucial for environmental sustainability. This review systematically explores the interaction between rising atmospheric CO2 concentrations and soil microbial populations, with possible feedback effects on climate change and terrestrial carbon (C) cycling through a meta-analytical approach. Furthermore, it investigates the enzymatic activities related to carbon acquisition, gene expression patterns governing carbon and nitrogen metabolism, and metagenomic and meta-transcriptomic dynamics in response to elevated CO2 levels. The study reveals that elevated CO2 levels substantially influence soil microbial communities, increasing microbial biomass C and respiration rate by 15 % and upregulating genes involved in carbon and nitrogen metabolism by 12 %. Despite a 14 % increase in C-acquiring enzyme activity, there is a 5 % decrease in N-acquiring enzyme activity, indicating complex microbial responses to CO2 changes. Additionally, fungal marker ratios increase by 14 % compared to bacterial markers, indicating potential ecosystem changes. However, the current inadequacy of data on metagenomic and meta-transcriptomic processes underscores the need for further research. Understanding soil microbial feedback mechanisms is crucial for elucidating the role of rising CO2 levels in carbon sequestration and climate regulation. Consequently, future research should prioritize a comprehensive elucidation of soil microbial carbon cycling, greenhouse gas emission dynamics, and their underlying drivers.

Unveiling the hidden world: How arbuscular mycorrhizal fungi and its regulated core fungi modify the composition and metabolism of soybean rhizosphere microbiome

BACKGROUND

The symbiosis between arbuscular mycorrhizal fungi (AMF) and plants often stimulates plant growth, increases agricultural yield, reduces costs, thereby providing significant economic benefits. AMF can also benefit plants through affecting the rhizosphere microbial community, but the underlying mechanisms remain unclear. Using Rhizophagus intraradices as a model AMF species, we assessed how AMF influences the bacterial composition and functional diversity through 16 S rRNA gene sequencing and non-targeted metabolomics analysis in the rhizosphere of aluminum-sensitive soybean that were inoculated with pathogenic fungus Nigrospora oryzae and phosphorus-solubilizing fungus Talaromyces verruculosus in an acidic soil.

RESULTS

The inoculation of R. intraradices, N. oryzae and T. verruculosus didn't have a significant influence on the levels of soil C, N, and P, or various plant characteristics such as seed weight, crude fat and protein content. However, their inoculation affected the structure, function and nutrient dynamics of the resident bacterial community. The co-inoculation of T. verruculosus and R. intraradices increased the relative abundance of Pseudomonas psychrotolerans, which was capable of N-fixing and was related to cry-for-help theory (plants signal for beneficial microbes when under stress), within the rhizosphere. R. intraradices increased the expression of metabolic pathways associated with the synthesis of unsaturated fatty acids, which was known to enhance plant resistance under adverse environmental conditions. The inoculation of N. oryzae stimulated the stress response inside the soil environment by enriching the polyene macrolide antifungal antibiotic-producing bacterial genus Streptomyces in the root endosphere and upregulating two antibacterial activity metabolic pathways associated with steroid biosynthesis pathways in the rhizosphere. Although inoculation of pathogenic fungus N. oryzae enriched Bradyrhizobium and increased soil urease activity, it had no significant effects on biomass and N content of soybean. Lastly, the host niches exhibited differences in the composition of the bacterial community, with most N-fixing bacteria accumulating in the endosphere and Rhizobium vallis only detected in the endosphere.

CONCLUSIONS

Our findings demonstrate that intricate interactions between AMF, associated core fungi, and the soybean root-associated ecological niches co-mediate the regulation of soybean growth, the dynamics of rhizosphere soil nutrients, and the composition, function, and metabolisms of the root-associated microbiome in an acidic soil.

Diversified Vegetation Cover Alleviates Microbial Resource Limitations within Soil Aggregates in Tailings

Resource demand by soil microorganisms critically influences microbial metabolism and then influences ecosystem resilience and multifunctionality. The ecological remediation of abandoned tailings is a topic of broad interest, yet our understanding of microbial metabolic status in restored soils, particularly at the aggregate scale, remains limited. This study investigated microbial resources within soil aggregates from revegetated tailings and applied a vector model of ecoenzymatic stoichiometry to examine how different vegetation patterns (grassland, forest, or bare land control) impact microbial resource limitation. Five-year vegetation restoration significantly elevated carbon (C) and nitrogen (N) concentrations and their stoichiometric ratios in soil aggregates (approximately 2-fold), although these increases were not translated to in the microbial biomass and its stoichiometry. The activities of C- and phosphorus (P)-acquiring extracellular enzymes in these aggregates increased substantially postvegetation, with the most pronounced escalation in macroaggregates (>0.25 mm). The vector model results indicated soil microbial metabolism was colimited by C and P, most acutely in microaggregates (<0.25 mm). This colimitation was exacerbated by monotypic vegetation cover but mitigated under diversified vegetation cover. Soil nutrient stoichiometric ratios in vegetation restoration controlled microbial resource limitation, overshadowing the impact of heavy metals. Our findings underscore that optimizing resource allocation within soil aggregates through strategic revegetation can enhance microbial metabolism in tailings, which advocates for the implementation of diverse vegetation covers as a viable strategy to improve the ecological development of degraded landscapes.

Asymmetric winter warming reduces microbial carbon use efficiency and growth more than symmetric year-round warming in alpine soils

Asymmetric seasonal warming trends are evident across terrestrial ecosystems, with winter temperatures rising more than summer ones. Yet, the impact of such asymmetric seasonal warming on soil microbial carbon metabolism and growth remains poorly understood. Using 18O isotope labeling, we examined the effects of a decade-long experimental seasonal warming on microbial carbon use efficiency (CUE) and growth in alpine grassland ecosystems. Moreover, the quantitative stable isotope probing with 18O-H2O was employed to evaluate taxon-specific bacterial growth in these ecosystems. Results show that symmetric year-round warming decreased microbial growth rate by 31% and CUE by 22%. Asymmetric winter warming resulted in a further decrease in microbial growth rate of 27% and microbial CUE of 59% compared to symmetric year-round warming. Long-term warming increased microbial carbon limitations, especially under asymmetric winter warming. Long-term warming suppressed the growth rates of most bacterial genera, with asymmetric winter warming having a stronger inhibition on the growth rates of specific genera (e.g., Gp10, Actinomarinicola, Bosea, Acidibacter, and Gemmata) compared to symmetric year-round warming. Bacterial growth was phylogenetically conserved, but this conservation diminished under warming conditions, primarily due to shifts in bacterial physiological states rather than the number of bacterial species and community composition. Overall, long-term warming escalated microbial carbon limitations, decreased microbial growth and CUE, with asymmetric winter warming having a more pronounced effect. Understanding these impacts is crucial for predicting soil carbon cycling as global warming progresses.

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.

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.

Divergent contributions of microbes and plants to soil organic carbon in the drawdown area of a large reservoir: Impacts of periodic flooding and drying

The distribution patterns and accumulation mechanisms of plant and microbial residues, along with their potential contributions to soil organic carbon (SOC), remain subjects of considerable debate, particularly within drawdown areas affected by reservoir operation. In this study, surface soil samples (0-10 cm) were collected from three different elevations within the drawdown area of the Three Gorges Reservoir. Amino sugars and lignin phenols served as biomarkers for microbial residues and plant-derived materials, respectively. The results revealed that with increasing duration of flooding, the content of amino sugars increased from 0.26 mg g-1 to 0.64 mg g-1, whereas the content of lignin phenols decreased from 204.09 mg kg-1 to 37.93 mg kg-1. Moreover, as the duration of flooding increased, the contribution of microbial necromass carbon (MNC) to SOC rose from 29% to 47%, while the contribution of plant-derived carbon to SOC gradually declined. Plants biomass and iron minerals influenced the accumulation of lignin phenols, whereas amino sugars were affected by plants biomass, microbial biomass carbon and nitrogen, and clay minerals. The periodic flooding and drying events induced alterations in carbon inputs and environmental characteristics within the drawdown area, resulting in fluctuations in the contributions of plants and MNC to SOC in this region. The findings of this study highlight the critical role played by both plant- and microbial-derived carbon in the retention and turnover of SOC within the terrestrial-aquatic transition zone.

Chromium(VI) Adsorption and Reduction in Soils under Anoxic Conditions: The Relative Roles of Iron (oxyhr)oxides, Iron(II), Organic Matters, and Microbes

Chromium (Cr) transformation in soils mediated by iron (Fe) (oxyhr)oxides, Fe(II), organic matter (OM), and microbes is largely unexplored. Here, their coupling processes and mechanisms were investigated during anoxic incubation experiments of four Cr(VI) spiked soil samples with distinct physicochemical properties from the tropical and subtropical regions of China. It demonstrates that easily oxidizable organic carbon (EOC, 55-84%) and microbes (16-48%) drive Cr(VI) reduction in soils enriched with goethite and/or hematite, among which in dryland soils microbial sulfate reduction may also be involved. In contrast, EOC (38 ± 1%), microbes (33 ± 1%), and exchangeable and poorly crystalline Fe (oxyhr)oxide-associated Fe(II) (29 ± 3%) contribute to Cr(VI) reduction in paddy soils enriched with ferrihydrite. Additionally, exogenous Fe(II) and microbes significantly enhance Cr(VI) reduction in ferrihydrite- and goethite-rich soils, and Fe(II) greatly promotes but microbes slightly inhibit Cr passivation. Both Fe(II) and microbes, especially the latter, promote OM mineralization and result in the most substantial OM loss in ferrihydrite-rich paddy soils. During the incubation, part of the ferrihydrite converts to goethite but microbes may hinder the transformation. These results provide deep insights into the geochemical fates of redox-sensitive heavy metals mediated by the complicated effects of Fe, OM, and microbes in natural and engineered environments.

Irradiance level and elevation shape the soil microbiome communities of Coffea arabica L

BACKGROUND

The nexus plant-microbe-environment is essential to understand the ecosystem processes shaping plant health and fitness. Within this triangle, soils and associated microflora are among the key ecosystem's drivers, underpinning plant productivity and evolution. In this study, we conducted a comprehensive analysis (physicochemical properties, enzyme activities, and taxonomic diversity) of soils under the canopy projection of Coffea arabica trees along a gradient of elevation (600, 800, and 900 m) and shade (0, 50, 100%).

RESULTS

While shade had no influence on most parameters, altitude shaped the dynamics of microbial communities. Available phosphorus, soil organic carbon, and nitrate were significantly higher at 800 m, likely due to the higher activities of β-glucosidase and phosphatases at this altitude. Microbial biomass (carbon and nitrogen) and moisture were significantly higher at 600 and 900 m, which might be attributed to the abundance and richness of soil microorganisms. Indeed, metabarcoding analysis revealed a complex pattern of microbial consortia (bacteria, archaea, fungi) at the three altitudes, with the lowest index of richness recorded at 800 m. The highest number of Amplicon Sequence Variants was observed in bacteria, whose functional analysis revealed distinct metabolic adaptations across different altitudes. At 900 m, the main functional attributes favored the responses to environmental stimuli and microbial interactions; at 800 m, the predominant metabolic pathways were related to organic matter, fermentation, and bioremediation; and at the lower 600 m, the pathways shifted towards the breakdown of plant-derived compounds (e.g. geraniol, limonene, and pinene degradation).

CONCLUSION

Overall, the results indicate a higher effectiveness of the microbial consortium at 800 m, which might result in better nutrient cycling. The study highlights the importance of canopy shade species and elevation for the composition of microbial consortia in C. arabica, unveiling ecological functions beyond plant health, with implications for bio-based solutions and biotechnology.

Lily viruses regulate the viral community of the Lanzhou lily rhizosphere and indirectly affect rhizosphere carbon and nitrogen cycling

The rhizosphere, where plant roots interact intensely with the soil, is a crucial but understudied area in terms of the impact of virus infection. In this study, we investigated the effects of lily symptomless virus (LSV) and cucumber mosaic virus (CMV) on the Lanzhou lily (Lilium davidii var. unicolor) rhizosphere using metagenomics and bioinformatics analysis. We found that virus infection significantly altered soil pH, inorganic carbon, nitrate nitrogen, and total sulfur. Co-infection with LSV and CMV had a greater influence than single infections on the α- and β-diversity of the rhizosphere viral community in which the absolute abundance of certain virus families (Siphoviridae, Podoviridae, and Myoviridae) increased significantly, whereas bacteria, fungi, and archaea remained relatively unaffected. These altered virus populations influenced the rhizosphere microbial carbon and nitrogen cycles by exerting top-down control on bacteria. Co-infection potentially weakened rhizosphere carbon fixation and promoted processes such as methane oxidation, nitrification, and denitrification. In addition, the co-occurrence network of bacteria and viruses in the rhizosphere revealed substantial changes in microbial community composition under co-infection. Our partial-least-squares path model confirmed that the diversity of the rhizosphere viral community indirectly regulated the carbon and nitrogen cycling functions of the microbial community, thus affecting the accumulation of carbon and nitrogen nutrients in the soil. Our results are the first report of the effects of virus infection on the lily rhizosphere, particularly for co-infection; they therefore complement research on the plant virus pathogenic mechanisms, and increase our understanding of the ecological role of rhizosphere soil viruses.

Unraveling the dynamic interplay of microbial communities associated to Lupinus angustifolius in response to environmental and cultivation conditions

Microorganisms form dynamic communities with plants, providing benefits such as nutrient acquisition and stress resilience. Understanding how these microorganisms are affected by environmental factors such as growth conditions and soil characteristics are essential for harnessing these communities for sustainable agriculture practices and their response to climate change. The microbiome associated to Lupinus angustifolius, a legume native in Europe, with a high protein value and stress resilience was characterized for the first time. Using 16S rRNA gene and ITS amplicon sequencing, we characterized the compositional and temporal changes of the bacterial and fungal communities associated to the soil, rhizosphere, and plant compartments where Lupinus angustifolius grows naturally. Our results suggest that the main difference in the soil microbial communities is related to the edaphic properties, although environmental factors such as temperature, humidity or rainfall also influenced the composition of the soil microbial communities. We also characterized the bacterial communities associated with the rhizosphere, roots, nodules, and leaves of wild plants collected in the field and compared them against plants obtained under greenhouse conditions. In the plant compartments, the bacterial composition appeared to be more affected by the growing conditions (field vs greenhouse), than by soil characteristics or location. These results can be used to identify key taxa that may play crucial roles in the development and adaptation of the host plant and its associated microbiota to environmental changes and highlight the importance of characterizing the plant microbiomes in their natural habitats. Soil, influenced by climatic seasons, shapes the plant microbiome assembly. Lupinus recruits a core microbiome across rhizosphere, roots, nodules, and leaves, that is stable across locations. However, cultivation conditions may alter microbiome dynamics, impacting the adaptability of its components. Wild plants show a resilient and adaptable microbiome while germination and cultivation in greenhouse conditions alter its composition and vulnerability.

Microbial necromass and glycoproteins for determining soil carbon formation under arbuscular mycorrhiza symbiosis

Arbuscular mycorrhizal fungi (AMF) form symbioses with most terrestrial plants and critically modulate soil organic carbon (C) dynamics. Whether AMF promote soil C storage and stability is, however, largely unknown. Since microbial necromass C (MNC) and glomalin-related soil protein (GRSP) are stable microbial-derived C in soils, we therefore evaluated how AMF symbiosis alters both soil C pools and their contributions to soil organic C (SOC) under nitrogen fertilization, based on a 16-weeks mesocosm experiment using a mutant tomato with highly reduced AMF symbiosis. Results showed that SOC content is 4.5 % higher following AMF symbiosis. Additionally, the content of MNC and total GRSP were 47.5 % and 22.3 % higher under AMF symbiosis than at AMF absence, respectively. The accumulations of GRSP and microbial necromass in soil were closely associated with mineral-associated organic C and the abundance of AMF. The increased soil living microbial biomass under AMF symbiosis was mainly derived from AMF biomass, and fungal necromass C significantly contributed to SOC accumulation, as evidenced by the higher fungal:bacterial necromass C ratio under AMF symbiosis. On the contrary, bacterial necromass was degraded to compensate for the increased microbial nutrient demand because of the aggravated nutrient limitation under AMF symbiosis, leading to a decrease in bacterial necromass. Redundancy analysis showing that bacterial necromass was negatively correlated with soil C:N ratio supported this argument. Moreover, the relative change rate of total GRSP was consistently greater in nitrogen-limited soil than that of microbial necromass. Our findings suggested GRSP accumulates faster and contributes more to SOC pools under AMF symbiosis than microbial necromass. The positive correlation between the contributions of GRSP and MNC to SOC further provided valuable information in terms of enhancing our understanding of mechanisms underlying the maintenance of SOC stocks through microbial-derived C.

Long-term sheep grazing reduces fungal necromass carbon contribution to soil organic carbon in the desert steppe

Grazing has been shown to impact the soil environment and microbial necromass carbon (MNC), which in turn regulates soil organic carbon (SOC). However, the carbon sequestration potential of fungi and bacteria under different stocking rates remains unclear, limiting our understanding of soil carbon sequestration in grazing management. In 2004, we established grazing experiments in the desert steppe of northern China with four stocking rates. Our findings indicate that MNC decreased under moderate and heavy grazing, while light grazing did not significantly differ from no grazing. Notably, the reduction in fungal necromass carbon, rather than bacterial necromass carbon, was primarily responsible for the decreased contribution of MNC to SOC. This difference is attributed to the varying effects of sheep grazing on fungal and bacterial community characteristics, including richness, diversity, and composition. Thus, to accurately predict carbon dynamics in grassland ecosystems, it is essential to consider that the ecological impacts and carbon sequestration potential of microbial communities may vary with different grazing management practices.

Tracking microbial movement in saturated media with spectral induced polarization

Pathogenic microorganisms in the subsurface can contaminate soil and water supplies, potentially posing great danger to human health. Early contamination detection routines rely on sparse direct sampling which is spatiotemporally limited. Thus, the path of microorganisms in the subsurface remains ambiguous and this can cause delays in detection of biohazardous threats. The geophysical spectral induced polarization (SIP) technique, sensitive to microbes' presence and activity in porous media, is a promising method to monitor microbial transport pathways. Here we evaluated the efficiency of SIP in monitoring the chemotactic movement of Sporosarcina pasteurii in saturated porous media. A cylindrical sample holder was packed with Ottawa sand and saturated with sterile KCl solution. The sample holder was oriented vertically and S. pasteurii was introduced at the bottom, forcing the movement of the microbes against gravity, towards a carbon source available at the top of the column. Temporal SIP measurements were collected at 3 regions of the sample holder: bottom (microbial injection point), middle and top (carbon source). Both the real (σ') and imaginary (σ″) conductivity parts of the SIP signal increased over time with the σ″ showing a peak signal magnitude following the upward movement of the microbes. We repeated the experiment excluding the carbon source in experiment 2 and omitting microbial injection in experiment 3. However, we did not observe any significant SIP signal changes in these two experiments. This is the first study to indicate the strong SIP signal correlation with microbial chemotaxis.

Necromass responses to warming: A faster microbial turnover in favor of soil carbon stabilisation

Microbial byproducts and residues (hereafter 'necromass') potentially play the most critical role in soil organic carbon (SOC) sequestration. However, little is known about the influence of climate warming on necromass accumulation in the agroecosystem and the underlying mechanisms associated with microbial life strategies. In order to address these knowledge gaps, we used amino sugars as biomarkers of microbial necromass, and investigated their variation through an 8-year trial in an agroecosystem with two warming levels (+1.6 and + 3.2 °C) compared to ambient temperature. The results showed that the lower warming level had no impact on total microbial necromass carbon. Conversely, warming the soil 3.2 °C above ambient increased total microbial necromass by 17 % and its contribution to SOC by 21.3 %, mainly by increasing fungal necromass (+19.8 %), whereas +3.2 °C warming had no impact on bacterial necromass. At the phylum level, compared with the ambient control, +3.2 °C warming induced an increase in the abundance of Proteobacteria and a decrease in both Acidobacteria and Actinobacteria, whereas in the fungal community, Ascomycota increased and Mortierellomycota decreased. This indicates that r-strategists outcompete K-strategists in warmer climates, which led to increased microbial necromass production and accumulation, as supported by the positive correlation between r-strategists and microbial necromass. Stronger microbial competition for resources also resulted in a higher biomass turnover rate, greater cell death, and greater production of microbial necromass. This was supported by the lower bacterial and fungal network complexity and trophic links under warming conditions. In addition, the necromass generated from accelerated microbial turnover further offsets warming-induced deceases in microbial biomass. Consequently, bulk SOC did not change, despite microbial necromass having a much greater response to warming than the soil C pool. Therefore, future climate warming may influence the composition and persistence of SOC during microbial degradation.

Community structure, diversity and function of endophytic and soil microorganisms in boreal forest

Introduction

Despite extensive studies on soil microbial community structure and functions, the significance of plant-associated microorganisms, especially endophytes, has been overlooked. To comprehensively anticipate future changes in forest ecosystem function under future climate change scenarios, it is imperative to gain a thorough understanding of the community structure, diversity, and function of both plant-associated microorganisms and soil microorganisms.

Methods

In our study, we aimed to elucidate the structure, diversity, and function of leaf endophytes, root endophytes, rhizosphere, and soil microbial communities in boreal forest. The microbial structure and composition were determined by high-throughput sequencing. FAPROTAX and FUNGuild were used to analyze the microbial functional groups.

Results

Our findings revealed significant differences in the community structure and diversity of fungi and bacteria across leaves, roots, rhizosphere, and soil. Notably, we observed that the endophytic fungal or bacterial communities associated with plants comprised many species distinct from those found in the soil microbial communities, challenging the assumption that most of endophytic fungal or bacterial species in plants originate from the soil. Furthermore, our results indicated noteworthy differences in the composition functional groups of bacteria or fungi in leaf endophytes, root endophytes, rhizosphere, and soil, suggesting distinct roles played by microbial communities in plants and soil.

Discussion

These findings underscore the importance of recognizing the diverse functions performed by microbial communities in both plant and soil environments. In conclusion, our study emphasizes the necessity of a comprehensive understanding of the structure and function microbial communities in both plants and soil for assessing the functions of boreal forest ecosystems.

Dynamic in situ detection in iRhizo-Chip reveals diurnal fluctuations of Bacillus subtilis in the rhizosphere

Effective colonization by microbe in the rhizosphere is critical for establishing a beneficial symbiotic relationship with the host plant. Bacillus subtilis, a soil-dwelling bacterium that is commonly found in association with plants and their rhizosphere, has garnered interest for its potential to enhance plant growth, suppress pathogens, and contribute to sustainable agricultural practices. However, research on the dynamic distribution of B. subtilis within the rhizosphere and its interaction mechanisms with plant roots remains insufficient due to limitations in existing in situ detection methodologies. To achieve dynamic in situ detection of the rhizosphere environment, we established iRhizo-Chip, a microfluidics-based platform. Using this device to investigate microbial behavior within the rhizosphere, we found obvious diurnal fluctuations in the growth of B. subtilis in the rhizosphere. Temporal dynamic analysis of rhizosphere dissolved oxygen (DO), pH, dissolved organic carbon, and reactive oxygen species showed that diurnal fluctuations in the growth of B. subtilis are potentially related to a variety of environmental factors. Spatial dynamic analysis also showed that the spatial distribution changes of B. subtilis and DO and pH were similar. Subsequently, through in vitro control experiments, we proved that rhizosphere DO and pH are the main driving forces for diurnal fluctuations in the growth of B. subtilis. Our results show that the growth of B. subtilis is driven by rhizosphere DO and pH, resulting in diurnal fluctuations, and iRhizo-Chip is a valuable tool for studying plant rhizosphere dynamics.

Spontaneous interactions between typical antibiotics and soil enzyme: Insights from multi-spectroscopic approaches, XPS technology, molecular modeling, and joint toxic actions

A large amount of antibiotics enters the soil environment and accumulates therein as individuals and mixtures, threatening the soil safety. However, there is little information regarding the influence of single and mixed antibiotics on key soil proteins at molecular level. In this study, setting sulfadiazine (SD) and tetracycline hydrochloride (TC) as the representative antibiotics, the interactions between these agents and α-amylase (an important hydrolase in soil carbon cycle) were investigated through multi-spectroscopic approaches, X-ray photoelectron spectrometry, and molecular modeling. It was found that both SD and TC spontaneously bound to α-amylase with 1:1 stoichiometry mainly via forming stable chemical bonds. The interactions altered the polarity of aromatic amino acids, protein backbone, secondary structure, hydrophobicity and activity of α-amylase. The SD-TC mixtures were designed based on the direct equipartition ray to comprehensively characterize the possible concentration distribution, and interactive effects indicated that the mixtures antagonistically impacted α-amylase. These findings reveal the binding characteristics between α-amylase and typical antibiotics, which probably influence the ecological functions of α-amylase in soil. This study clarifies the potential harm of antibiotics on soil functional enzyme, which is significant for the environmental risk assessment of antibiotics and their mixtures.

Sandy loam soil maintains better physicochemical parameters and more abundant beneficial microbiomes than clay soil in Stevia rebaudiana cultivation

Depending on the texture of soil, different physicochemical and microbiological parameters are characterized, and these characteristics are influenced by crop cultivation. Stevia, a popular zero-calorie sweetener crop, is widely cultivated around the world on various soil textures. Sandy loam and clay soil show great differences in physicochemical and biological parameters and are often used for Stevia cultivation. To understand the effects of Stevia cultivation on soil physicochemical and biological features, we investigated the changes of physicochemical and microbiological parameters in sandy loam and clay soil following Stevia cultivation. This study was carried out through different physiological and biochemical assays and microbiomic analysis. The results indicated that the sandy loam soil had significantly lower pH and higher nutrient content in the rhizosphere and bulk soils after the Stevia cultivation. The sandy loam soil maintained higher bacterial diversity and richness than the clay soil after Stevia harvest. Beneficial bacteria such as Dongia, SWB02, Chryseolinea, Bryobacter and Devosia were enriched in the sandy loam soil; however, bacteria such as RB41, Haliangium and Ramlibacter, which are unfavorable for nutrient accumulation, predominated in clay soil. Redundancy analysis indicated that the variation in the composition of bacterial community was mainly driven by soil pH, organic matter, total nitrogen, available phosphorus, and microbial biomass phosphorus. This study provides a deeper understanding of physicochemical and microbiological changes in different soil textures after Stevia cultivation and guidance on fertilizer management for Stevia rotational cultivation.

Growth rate as a link between microbial diversity and soil biogeochemistry

Measuring the growth rate of a microorganism is a simple yet profound way to quantify its effect on the world. The absolute growth rate of a microbial population reflects rates of resource assimilation, biomass production and element transformation-some of the many ways in which organisms affect Earth's ecosystems and climate. Microbial fitness in the environment depends on the ability to reproduce quickly when conditions are favourable and adopt a survival physiology when conditions worsen, which cells coordinate by adjusting their relative growth rate. At the population level, relative growth rate is a sensitive metric of fitness, linking survival and reproduction to the ecology and evolution of populations. Techniques combining omics and stable isotope probing enable sensitive measurements of the growth rates of microbial assemblages and individual taxa in soil. Microbial ecologists can explore how the growth rates of taxa with known traits and evolutionary histories respond to changes in resource availability, environmental conditions and interactions with other organisms. We anticipate that quantitative and scalable data on the growth rates of soil microorganisms, coupled with measurements of biogeochemical fluxes, will allow scientists to test and refine ecological theory and advance process-based models of carbon flux, nutrient uptake and ecosystem productivity. Measurements of in situ microbial growth rates provide insights into the ecology of populations and can be used to quantitatively link microbial diversity to soil biogeochemistry.

Green manure (Ophiopogon japonicus) cover promotes tea plant growth by regulating soil carbon cycling

Introduction

In mountainous tea plantations, which are the primary mode of tea cultivation in China, issues such as soil erosion and declining soil fertility are particularly severe. Although green manure cover is an effective agricultural measure for restoring soil fertility, its application in mountainous tea plantations has been relatively understudied.

Methods

This study investigated the effects of continuous green manure cover using the slope-protecting plant Ophiopogon japonicus on tea plant growth and soil microbial community structure. We implemented three treatments: 1 year of green manure coverage, 2 years of coverage, and a control, to study their effects on tea plant growth, soil physicochemical properties, and soil bacterial and fungal communities.

Results

Results demonstrate that green manure coverage significantly promote the growth of tea plants, enhanced organic matter and pH levels in soil, and various enzyme activities, including peroxidases and cellulases. Further functional prediction results indicate that green manure coverage markedly promoted several carbon cycling functions in soil microbes, including xylanolysis, cellulolysis, degradation of aromatic compounds, and saprotrophic processes. LEfSe analysis indicated that under green manure cover, the soil tends to enrich more beneficial microbial communities with degradation functions, such as Sphingomonas, Sinomonas, and Haliangium (bacteria), and Penicillium, Apiotrichum, and Talaromyce (fungi). In addition. Random forest and structural equation models indicated that carbon cycling, as a significant differentiating factor, has a significant promoting effect on tea plant growth.

Discussion

In the management practices of mountainous tea plantations, further utilizing slope-protecting plants as green manure can significantly influence the soil microbial community structure and function, enriching microbes involved in the degradation of organic matter and aromatic compounds, thereby positively impacting tea tree growth and soil nutrient levels.

Evaluation of the phytotoxicity and accumulation potential of nitro-polycyclic aromatic hydrocarbon, 3-nitrofluoranthene, on water status, photosystem II efficiency, antioxidant activity and ROS accumulation in Salvinia natans

Organic pollutants, which have become one of the most striking problems of today, raise concerns about the spread of polyaromatic hydrocarbon (PAH) compounds into ecosystems and their toxic effects on living organisms. The purpose of this study was to determine how harmful 3-nitrofluoranthene (3-NF) exposure was to Salvinia natans, a freshwater macrophyte. Furthermore, it clarifies how this aquatic plant, which is frequently used in phytoremediation of water contaminants and wastewater treatments, interacts with PAHs and contributes to the development of bioremediation methods. In S. natans exposed to stress (10 μM (3-NF10), 25 μM (3-NF25), 50 μM (3-NF50), 100 μM (3-NF100), 250 μM (3-NF250), 500 μM (3-NF500), 1000 μM (3-NF1000) 3-nitrofluoranthene), 3-NF accumulation, oxidative stress indicators, photosynthetic efficiency, and antioxidant system activity alterations were investigated for this objective. The findings demonstrated that S. natans could effectively accumulate 3-NF, and at a concentration of 1000 μM, the 3-NF content in the leaves reached approximately 1112 mg/kg. While its adverse effects on growth (RGR) and photosynthesis (Fv/Fm) remained mild up to a concentration of 250 μM, the severity of the inhibitions increased at higher concentrations. On the other hand, exposure to 3-NF triggered the antioxidant system in S. natans plants and resulted in an increase of 60 %, 80 %, 47 % and 27 % in superoxide dismutase (SOD) activity in 3-NF10-25-50-100 groups, respectively. Conversely, in comparison to control plants, higher concentrations of 3-NF treatments resulted in insufficient antioxidant activity, increased lipid peroxidation (TBARS concentration), and hydrogen peroxide (H2O2). In conclusion, S. natans plants tolerated 3-NF accumulation up to 250 μM concentration despite limitations in growth suppression and photosynthetic capacity, proving that S. natans has the potential to be used in phytoextraction studies of 3-NF-polluted waters.

Plant diversity drives positive microbial associations in the rhizosphere enhancing carbon use efficiency in agricultural soils

Expanding and intensifying agriculture has led to a loss of soil carbon. As agroecosystems cover over 40% of Earth's land surface, they must be part of the solution put in action to mitigate climate change. Development of efficient management practices to maximize soil carbon retention is currently limited, in part, by a poor understanding of how plants, which input carbon to soil, and microbes, which determine its fate there, interact. Here we implement a diversity gradient by intercropping undersown species with barley in a large field trial, ranging from one to eight undersown species. We find that increasing plant diversity strengthens positive associations within the rhizosphere soil microbial community in relation to negative associations. These associations, in turn, enhance community carbon use efficiency. Jointly, our results highlight how increasing plant diversity in agriculture can be used as a management strategy to enhance carbon retention potential in agricultural soils.

Permafrost carbon cycle and its dynamics on the Tibetan Plateau

Our knowledge on permafrost carbon (C) cycle is crucial for understanding its feedback to climate warming and developing nature-based solutions for mitigating climate change. To understand the characteristics of permafrost C cycle on the Tibetan Plateau, the largest alpine permafrost region around the world, we summarized recent advances including the stocks and fluxes of permafrost C and their responses to thawing, and depicted permafrost C dynamics within this century. We find that this alpine permafrost region stores approximately 14.1 Pg (1 Pg=1015 g) of soil organic C (SOC) in the top 3 m. Both substantial gaseous emissions and lateral C transport occur across this permafrost region. Moreover, the mobilization of frozen C is expedited by permafrost thaw, especially by the formation of thermokarst landscapes, which could release significant amounts of C into the atmosphere and surrounding water bodies. This alpine permafrost region nevertheless remains an important C sink, and its capacity to sequester C will continue to increase by 2100. For future perspectives, we would suggest developing long-term in situ observation networks of C stocks and fluxes with improved temporal and spatial coverage, and exploring the mechanisms underlying the response of ecosystem C cycle to permafrost thaw. In addition, it is essential to improve the projection of permafrost C dynamics through in-depth model-data fusion on the Tibetan Plateau.

A smartphone-based approach for comprehensive soil microbiome profiling

The soil microbiome is crucial for nutrient cycling, health, and plant growth. This study presents a smartphone-based approach as a low-cost and portable alternative to traditional methods for classifying bacterial species and characterizing microbial communities in soil samples. By harnessing bacterial autofluorescence detection and machine learning algorithms, the platform achieved an average accuracy of 88% in distinguishing common soil-related bacterial species despite the lack of biomarkers, nucleic acid amplification, or gene sequencing. Furthermore, it successfully identified dominant species within various bacterial mixtures with an accuracy of 76% and three-level soil health identification at an accuracy of 80%-82%, providing insights into microbial community dynamics. The influence of other soil conditions (pH and moisture) was relatively minor, showcasing the platform's robustness. Various field soil samples were also tested with this platform at 80% accuracy compared with the laboratory analyses, demonstrating the practicality and usability of this approach for on-site soil analysis. This study highlights the potential of the smartphone-based system as a valuable tool for soil assessment, microbial monitoring, and environmental management.

Limiting Resources Define the Global Pattern of Soil Microbial Carbon Use Efficiency

Microbial carbon (C) use efficiency (CUE) delineates the proportion of organic C used by microorganisms for anabolism and ultimately influences the amount of C sequestered in soils. However, the key factors controlling CUE remain enigmatic, leading to considerable uncertainty in understanding soil C retention and predicting its responses to global change factors. Here, we investigate the global patterns of CUE estimate by stoichiometric modeling in surface soils of natural ecosystems, and examine its associations with temperature, precipitation, plant-derived C and soil nutrient availability. We found that CUE is determined by the most limiting resource among these four basic environmental resources within specific climate zones (i.e., tropical, temperate, arid, and cold zones). Higher CUE is common in arid and cold zones and corresponds to limitations in temperature, water, and plant-derived C input, while lower CUE is observed in tropical and temperate zones with widespread limitation of nutrients (e.g., nitrogen or phosphorus) in soil. The contrasting resource limitations among climate zones led to an apparent increase in CUE with increasing latitude. The resource-specific dependence of CUE implies that soils in high latitudes with arid and cold environments may retain less organic C in the future, as warming and increased precipitation can reduce CUE. In contrast, oligotrophic soils in low latitudes may increase organic C retention, as CUE could be increased with concurrent anthropogenic nutrient inputs. The findings underscore the importance of resource limitations for CUE and suggest asymmetric responses of organic C retention in soils across latitudes to global change factors.

Soil keystone viruses are regulators of ecosystem multifunctionality

Ecosystem multifunctionality reflects the capacity of ecosystems to simultaneously maintain multiple functions which are essential bases for human sustainable development. Whereas viruses are a major component of the soil microbiome that drive ecosystem functions across biomes, the relationships between soil viral diversity and ecosystem multifunctionality remain under-studied. To address this critical knowledge gap, we employed a combination of amplicon and metagenomic sequencing to assess prokaryotic, fungal and viral diversity, and to link viruses to putative hosts. We described the features of viruses and their potential hosts in 154 soil samples from 29 farmlands and 25 forests distributed across China. Although 4,460 and 5,207 viral populations (vOTUs) were found in the farmlands and forests respectively, the diversity of specific vOTUs rather than overall soil viral diversity was positively correlated with ecosystem multifunctionality in both ecosystem types. Furthermore, the diversity of these keystone vOTUs, despite being 10-100 times lower than prokaryotic or fungal diversity, was a better predictor of ecosystem multifunctionality and more strongly associated with the relative abundances of prokaryotic genes related to soil nutrient cycling. Gemmatimonadota and Actinobacteria dominated the host community of soil keystone viruses in the farmlands and forests respectively, but were either absent or showed a significantly lower relative abundance in that of soil non-keystone viruses. These findings provide novel insights into the regulators of ecosystem multifunctionality and have important implications for the management of ecosystem functioning.

Critical steps in the restoration of coal mine soils: Microbial-accelerated soil reconstruction

Soil reconstruction is a critical step in the restoration of environments affected by mining activities. This paper provides a comprehensive review of the significant role that microbial processes play in expediting soil structure formation, particularly within the context of mining environment restoration. Coal gangue and flotation tailings, despite their low carbon content and large production volumes, present potential substrates for soil reclamation. These coal-based solid waste materials can be utilized as substrates to produce high-quality soil and serve as an essential carbon source to enhance poor soil conditions. However, extracting active organic carbon components from coal-based solid waste presents a significant challenge due to its complex mineral composition. This article offers a thorough review of the soilization process of coal-based solid waste under the influence of microorganisms. It begins by briefly introducing the primary role of in situ microbial remediation technology in the soilization process. It then elaborates on various improvements to soil structure under the influence of microorganisms, including the enhancement of soil aggregate structure and soil nutrients. The article concludes with future recommendations aimed at improving the efficiency of soil reconstruction and restoration, reducing environmental risks, and promoting its application in complex environments. This will provide both theoretical and practical support for more effective environmental restoration strategies.

Bioenergetic mapping of 'healthy microbiomes' via compound processing potential imprinted in gut and soil metagenomes

Despite mounting evidence of their importance in human health and ecosystem functioning, the definition and measurement of 'healthy microbiomes' remain unclear. More advanced knowledge exists on health associations for compounds used or produced by microbes. Environmental microbiome exposures (especially via soils) also help shape, and may supplement, the functional capacity of human microbiomes. Given the synchronous interaction between microbes, their feedstocks, and micro-environments, with functional genes facilitating chemical transformations, our objective was to examine microbiomes in terms of their capacity to process compounds relevant to human health. Here we integrate functional genomics and biochemistry frameworks to derive new quantitative measures of in silico potential for human gut and environmental soil metagenomes to process a panel of major compound classes (e.g., lipids, carbohydrates) and selected biomolecules (e.g., vitamins, short-chain fatty acids) linked to human health. Metagenome functional potential profile data were translated into a universal compound mapping 'landscape' based on bioenergetic van Krevelen mapping of function-level meta-compounds and corresponding functional relative abundances, reflecting imprinted genetic capacity of microbiomes to metabolize an array of different compounds. We show that measures of 'compound processing potential' associated with human health and disease (examining atherosclerotic cardiovascular disease, colorectal cancer, type 2 diabetes and anxious-depressive behavior case studies), and displayed seemingly predictable shifts along gradients of ecological disturbance in plant-soil ecosystems (three case studies). Ecosystem quality explained 60-92 % of variation in soil metagenome compound processing potential measures in a post-mining restoration case study dataset. With growing knowledge of the varying proficiency of environmental microbiota to process human health associated compounds, we might design environmental interventions or nature prescriptions to modulate our exposures, thereby advancing microbiota-oriented approaches to human health. Compound processing potential offers a simplified, integrative approach for applying metagenomics in ongoing efforts to understand and quantify the role of microbiota in environmental- and human-health.

Dynamic response of allelopathic potency of Taxus cuspidata Sieb. et Zucc. mediated by allelochemicals in Ficus carica Linn. root exudates

In a mixed forest, certain plants can release allelochemicals that exert allelopathic effects on neighboring plants, thereby facilitating interspecific coexistence of two species. Previous studies have demonstrated that allelochemicals released from Ficus carica Linn. roots in mixed forest of F. carica and Taxus cuspidata Sieb. et Zucc. has phase characteristics over time, which can improve the soil physicochemical properties, enzyme activity and microbial diversity, thus promoting the growth of T. cuspidata. Based on the irrigation of exogenous allelochemicals, changes in soil fertility (soil physical and chemical properties, soil enzyme activity and soil microelement content) were observed in response to variations in allelochemicals during five phases of irrigation: initial disturbance phase (0-2 d), physiological compensation phase (2-8 d), screening phase (8-16 d), restore phase (16-32 d) and maturity phase (32-64 d), which was consistent with the response of soil microorganisms. The allelopathic response of growth physiological indexes of T. cuspidata, however, exhibited a slight lag behind the soil fertility, with distinct phase characteristics becoming evident on the 4th day following irrigation of allelochemicals. The findings demonstrated that the allelochemicals released by the root of F. carica induced a synergistic effect on soil fertility and microorganisms, thereby facilitating the growth of T. cuspidata. This study provides a comprehensive elucidation of the phased dynamic response-based allelopathic mechanism employed by F. carica to enhance the growth of T. cuspidata, thus establishing a theoretical basis for optimizing forest cultivation through allelopathic pathways.

Bacillus species are core microbiota of resistant maize cultivars that induce host metabolic defense against corn stalk rot

BACKGROUND

Microbes colonizing each compartment of terrestrial plants are indispensable for maintaining crop health. Although corn stalk rot (CSR) is a severe disease affecting maize (Zea mays) worldwide, the mechanisms underlying host-microbe interactions across vertical compartments in maize plants, which exhibit heterogeneous CSR-resistance, remain largely uncharacterized.

RESULTS

Here, we investigated the microbial communities associated with CSR-resistant and CSR-susceptible maize cultivars using multi-omics analysis coupled with experimental verification. Maize cultivars resistant to CSR reshaped the microbiota and recruited Bacillus species with three phenotypes against Fusarium graminearum including niche pre-emption, potential secretion of antimicrobial compounds, and no inhibition to alleviate pathogen stress. By inducing the expression of Tyrosine decarboxylase 1 (TYDC1), encoding an enzyme that catalyzes the production of tyramine and dopamine, Bacillus isolates that do not directly suppress pathogen infection induced the synthesis of berberine, an isoquinoline alkaloid that inhibits pathogen growth. These beneficial bacteria were recruited from the rhizosphere and transferred to the stems but not grains of the CSR-resistant plants.

CONCLUSIONS

The current study offers insight into how maize plants respond to and interact with their microbiome and lays the foundation for preventing and treating soil-borne pathogens. Video Abstract.

Single-cell measurement of microbial growth rate with Raman microspectroscopy

Rates of microbial growth are fundamental to understanding environmental geochemistry and ecology. However, measuring the heterogeneity of microbial activity at the single-cell level, especially within complex populations and environmental matrices, remains a forefront challenge. Stable isotope probing (SIP) is a method for assessing microbial growth and involves measuring the incorporation of an isotopic label into microbial biomass. Here, we assess Raman microspectroscopy as a SIP technique, specifically focusing on the measurement of deuterium (2H), a tracer of microbial biomass production. We correlatively measured cells grown in varying concentrations of deuterated water with both Raman spectroscopy and nanoscale secondary ion mass spectrometry (nanoSIMS), generating isotopic calibrations of microbial 2H. Relative to Raman, we find that nanoSIMS measurements of 2H are subject to substantial dilution due to rapid exchange of H during sample washing. We apply our Raman-derived calibration to a numerical model of microbial growth, explicitly parameterizing the factors controlling growth rate quantification and demonstrating that Raman-SIP can sensitively measure the growth of microorganisms with doubling times ranging from hours to years. The measurement of single-cell growth with Raman spectroscopy, a rapid, nondestructive technique, represents an important step toward application of single-cell analysis into complex sample matrices or cellular assemblages.

Bacteria-Like Gaiella Accelerate Soil Carbon Loss by Decomposing Organic Matter of Grazing Soils in Alpine Meadows on the Qinghai-Tibet Plateau

The alpine meadows of the Qinghai-Tibet Plateau have significant potential for storing soil carbon, which is important to global carbon sequestration. Grazing is a major threat to its potential for carbon sequestration. However, grazing poses a major threat to this potential by speeding up the breakdown of organic matter in the soil and releasing carbon, which may further lead to positive carbon-climate change feedback and threaten ecological security. Therefore, in order to accurately explore the driving mechanism and regulatory factors of soil organic matter decomposition in grazing alpine meadows on the Qinghai-Tibet Plateau, we took the grazing sample plots of typical alpine meadows as the research object and set up grazing intensities of different life cycles, aiming to explore the relationship and main regulatory factors of grazing on soil organic matter decomposition and soil microorganisms. The results show the following: (1) soil microorganisms, especially Acidobacteria and Acidobacteria, drove the decomposition of organic matter in the soil, thereby accelerating the release of soil carbon, which was not conducive to soil carbon sequestration in grassland; (2) the grazing triggering effect formed a positive feedback with soil microbial carbon release, accelerating the decomposition of organic matter and soil carbon loss; and (3) the grazing ban and light grazing were more conducive to slowing down soil organic matter decomposition and increasing soil carbon sequestration.

Genotype-by-genotype interkingdom cross-talk between symbiotic nitrogen fixing Sinorhizobium meliloti strains and Trichoderma species

In the understanding of the molecular interaction between plants and their microbiome, a key point is to identify simplified models of the microbiome including relevant bacterial and fungal partners which could also be effective in plant growth promotion. Here, as proof-of-concept, we aim to identify the possible molecular interactions between symbiotic nitrogen-fixing rhizobia and soil fungi (Trichoderma spp.), hence shed light on synergistic roles rhizospheric fungi could have in the biology of symbiotic nitrogen fixation bacteria. We selected 4 strains of the model rhizobium Sinorhizobium meliloti and 4 Trichoderma species (T. velutinum, T. tomentosum, T. gamsii and T. harzianum). In an experimental scheme of 4 ×4 strains x species combinations, we investigated the rhizobia physiological and transcriptomic responses elicited by fungal spent media, as well as spent media effects on rhizobia-host legume plant (alfalfa, Medicago sativa L.) symbiosis. Fungal spent media had large effects on rhizobia, specific for each fungal species and rhizobial strains combination, indicating a generalized rhizobia genotype x fungal genotype interaction, including synergistic, neutral and antagonistic effects on alfalfa symbiotic phenotypes. Differential expression of a high number of genes was shown in rhizobia strains with up to 25% of total genes differentially expressed upon treatment of cultures with fungal spent media. Percentages over total genes and type of genes differentially expressed changed according to both fungal species and rhizobial strain. To support the hypothesis of a relevant rhizobia genotype x fungal genotype interaction, a nested Likelihood Ratio Test indicated that the model considering the fungus-rhizobium interaction explained 23.4% of differentially expressed genes. Our results provide insights into molecular interactions involving nitrogen-fixing rhizobia and rhizospheric fungi, highlighting the panoply of genes and genotypic interactions (fungus, rhizobium, host plant) which may concur to plant symbiosis.

Plant diversity is more important than soil microbial diversity in explaining soil multifunctionality in Qinghai-Tibetan plateau wetlands

The Qinghai-Tibetan Plateau harbors rich and diverse wetlands that provide multiple ecological functions simultaneously. Although the relationships between biodiversity and wetland functioning have been well studied in recent decades, the links between the multiple features of plant and microbial communities and soil multifunctionality (SMF) remain unknown in the high-altitude wetlands that are extremely sensitive to human disturbance. Here, using the single function, averaging, weighted, and multiple-threshold methods, we calculated the SMF of Qinghai-Tibetan wetlands based on 15 variables associated with soil nutrient status, nutrient cycle, and greenhouse gas emission. We then related SMF to multidimensional (species, phylogenetic, and functional) diversity of plants and soil microorganisms and microbial network modules. The results showed that plant diversity explained more variance in SMF than soil microbial diversity, and plant species richness and phylogenetic distance were positive predictors of SMF. Bacterial network modules were more positively related to SMF than fungal network modules, and the alpha diversity of bacterial network modules contributed more to SMF than the diversity of the whole bacterial community. Pediococcus, Hirsutella, and Rhodotorula were biomarkers for SMF and had significant relationships with nitrogen mineralization and greenhouse gas emissions. Together, these results highlight the importance of plant diversity and bacterial network modules in determining the SMF, which are crucial to predicting the response of ecosystem functioning to biodiversity loss under intensifying anthropogenic activities.

Dual roles of microbes in mediating soil carbon dynamics in response to warming

Understanding the alterations in soil microbial communities in response to climate warming and their controls over soil carbon (C) processes is crucial for projecting permafrost C-climate feedback. However, previous studies have mainly focused on microorganism-mediated soil C release, and little is known about whether and how climate warming affects microbial anabolism and the subsequent C input in permafrost regions. Here, based on a more than half-decade of in situ warming experiment, we show that compared with ambient control, warming significantly reduces microbial C use efficiency and enhances microbial network complexity, which promotes soil heterotrophic respiration. Meanwhile, microbial necromass markedly accumulates under warming likely due to preferential microbial decomposition of plant-derived C, further leading to the increase in mineral-associated organic C. Altogether, these results demonstrate dual roles of microbes in affecting soil C release and stabilization, implying that permafrost C-climate feedback would weaken over time with dampened response of microbial respiration and increased proportion of stable C pool.

Initial Litter Chemistry and UV Radiation Drive Chemical Divergence in Litter during Decomposition

Litter's chemical complexity influences carbon (C) cycling during its decomposition. However, the chemical and microbial mechanisms underlying the divergence or convergence of chemical complexity under UV radiation remain poorly understood. Here, we conducted a 397-day field experiment using 13C cross-polarization magic-angle spinning nuclear magnetic resonance (13C-CPMAS NMR) to investigate the interactions among the initial chemistry, microbial communities, and UV radiation during decomposition. Our study found that the initial concentrations of O-substituted aromatic C, di-O-alkyl C, and O-alkyl C in Deschampsia caespitosa were higher than those in Kobresia tibetica. Litter's chemical composition exhibited divergent patterns based on the initial chemistry, UV radiation, and decay time. Specifically, D. caespitosa consistently displayed higher concentrations of di-O-alkyl C and O-alkyl C compared to K. tibetica, regardless of the UV exposure and decay time. Additionally, litter's chemical complexity was positively correlated with changes in the extracellular enzyme activities, particularly those involved in lignin, cellulose, and hemicellulose degradation, which accounted for 9%, 20%, and 4% of the variation in litter's chemical complexity, respectively. These findings highlighted the role of distinct microbial communities in decomposing different C components through catabolism, leading to chemical divergence in litter. During the early decomposition stages, oligotrophic Planctomycetes and Acidobacteria metabolized O-alkyl C and di-O-alkyl C under UV-blocking conditions. In contrast, copiotrophic Actinobacteria and Chytridiomycota utilized these components under UV radiation exposure, reflecting their ability to thrive under UV stress conditions due to their rapid growth strategies in environments rich in labile C. Our study revealed that the inherent differences in the initial O-alkyl C and di-O-alkyl C contributed to the chemical divergence, while UV radiation further influenced this divergence by shifting the microbial community composition from oligotrophic to copiotrophic species. Thus, differences in the initial litter chemistry, microbial community, and UV radiation affected the quantity and quality of plant-derived C during decomposition.

The Ability of Different Tea Tree Germplasm Resources in South China to Aggregate Rhizosphere Soil Characteristic Fungi Affects Tea Quality

It is generally recognized that the quality differences in plant germplasm resources are genetically determined, and that only a good "pedigree" can have good quality. Ecological memory of plants and rhizosphere soil fungi provides a new perspective to understand this phenomenon. Here, we selected 45 tea tree germplasm resources and analyzed the rhizosphere soil fungi, nutrient content and tea quality. We found that the ecological memory of tea trees for soil fungi led to the recruitment and aggregation of dominant fungal populations that were similar across tea tree varieties, differing only in the number of fungi. We performed continuous simulation and validation to identify four characteristic fungal genera that determined the quality differences. Further analysis showed that the greater the recruitment and aggregation of Saitozyma and Archaeorhizomyces by tea trees, the greater the rejection of Chaetomium and Trechispora, the higher the available nutrient content in the soil and the better the tea quality. In summary, our study presents a new perspective, showing that ecological memory between tea trees and rhizosphere soil fungi leads to differences in plants' ability to recruit and aggregate characteristic fungi, which is one of the most important determinants of tea quality. The artificial inoculation of rhizosphere fungi may reconstruct the ecological memory of tea trees and substantially improve their quality.

Cross-kingdom nutrient exchange in the plant-arbuscular mycorrhizal fungus-bacterium continuum

The association between plants and arbuscular mycorrhizal fungi (AMF) affects plant performance and ecosystem functioning. Recent studies have identified AMF-associated bacteria as cooperative partners that participate in AMF-plant symbiosis: specific endobacteria live inside AMF, and hyphospheric bacteria colonize the soil that surrounds the extraradical hyphae. In this Review, we describe the concept of a plant-AMF-bacterium continuum, summarize current advances and provide perspectives on soil microbiology. First, we review the top-down carbon flow and the bottom-up mineral flow (especially phosphorus and nitrogen) in this continuum, as well as how AMF-bacteria interactions influence the biogeochemical cycling of nutrients (for example, carbon, phosphorus and nitrogen). Second, we discuss how AMF interact with hyphospheric bacteria or endobacteria to regulate nutrient exchange between plants and AMF, and the possible molecular mechanisms that underpin this continuum. Finally, we explore future prospects for studies on the hyphosphere to facilitate the utilization of AMF and hyphospheric bacteria in sustainable agriculture.

Soil bacteriome diversity and composition of rooftop and surface gardens in urban and peri-urban areas of Bangladesh

Soil microbiome science, rapidly evolving, predominantly focuses on field crop soils. However, understanding garden soil microbiomes is essential for enhancing food production sustainability in garden environments. This study aimed to unveil the bacteriome diversity and composition in rooftop garden soils (RGS) and surface garden soils (SGS) across urban (Dhaka North and Dhaka South City Corporations) and peri-urban (Gazipur City Corporation) areas of Dhaka Division, Bangladesh. We analyzed 11 samples, including six RGS and five SGS samples from 11 individual gardens using 16S rRNA (V3-V4 region) gene-based amplicon sequencing. A total of 977 operational taxonomic units (OTUs), including 270 and 707 in RGS and SGS samples, respectively, were identified. The observed OTUs were represented by 21 phyla, 45 classes, 84 orders, 173 families, and 293 genera of bacteria. Alpha diversity indices revealed significantly higher bacterial diversity in SGS samples (p = 0.01), while beta diversity analyses indicated distinct bacteriome compositions between RGS and SGS samples (p = 0.028, PERMANOVA). Despite substantial taxonomic variability between sample categories, there was also a considerable presence of shared bacterial taxa. At the phylum level, Bacilliota (61.14%), Pseudomonadota (23.42%), Actinobacteria (6.33%), and Bacteroidota (3.32%) were the predominant bacterial phyla (comprising > 94.0% of the total abundances) in both types of garden soil samples. Of the identified genera, Bacillus (69.73%) and Brevibacillus (18.81%) in RGS and Bacillus (19.22%), Methylophaga (19.21%), Acinetobacter (6.27%), Corynebacterium (5.06%), Burkholderia (4.78%), Paracoccus (3.98%) and Lysobacter (2.07%) in SGS were the major bacterial genera. Importantly, we detected that 52.90% of genera were shared between RGS and SGS soil samples. Our data reveal unique and shared bacteriomes with probiotic potential in soil samples from both rooftop and surface gardens. Further studies should explore the functional roles of shared bacterial taxa in garden soils and how urban environmental factors affect microbiome composition to optimize soil health and sustainable food production.

Agronomic performance and technological quality of sugarcane submitted to different poultry litter dosages

Sugarcane is a central crop for sugar and ethanol production. Investing in sustainable practices can enhance productivity, technological quality, mitigate impacts, and contribute to a cleaner energy future. Among the factors that help increase the productivity of sugarcane, the physical, chemical and biological parameters of the soil are amongst the most important. The use of poultry litter has been an important alternative for soil improvement, as it acts as a soil conditioner. Therefore, this work aimed to verify the best doses of poultry litter for the vegetative, reproductive and technological components of sugarcane. The experiment was carried out at Usina Denusa Destilaria Nova União S/A in the municipality of Jandaia, GO. The experimental design used was a complete randomized block design with four replications: 5 × 4, totaling 20 experimental units. The evaluated factor consisted of four doses of poultry litter plus the control (0 (control), 2, 4, 6 and 8 t ha-1). In this study, were evaluated the number of tillers, lower stem diameter, average stem diameter, upper stem diameter, plant height, stem weight and productivity. The technological variables of total recoverable sugar, recoverable sugar, Brix, fiber, purity and percentage of oligosaccharides were also evaluated. It was observed, within the conditions of this experiment, that the insertion of poultry litter did not interfere significantly in most biometric, productive and technological variables of the sugarcane. But it can also be inferred that there was a statistical trend toward better results when the sugarcane was cultivated with 4 t ha-1 of poultry litter.

A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts

Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities and interactions with the soil microbiome remains limited. Here we present the Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and composed of 616,935 uncultivated viral genomes and 38,508 unique viral operational taxonomic units. Rarefaction curves from the Global Soil Virus Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared viral operational taxonomic units across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents an extensive characterization of soil viral diversity and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.

Spatial distribution and drivers of arbuscular mycorrhizal fungi on the Tibetan Plateau

Introduction

Arbuscular mycorrhizal fungi (AMF) are pivotal in plant resource acquisition, mediating plant interactions, and influencing soil carbon dynamics. However, their biogeographical distribution in Tibetan alpine grasslands remains understudied.

Methods

In this research, we examined the distribution pattern of AMF communities and their key determinants along a 2000-km transect across the Tibetan plateau, encompassing 7 alpine meadows and 8 alpine steppes.

Results

Our findings indicate that AMF community diversity and composition exhibit similarities between alpine meadows and alpine steppes, primarily influenced by latitude and evapotranspiration. At the genus level, Glomus predominated in both alpine meadow (36.49%±2.67%) and alpine steppe (41.87%±2.36%) soils, followed by Paraglomus (27.14%±3.69%, 32.34%±3.28%). Furthermore, a significant decay relationship of AMF community was observed over geographical distance. Null model analyses revealed that random processes predominantly (>50%) drove the assembly of AMF communities.

Discussion

In summary, our study elucidates the spatial distribution pattern of AMF in Tibetan plateau grasslands and underscores the significant influence of geographical and climatic factors on AMF community dynamics.

Unearthing new learning opportunities: adapting and innovating through the 'Antibiotics under our feet' citizen science project in Scotland during COVID-19

'Antibiotics under our feet' is a Scottish citizen science project that aimed to raise science capital in primary school learners and their teachers through measurement of microbial diversity in urban soil samples in the search for novel antimicrobial compounds. Resistance to antibiotics is rising, posing a global threat to human health. Furthermore, science, technology, engineering and mathematics (STEM) skills are in crisis, jeopardising our capacity to mobilise as a society to fight antimicrobial resistance (AMR). Originally conceived as a response to the AMR and STEM emergencies, our project was hit by the unprecedented challenge of engaging with schools during the COVID-19 pandemic. We describe how we adapted our project to enable remote participation from primary schools and youth groups, utilising COVID-19 response initiatives as opportunities for multi-level co-creation of resources with learners in primary, secondary, and higher education. We produced portable kit boxes for soil sample collection with learning activities and videos linked to the Scottish Curriculum for Excellence. We also addressed glaring project specific content gaps relating to microbiology on English and Simple English Wikipedia. Our hybrid model of working extended our geographical reach and broadened inclusion. We present here the inception, implementation, digital resource outputs, and discussion of pedagogical aspects of 'Antibiotics under our feet'. Our strategies and insights are applicable post-pandemic for educators to develop STEM skills using soil, microbes, and antibiotics as a theme.

Ectomycorrhizal fungi alter soil food webs and the functional potential of bacterial communities

Most of Earth's trees rely on critical soil nutrients that ectomycorrhizal fungi (EcMF) liberate and provide, and all of Earth's land plants associate with bacteria that help them survive in nature. Yet, our understanding of how the presence of EcMF modifies soil bacterial communities, soil food webs, and root chemistry requires direct experimental evidence to comprehend the effects that EcMF may generate in the belowground plant microbiome. To this end, we grew Pinus muricata plants in soils that were either inoculated with EcMF and native forest bacterial communities or only native bacterial communities. We then profiled the soil bacterial communities, applied metabolomics and lipidomics, and linked omics data sets to understand how the presence of EcMF modifies belowground biogeochemistry, bacterial community structure, and their functional potential. We found that the presence of EcMF (i) enriches soil bacteria linked to enhanced plant growth in nature, (ii) alters the quantity and composition of lipid and non-lipid soil metabolites, and (iii) modifies plant root chemistry toward pathogen suppression, enzymatic conservation, and reactive oxygen species scavenging. Using this multi-omic approach, we therefore show that this widespread fungal symbiosis may be a common factor for structuring soil food webs.IMPORTANCEUnderstanding how soil microbes interact with one another and their host plant will help us combat the negative effects that climate change has on terrestrial ecosystems. Unfortunately, we lack a clear understanding of how the presence of ectomycorrhizal fungi (EcMF)-one of the most dominant soil microbial groups on Earth-shapes belowground organic resources and the composition of bacterial communities. To address this knowledge gap, we profiled lipid and non-lipid metabolites in soils and plant roots, characterized soil bacterial communities, and compared soils amended either with or without EcMF. Our results show that the presence of EcMF changes soil organic resource availability, impacts the proliferation of different bacterial communities (in terms of both type and potential function), and primes plant root chemistry for pathogen suppression and energy conservation. Our findings therefore provide much-needed insight into how two of the most dominant soil microbial groups interact with one another and with their host plant.

Recruitment and Aggregation Capacity of Tea Trees to Rhizosphere Soil Characteristic Bacteria Affects the Quality of Tea Leaves

There are obvious differences in quality between different varieties of the same plant, and it is not clear whether they can be effectively distinguished from each other from a bacterial point of view. In this study, 44 tea tree varieties (Camellia sinensis) were used to analyze the rhizosphere soil bacterial community using high-throughput sequencing technology, and five types of machine deep learning were used for modeling to obtain characteristic microorganisms that can effectively differentiate different varieties, and validation was performed. The relationship between characteristic microorganisms, soil nutrient transformation, and tea quality formation was further analyzed. It was found that 44 tea tree varieties were classified into two groups (group A and group B) and the characteristic bacteria that distinguished them came from 23 genera. Secondly, the content of rhizosphere soil available nutrients (available nitrogen, available phosphorus, and available potassium) and tea quality indexes (tea polyphenols, theanine, and caffeine) was significantly higher in group A than in group B. The classification result based on both was consistent with the above bacteria. This study provides a new insight and research methodology into the main reasons for the formation of quality differences among different varieties of the same plant.

Conceptualizing soil fauna effects on labile and stabilized soil organic matter

Fauna is highly abundant and diverse in soils worldwide, but surprisingly little is known about how it affects soil organic matter stabilization. Here, we review how the ecological strategies of a multitude of soil faunal taxa can affect the formation and persistence of labile (particulate organic matter, POM) and stabilized soil organic matter (mineral-associated organic matter, MAOM). We propose three major mechanisms - transformation, translocation, and grazing on microorganisms - by which soil fauna alters factors deemed essential in the formation of POM and MAOM, including the quantity and decomposability of organic matter, soil mineralogy, and the abundance, location, and composition of the microbial community. Determining the relevance of these mechanisms to POM and MAOM formation in cross-disciplinary studies that cover individual taxa and more complex faunal communities, and employ physical fractionation, isotopic, and microbiological approaches is essential to advance concepts, models, and policies focused on soil organic matter and effectively manage soils as carbon sinks, nutrient stores, and providers of food.

Long-term vegetation restoration promotes lignin phenol preservation and microbial anabolism in forest plantations: Implications for soil organic carbon dynamics

Vegetation restoration contributes to soil organic carbon (C; SOC) sequestration through the accumulation of plant and microbial residues, but the mechanisms underlying this microbially mediated process are not well resolved. To depict the dynamics of plant- and microbial-derived C in restored forest ecosystems, soil samples were collected from Robinia pseudoacacia plantations of different stand ages (15, 25, 35, 45 years old) established on degraded wheat fields. The results showed that the degree of lignin phenol oxidation decreased with increasing stand age (P < 0.05), and hemicellulose-degrading genes were detected at higher relative abundances than other functional gene categories, indicating selective preservation of recalcitrant lignin phenols. Despite both glucosamine (R2 = 0.61, P < 0.001) and muramic acid (R2 = 0.37, P < 0.001) contents trending upward over time, fungal residual C accounted for a greater proportion of SOC compared with bacterial residual C. Accordingly, fungal residual C, which exhibited a similar response pattern as total microbial residual C to vegetation restoration, was considered a major contributor to the SOC pool. These results provided evidence that long-term vegetation restoration enhanced SOC sequestration in R. pseudoacacia forest by promoting the preservation of plant-derived lignin phenols and concomitant microbial anabolism. Partial least squares-discriminant analysis identified two important ecological clusters (i.e., modules) in the fungal network that profoundly influenced lignin phenol oxidation (P < 0.05) and microbial residual C accumulation (P < 0.01). Among the dominant taxa in microbial networks, the bacterial phyla Proteobacteria and Acidobacteriota had potential to degrade recalcitrant C compounds (e.g., cellulose, lignin), whereas the fungal phylum Ascomycota could outcompete for labile C fractions (e.g., dissolved organic C). Findings of this study can enable a mechanistic understanding of SOC stability driven by microbial turnover in restored forest ecosystems.

Species-specific predation determines the feeding impacts of six soil protist species on bacterial and eukaryotic prey

Predatory protists play a central role in nutrient cycling and are involved in other ecosystem functions by predating the microbiome. While most soil predatory protist species arguably are bacterivorous, some protist species can prey on eukaryotes. However, studies about soil protist feeding mainly focused on bacteria as prey and rarely tested both bacteria and eukaryotes as potential prey. In this study, we aimed to decipher soil predator-prey interactions of three amoebozoan and three heterolobosean soil protists and potential bacterial (Escherichia coli; 0.5-1.5 µm), fungal (Saccharomyces cerevisiae; 5-7 µm) and protist (Plasmodiophora brassicae; 3-5 µm) prey, either as individual prey or in all their combinations. We related protist performance (relative abundance) and prey consumption (qPCR) to the protist phylogenetic group and volume. We showed that for the six soil protist predators, the most suitable prey was E. coli, but some species also grew on P. brassicae or S. cerevisiae. While protist relative abundances and growth rates depended on prey type in a protist species-specific manner, phylogenetic groups and volume affected prey consumption. Yet we conclude that protist feeding patterns are mainly species-specific and that some known bacterivores might be more generalist than expected, even preying on eukaryotic plant pathogens such as P. brassicae.