Direct evidence for the role of microbial community composition in the formation of soil organic matter composition and persistence

Arbuscular mycorrhiza convey significant plant carbon to a diverse hyphosphere microbial food web and mineral-associated organic matter

Arbuscular mycorrhizal fungi (AMF) transport substantial plant carbon (C) that serves as a substrate for soil organisms, a precursor of soil organic matter (SOM), and a driver of soil microbial dynamics. Using two-chamber microcosms where an air gap isolated AMF from roots, we 13CO2-labeled Avena barbata for 6 wk and measured the C Rhizophagus intraradices transferred to SOM and hyphosphere microorganisms. NanoSIMS imaging revealed hyphae and roots had similar 13C enrichment. SOM density fractionation, 13C NMR, and IRMS showed AMF transferred 0.77 mg C g-1 of soil (increasing total C by 2% relative to non-mycorrhizal controls); 33% was found in occluded or mineral-associated pools. In the AMF hyphosphere, there was no overall change in community diversity but 36 bacterial ASVs significantly changed in relative abundance. With stable isotope probing (SIP)-enabled shotgun sequencing, we found taxa from the Solibacterales, Sphingobacteriales, Myxococcales, and Nitrososphaerales (ammonium oxidizing archaea) were highly enriched in AMF-imported 13C (> 20 atom%). Mapping sequences from 13C-SIP metagenomes to total ASVs showed at least 92 bacteria and archaea were significantly 13C-enriched. Our results illustrate the quantitative and ecological impact of hyphal C transport on the formation of potentially protective SOM pools and microbial roles in the AMF hyphosphere soil food web.

Soil bacterial community characteristics and its effect on organic carbon under different fertilization treatments

Introduction

By implementing small-scale and efficient fertilization techniques, it is possible to enhance the activity of microorganisms, thereby improving soil carbon sequestration and ecological value in agriculture.

Methods

In this study, field experiments were conducted using various types of fertilizers: organic fertilizer, microbial fungal fertilizer, composite fertilizer, and an unfertilized control (CK). Additionally, different dosages of compound fertilizers were applied, including 0.5 times compound fertilizers, constant compound fertilizers, 1.5 times compound fertilizers and CK. Using advanced technologies such as Illumina MiSeq high-throughput sequencing, PICRUSt2 prediction, Anosim analysis, redundancy analysis, canonical correlation analysis, and correlation matrix, soil organic carbon (SOC) content and components, bacterial diversity, metabolic functions, and interaction mechanisms were examined in different fields.

Results and Discussion

The results showed pronounced effects of various fertilization modes on SOC and the bacterial community, particularly in the topsoil layer (0-20 cm). Organic fertilizer treatments increased the richness and diversity of bacterial communities in the soil. However, conventional doses and excessive application of compound fertilizers reduced the diversity of soil bacterial communities and SOC content. Additionally, different fertilization treatments led to an increase in easily oxidizable organic carbon (EOC) contents. Interestingly, the relationship between SOC components and soil bacteria exhibited inconsistency. EOC was positively correlated with the bacterial diversity index. Additionally, Chloroflexi exhibited a negative correlation with both SOC and its components. The influence of metabolismon primary metabolic functions on the content of SOC components in the soil was more notable. It included seven types of tertiary functional metabolic pathways significantly correlated with SOC components (p < 0.05).

Purpose and Significance

These findings enhance the understanding of the relative abundance of bacterial communities, particularly those related to the carbon cycle, by adjusting agricultural fertilization patterns. This adjustment serves as a reference for enhancing carbon sinks and reducing emissions in agricultural soils.

Microbial perspective of inhibited carbon turnover in Tangel humus of the Northern Limestone Alps

Tangel humus primarily occurs in montane and subalpine zones of the calcareous Alps that exhibit low temperatures and high precipitation sums. This humus form is characterized by inhibited carbon turnover and accumulated organic matter, leading to the typical thick organic layers. However, the reason for this accumulation of organic matter is still unclear, and knowledge about the microbial community within Tangel humus is lacking. Therefore, we investigated the prokaryotic and fungal communities along with the physical and chemical properties within a depth gradient (0-10, 10-20, 20-30, 30-40, 40-50 cm) of a Tangel humus located in the Northern Limestone Alps. We hypothesized that humus properties and microbial activity, biomass, and diversity differ along the depth gradient and that microbial key players refer to certain humus depths. Our results give the first comprehensive information about microbiota within the Tangel humus and establish a microbial zonation of the humus. Microbial activity, biomass, as well as microbial alpha diversity significantly decreased with increasing depths. We identified microbial biomarkers for both, the top and the deepest depth, indicating different, microbial habitats. The microbial characterization together with the established nutrient deficiencies in the deeper depths might explain reduced C-turnover and Tangel humus formation.

Transport Behavior of Cd2+ in Highly Weathered Acidic Soils and Shaping in Soil Microbial Community Structure

The mining and smelting site soils in South China present excessive Cd pollution. However, the transport behavior of Cd in the highly weathered acidic soil layer at the lead-zinc smelting site remains unclear. Here, under different conditions of simulated infiltration, the migration behavior of Cd2+ in acid smelting site soils at different depths was examined. The remodeling effect of Cd2+ migration behavior on microbial community structure and the dominant microorganisms in lead-zinc sites soils was analyzed using high-throughput sequencing of 16S rRNA gene amplicons. The results revealed a specific flow rate in the range of 0.3-0.5 mL/min that the convection and dispersion have no obvious effect on Cd2+ migration. The variation of packing porosity could only influence the migration behavior by changing the average pore velocity, but cannot change the adsorption efficiency of soil particles. The Cd has stronger migration capacity under the reactivation of acidic seepage fluid. However, in the alkaline solution, the physical properties of soil, especially pores, intercept the Cd compounds, further affecting their migration capacity. The acid-site soil with high content of SOM, amorphous Fe oxides, crystalline Fe/Mn/Al oxides, goethite, and hematite has stronger ability to adsorb and retain Cd2+. However, higher content of kaolinite in acidic soil will increase the potential migration of Cd2+. Besides, the migration behavior of Cd2+ results in simplified soil microbial communities. Under Cd stress, Cd-tolerant genera (Bacteroides, Sphingomonas, Bradyrhizobium, and Corynebacterium) and bacteria with both acid-Cd tolerance (WCHB 1-84) were distinguished. The Ralstonia showed a high enrichment degree in alkaline Cd2+ infiltration solution (pH 10.0). Compared to the influence of Cd2+ stress, soil pH had a stronger ability to shape the microbial community in the soil during the process of Cd2+ migration.

The mechanism of microbial community succession and microbial co-occurrence network in soil with compost application

The application of organic and chemical fertilizer into soil can regulate microbial communities. However, the response mechanism of microbial communities in soil to compost and chemical fertilizer application remain unclear. In this study, compost made of tobacco leaves individually and combined with chemical fertilizer was applied, respectively, to investigate their effect on soil microorganisms during the pot-culture process. High-throughput sequence, neutral community model and null model were employed to clarify how soil microbial community respond to the application of compost and chemical fertilizer. Furthermore, random forest model was applied to predict the relationships between the plant agronomical traits and the soil microorganism during the pot-culture process. The results demonstrated that the simultaneous application of compost and chemical fertilizer increased significantly the richness and diversity of the microorganisms in soil (p < 0.05), groups C and D led to a significant reduction in the number of nodes and edges in the microbial network (77.78 %-96.57 %). The dominant bacteria in the application of 50 g fertilizer accounted for the highest proportion (40 %) and organic matter was the main factors driving the change in bacterial communities. Compared to the tilled soil, the microbial communities of the soil with the simultaneous application of compost and chemical fertilizer were more susceptible to stochastic processes, and soil microorganisms had less influence on the growth of crops during pot-culture. In conclusion, the simultaneous application of compost and fertilizer altered the ecological functions of soil microbial communities, leading to an enhanced stochastic process of community formation.

Metagenomics reveals the effects of glyphosate on soil microbial communities and functional profiles of C and P cycling in the competitive vegetation control process of Chinese fir plantation

Although considerable efforts have been devoted to investigate the behavior of glyphosate on microbiome in various environment, knowledge about the soil microbial community and functional profile in weeds control process of the Chinese fir plantation are limited. In this study, shotgun metagenomic sequencing was used to determine the abundance and diversity of microbial communities and functional genes after foliar application of glyphosate for 1, 2, 3 and 4 months in a Chinese fir plantation. The results showed that glyphosate increased the copy numbers (qPCR) of 16S rRNA gene for 16.9%, improved the bacterial diversity (Shannon index) and complexity of bacterial co-occurrence network, and changed the abundances of some bacterial and fungal taxa, but had no effects on ITS gene copy numbers, fungal Shannon index, and bacterial and fungal communities (PCoA). Glyphosate application significantly decreased the amount of microbial function potentials involved in organic P mineralization for 10.7%, chitin degradation for 13.1%, and CAZy gene families with an exception of PL for 11.5% at the first month, while did not affect the profile of microbial genes response to P and C cycling in longer term. In addition, glyphosate reduced the contents of soil TOC, DOC and NH4+-H for 17.6%, 52.3% and 44.6% respectively, and decreased the starch, soluble sugar, Zn and Fe of Chinese fir leaves for 20.6%, 19.8%, 32.8% and 48.4% respectively. Mantle test, Spearman's correlation, and PLS-PM model revealed the connections among soil properties, tree nutrients, bacterial and fungal communities, and microbial function potentials were influenced by glyphosate. While our findings need to be validated in other filed and mechanistic studies, they may indicate that the foliar application of glyphosate has a potential effect on Chinese fir seedlings, and this effect may contribute to the changes of the bacterial community and soil properties including AN, DON and NH4+-H.

Effects of different types of vegetation cover on soil microorganisms and humus characteristics of soda-saline land in the Songnen Plain

Introduction

In the soda-saline grasslands of the Songnen Plain, Jilin Province, China, the prohibition of grazing has led to significant changes in plant communities and soil properties. However, the intricate interplay between soil physical and chemical attributes, the soil microbial community, and their combined influence on soil humus composition remains poorly understood.

Methods

Our study aimed to evaluate the impact of natural vegetation restoration on soil properties, microbial community diversity, and composition in the soda-saline soil region of the Songnen Plain. We conducted assessments of soil physical and chemical properties, analyzed community diversity, and composition at a soil depth range of 0-20 cm. The study covered soils with dominant soda-saline vegetation species, including Suaeda glauca Bunge, Puccinellia chinampoensis Ohwi, Chloris virgata Swarta, Phragmites australis (Clay.), Leymus chinensis (Trin.), and Tzvelev. We compared these vegetated soils to bare land devoid of any plants.

Results

We found that soil organic content (SOC) in vegetation restoration areas was higher than in bare land, with SOC content varying between 3.64 and 11.15 g/kg in different vegetated areas. Notably, soil pH emerged as a pivotal factor, explaining 11.4% and 12.2% of the variance in soil bacteria and fungi, respectively. There were correlations between SOC content and the relative abundance of specific microbial groups, with Acidobacteria and Mortierella showing a positive correlation, while Actinobacteria, Gemmatimonadetes, and Ascomycota exhibited significant negative correlations with SOC.

Discussion

The disparities in SOC composition and content among the soda-saline vegetation types were primarily attributed to variations in pH. Consequently, reducing soil pH is identified as a critical step in the process of vegetation restoration in soda-saline land. Prohibiting grazing has the potential to increase soda-saline SOC content and enhance microbial diversity, with Leymus chinensis and Phragmites australis showing particularly promising results in terms of higher SOC carbon content and microbial diversity.

Investigating the eco-evolutionary response of microbiomes to environmental change

Microorganisms are the primary engines of biogeochemical processes and foundational to the provisioning of ecosystem services to human society. Free-living microbial communities (microbiomes) and their functioning are now known to be highly sensitive to environmental change. Given microorganisms' capacity for rapid evolution, evolutionary processes could play a role in this response. Currently, however, few models of biogeochemical processes explicitly consider how microbial evolution will affect biogeochemical responses to environmental change. Here, we propose a conceptual framework for explicitly integrating evolution into microbiome-functioning relationships. We consider how microbiomes respond simultaneously to environmental change via four interrelated processes that affect overall microbiome functioning (physiological acclimation, demography, dispersal and evolution). Recent evidence in both the laboratory and the field suggests that ecological and evolutionary dynamics occur simultaneously within microbiomes; however, the implications for biogeochemistry under environmental change will depend on the timescales over which these processes contribute to a microbiome's response. Over the long term, evolution may play an increasingly important role for microbially driven biogeochemical responses to environmental change, particularly to conditions without recent historical precedent.

Abiotic and Biotic Drivers of Soil Fungal Communities in Response to Dairy Manure Amendment

Modern agriculture often relies on large inputs of synthetic fertilizers to maximize crop yield potential, yet their intensive use has led to nutrient losses and impaired soil health. Alternatively, manure amendments provide plant available nutrients, build organic carbon, and enhance soil health. However, we lack a clear understanding of how consistently manure impacts fungal communities, the mechanisms via which manure impacts soil fungi, and the fate of manure-borne fungi in soils. We assembled soil microcosms using five soils to investigate how manure amendments impact fungal communities over a 60-day incubation. Further, we used autoclaving treatments of soils and manure to determine if observed changes in soil fungal communities were due to abiotic or biotic properties, and if indigenous soil communities constrained colonization of manure-borne fungi. We found that manure amended soil fungal communities diverged from nonamended communities over time, often in concert with a reduction in diversity. Fungal communities responded to live and autoclaved manure in a similar manner, suggesting that abiotic forces are primarily responsible for the observed dynamics. Finally, manure-borne fungi declined quickly in both live and autoclaved soil, indicating that the soil environment is unsuitable for their survival. IMPORTANCE Manure amendments in agricultural systems can impact soil microbial communities via supplying growth substrates for indigenous microbes or by introducing manure-borne taxa. This study explores the consistency of these impacts on soil fungal communities and the relative importance of abiotic and biotic drivers across distinct soils. Different fungal taxa responded to manure among distinct soils, and shifts in soil fungal communities were driven largely by abiotic factors, rather than introduced microbes. This work demonstrates that manure may have inconsistent impacts on indigenous soil fungi, and that abiotic properties of soils render them largely resistant to invasion by manure-borne fungi.

Rhizospheric soil organic carbon accumulated but its molecular groups redistributed via rhizospheric soil microorganisms along multi-root Cerasus humilis plantation chronosequence at the karst rocky desertification control area

Though the relationships between the microorganism communities and the edaphic factors in rhizosphere soil along the plantation chronosequence have been widely reported, few researches have appeared on the interrelationship about rhizospheric soil microorganism community and soil organic carbon (SOC) under multi-root Cerasus humilis plantations of different age. In our study, the rhizospheric soil microbial communities, soil physicochemistry, and SOC molecular groups in plantations of 1-, 3-, and 5-year-old Cerasus humilis were investigated in karst rocky desertification control area of southwest China. It was found that karst rhizospheric soil moisture, total nitrogen, available potassium, and 46-60 ppm N-alkyl/methoxyl C decreased; however, SOC and fungal:bacterial ratio decreased along multi-root Cerasus humilis plantation chronosequence. Proteobacteria, Actinobacteriota, Acidobacteriota, and Ascomycota were recognized as the top 4 phyla in the karst rhizospheric soil microbial co-occurrence network. Moreover, Cerasus humilis plantations exerted significantly direct effect on rhizospheric soil microbial communities and soil physicochemical properties exerted significantly direct effects on SOC molecular groups. Our results suggested that the increased Cerasus humilis plantation years will promote C sequestration (e.g., SOC) with the continued input of root litter, root exudates, and plant litter. The inputted and activated C can be preferentially consumed by rhizospheric soil microorganisms and converted into microbial-derived compounds, which are finally incorporated into recalcitrant SOC pools. Hence, Cerasus humilis redistributed SOC molecular groups via rhizospheric soil microorganisms, and increased ratio of fungi:bacteria in rhizosphere was associated with C sequestration which could not be regarded as a widespread rule. Though our study is the first attempt to recognize the interaction between rhizospheric soil microbial community and SOC molecular groups at the karst rocky desertification control area, it provides a baseline for further research that ecological restoration can promote soil C sequestration via soil microorganisms in the early period of eco-restoration at karst area.

Mini-review: Current and Future Perspectives on Microbially Focused Restoration Strategies in Tallgrass Prairies

Ecosystem restoration is a critical conservation strategy, especially for increasing resilience and resistance to climate change. Current restoration efforts that convert reclaimed agricultural land to native tallgrass prairies typically focus on aboveground communities, but it can take decades to restore soil microbial biodiversity and function using these strategies, if they recover at all. This incomplete restoration can have detrimental impacts on longer-term restoration goals, such as supporting late-successional plant species and facilitating soil carbon sequestration. Soil microorganisms are key components in determining the fate of organic material that enters the soil. They mediate decomposition rates and contribute to plant-microbe-soil interactions, produce microbial biomass, necromass, and metabolic products, and physically protect soil carbon through aggregation. Interactions with plants and controls over soil carbon vary widely depending on the specific microbial taxa present, their physiology, their functional capabilities, and their responses to environmental stressors. Thus, the ability for new restorations, prairie conservation corridors, and prairies planted in marginal lands to act as carbon sinks and help balance greenhouse gas emissions can depend on the success of microbial restoration. Next-generation sequencing approaches can support novel methods for evaluating existing restoration practices and developing microbially focused management strategies. This review summarizes the growing body of literature describing microbially focused tallgrass prairie restoration and considers when and how integrating next-generation sequencing approaches into management efforts can be beneficial. We provide a roadmap for future restoration efforts where microbial ecologists, restoration ecologists, and land managers can work together to meet their goals to promote climate-ready restored ecosystems.

Changes of Soil Dissolved Organic Matter and Its Relationship with Microbial Community along the Hailuogou Glacier Forefield Chronosequence

Glacier-retreated areas are ideal areas to study soil biogeochemical processes during vegetation succession, because of the limited effect of other environmental and climatic factors. In this study, the changes of soil dissolved organic matter (DOM) and its relationship with microbial communities along the Hailuogou Glacier forefield chronosequence were investigated. Both microbial diversity and DOM molecular chemodiversity recovered rapidly at the initial stage, indicating the pioneering role of microorganisms in soil formation and development. The chemical stability of soil organic matter enhanced with vegetation succession due to the retaining of compounds with high oxidation state and aromaticity. The molecular composition of DOM affected microbial communities, while microorganisms tended to utilize labile components to form refractory components. This complex relationship network between microorganisms and DOM components played an important role in the development of soil organic matter as well as the formation of stable soil carbon pool in glacier-retreated areas.

Environmental implication of MoS2 nanosheets: Effects on maize plant growth and soil microorganisms

Molybdenum disulfide (MoS₂) nanosheets have been used extensively in a variety of fields including medical and industrial. However, little is known about their toxicity effects, especially to edible plants. In this greenhouse study, maize (Zea mays) seedlings were exposed for 4 weeks, through the soil route, to 10 and 100 mg/kg of 2H MoS₂ nanosheets. Plant growth, physiological parameters (chlorophyll, antioxidants, and MDA), along with Mo and nutrient element contents were determined in plant tissues. Results showed that at both doses, the nanosheets decreased plant growth. Inductively coupled plasma-mass spectrometry data also showed that both 2H MoS₂ concentrations allowed Mo absorption and translocation by maize plants. Additionally, at 100 mg/kg the nanosheets significantly reduced Ca, Mg, Mn, and Zn in leaves, and Na in roots. Gene sequencing data of 16S rRNA showed, that MoS₂ nanosheets changed the soil microbial community structure, compared with the untreated control. In addition, nitrogen-fixing microorganisms such as Burkholderiales, Rhizobiales and Xanthobacteraceae were enriched. Overall, the data suggest that, even at low dose (10 mg/kg), the 2H MoS₂ nanosheets perturbed both the nutrient uptake by maize plants and the soil microbial communities.

Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils

The advance of high-throughput molecular biology tools allows in-depth profiling of microbial communities in soils, which possess a high diversity of prokaryotic microorganisms. Amplicon-based sequencing of 16S rRNA genes is the most common approach to studying the richness and composition of soil prokaryotes. To reliably detect different taxonomic lineages of microorganisms in a single soil sample, an adequate pipeline including DNA isolation, primer selection, PCR amplification, library preparation, DNA sequencing, and bioinformatic post-processing is required. Besides DNA sequencing quality and depth, the selection of PCR primers and PCR amplification reactions arguably have the largest influence on the results. This study tested the performance and potential bias of two primer pairs, i.e., 515F (Parada)-806R (Apprill) and 515F (Parada)-926R (Quince) in the standard pipelines of 16S rRNA gene Illumina amplicon sequencing protocol developed by the Earth Microbiome Project (EMP), against shotgun metagenome-based 16S rRNA gene reads. The evaluation was conducted using five differently managed soils. We observed a higher richness of soil total prokaryotes by using reverse primer 806R compared to 926R, contradicting to in silico evaluation results. Both primer pairs revealed various degrees of taxon-specific bias compared to metagenome-derived 16S rRNA gene reads. Nonetheless, we found consistent patterns of microbial community variation associated with different land uses, irrespective of primers used. Total microbial communities, as well as ammonia oxidizing archaea (AOA), the predominant ammonia oxidizers in these soils, shifted along with increased soil pH due to agricultural management. In the unmanaged low pH plot abundance of AOA was dominated by the acid-tolerant NS-Gamma clade, whereas limed agricultural plots were dominated by neutral-alkaliphilic NS-Delta/NS-Alpha clades. This study stresses how primer selection influences community composition and highlights the importance of primer selection for comparative and integrative studies, and that conclusions must be drawn with caution if data from different sequencing pipelines are to be compared.

Impact of twenty pesticides on soil carbon microbial functions and community composition

Pesticides are known to affect non-targeted soil microorganisms. Still, studies comparing the effect of multiple pesticides on a wide range of microbial endpoints associated with carbon cycling are scarce. Here, we employed fluorescence enzymatic assay and real-time PCR to evaluate the effect of 20 commercial pesticides, applied at their recommended dose and five times their recommended dose, on soil carbon cycling related enzymatic activities (α-1,4-glucosidase, β-1,4-glucosidase, β-d-cellobiohydrolase and β-xylosidase), and on the absolute abundance of functional genes (cbhl and chiA), in three different South Australian agricultural soils. The effects on cellulolytic and chitinolytic microorganisms, and the total microbial community composition were determined using shotgun metagenomic sequencing in selected pesticide-treated and untreated samples. The application of insecticides significantly increased the cbhl and chiA genes absolute abundance in the acidic soil. At the community level, insecticide fipronil had the greatest stimulating effect on cellulolytic and chitinolytic microorganisms, followed by fungicide metalaxyl-M and insecticide imidacloprid. A shift towards a fungal dominated microbial community was observed in metalaxyl-M treated soil. Overall, our results suggest that the application of pesticides might affect the soil carbon cycle and may disrupt the formation of soil organic matter and structure stabilisation.

Tracing Carbon Metabolism with Stable Isotope Metabolomics Reveals the Legacy of Diverse Carbon Sources in Soil

Carbon metabolism in soil remains poorly described due to the inherent difficulty of obtaining information on the microbial metabolites produced by complex soil communities. Our study demonstrates the use of stable isotope probing (SIP) to study carbon metabolism in soil by tracking 13 C from supplied carbon sources into metabolite pools and biomass.

Plant biodiversity promotes sustainable agriculture directly and via belowground effects

While the positive relationship between plant biodiversity and ecosystem functioning (BEF) is well established, the extent to which this is mediated via belowground microbial processes is poorly understood. Growing evidence suggests that plant community structure influences soil microbial diversity, which in turn promotes functions desired for sustainable agriculture. Here, we outline the 'plant-directed' and soil microbe-mediated mechanisms expected to promote positive BEF. We identify how this knowledge can be utilized in plant diversification schemes to maximize ecosystem functioning in agroecosystems, which are typically species poor and sensitive to biotic and abiotic stressors. In the face of resource overexploitation and global change, bridging the gaps between biodiversity science and agricultural practices is crucial to meet food security in the Anthropocene.