Composition Of Soil Microbiome Research Articles

The Impact of Climate Change on Immunity and Gut Microbiota in the Development of Disease.

According to the definition provided by the United Nations, "climate change" describes the persistent alterations in temperatures and weather trends. These alterations may arise naturally, such as fluctuations in the solar cycle. Nonetheless, since the 19th century, human activities have emerged as the primary agent for climate change, primarily attributed to the combustion of fossil fuels such as coal, oil, and gas. Climate change can potentially influence the well-being, agricultural production, housing, safety, and employment opportunities for all individuals. The immune system is an important interface through which global climate change affects human health. Extreme heat, weather events and environmental pollutants could impair both innate and adaptive immune responses, promoting inflammation and genomic instability, and increasing the risk of autoimmune and chronic inflammatory diseases. Moreover, climate change has an impact on both soil and gut microbiome composition, which can further explain changes in human health outcomes. This narrative review aims to explore the influence of climate change on human health and disease, focusing specifically on its effects on the immune system and gut microbiota. Understanding how these factors contribute to the development of physical and mental illness may allow for the design of strategies aimed at reducing the negative impact of climate and pollution on human health.

Shifts in structure and dynamics of the soil microbiome in biofuel/fuel blend-affected areas triggered by different bioremediation treatments.

The use of biofuels has grown in the last decades as a consequence of the direct environmental impacts of fossil fuel use. Elucidating structure, diversity, species interactions, and assembly mechanisms of microbiomes is crucial for understanding the influence of environmental disturbances. However, little is known about how contamination with biofuel/petrofuel blends alters the soil microbiome. Here, we studied the dynamics in the soil microbiome structure and composition of four field areas under long-term contamination with biofuel/fossil fuel blends (ethanol 10% and gasoline 90%-E10; ethanol 25% and gasoline 75%-E25; soybean biodiesel 20% and diesel 80%-B20) submitted to different bioremediation treatments along a temporal gradient. Soil microbiomes from biodiesel-polluted areas exhibited higher richness and diversity index values and more complex microbial communities than ethanol-polluted areas. Additionally, monitored natural attenuation B20-polluted areas were less affected by perturbations caused by bioremediation treatments. As a consequence, once biostimulation was applied, the degradation was slower compared with areas previously actively treated. In soils with low diversity and richness, the impact of bioremediation treatments on the microbiomes was greater, and as a result, the hydrocarbon degradation extent was higher. The network analysis showed that all abundant keystone taxa corresponded to well-known degraders, suggesting that the abundant species are core targets for biostimulation in soil remediation processes. Altogether, these findings showed that the knowledge gained through the study of microbiomes in contaminated areas may help design and conduct optimized bioremediation approaches, paving the way for future rationalized and efficient pollutant mitigation strategies.

Defensive alteration of root exudate composition by grafting Prunus sp. onto resistant rootstock contributes to reducing crown gall disease.

Grafting is a traditional and significant strategy to suppress soil-borne diseases, such as the crown gall disease caused by tumorigenic Agrobacterium and Rhizobium. Root exudates and the rhizosphere microbiome play critical roles in controlling crown gall disease, but their roles in suppressing crown gall disease in grafted plants remain unclear. Here, disease-susceptible cherry rootstock 'Gisela 6' and disease-resistant cherry rootstock 'Haiying 1' were grafted onto each other or self-grafted. The effect of their root exudates on the soil microbiome composition and the abundance of pathogenic Agrobacterium were studied. Grafting onto the disease-resistant rootstock helped to reduce the abundance of pathogenic Agrobacterium, accompanied by altering root exudation, enriching potential beneficial bacteria, and changing soil function. Then, the composition of the root exudates from grafted plants was analyzed and the potential compounds responsible for decreasing pathogenic Agrobacterium abundance were identified. Based on quantitative measurement of the concentrations of the compounds and testing the impacts of supplied pure chemicals on abundance and chemotaxis of pathogenic Agrobacterium and potential beneficial bacteria, the decreased valine in root exudates of the plant grafted onto resistant rootstock was found to contribute to decreasing Agrobacterium abundance, enriching some potential beneficial bacteria and suppressing crown gall disease. This study provides insights into the mechanism whereby grafted plants suppress soil-borne disease.

Single and combined effects of secondary polyethylene microplastic on the growth of Pak choi and the soil microbiome composition

Single and combined effects of secondary polyethylene microplastic on the growth of Pak choi and the soil microbiome composition

Soil microbiome feedbacks during disturbance-driven forest ecosystem conversion.

Disturbances cause rapid changes to forests, with different disturbance types and severities creating unique ecosystem trajectories that can impact the underlying soil microbiome. Pile burning-the combustion of logging residue on the forest floor-is a common fuel reduction practice that can have impacts on forest soils analogous to those following high-severity wildfire. Further, pile burning following clear-cut harvesting can create persistent openings dominated by nonwoody plants surrounded by dense regenerating conifer forest. A paired 60-year chronosequence of burn scar openings and surrounding regenerating forest after clear-cut harvesting provides a unique opportunity to assess whether belowground microbial processes mirror aboveground vegetation during disturbance-induced ecosystem shifts. Soil ectomycorrhizal fungal diversity was reduced the first decade after pile burning, which could explain poor tree seedling establishment and subsequent persistence of herbaceous species within the openings. Fine-scale changes in the soil microbiome mirrored aboveground shifts in vegetation, with short-term changes to microbial carbon cycling functions resembling a postfire microbiome (e.g. enrichment of aromatic degradation genes) and respiration in burn scars decoupled from substrate quantity and quality. Broadly, however, soil microbiome composition and function within burn scar soils converged with that of the surrounding regenerating forest six decades after the disturbances, indicating potential microbial resilience that was disconnected from aboveground vegetation shifts. This work begins to unravel the belowground microbial processes that underlie disturbance-induced ecosystem changes, which are increasing in frequency tied to climate change.

New perspectives on microbiome and nutrient sequestration in soil aggregates during long‐term grazing exclusion

AbstractGrazing exclusion alters grassland soil aggregation, microbiome composition, and biogeochemical processes. However, the long‐term effects of grazing exclusion on the microbial communities and nutrient dynamics within soil aggregates remain unclear. We conducted a 36‐year exclusion experiment to investigate how grazing exclusion affects the soil microbial community and the associated soil functions within soil aggregates in a semiarid grassland. Long‐term (36 years) grazing exclusion induced a shift in microbial communities, especially in the <2 mm aggregates, from high to low diversity compared to the grazing control. The reduced microbial diversity was accompanied by instability of fungal communities, extended distribution of fungal pathogens to >2 mm aggregates, and reduced carbon (C) sequestration potential thus revealing a negative impact of long‐term GE. In contrast, 11–26 years of grazing exclusion greatly increased C sequestration and promoted nutrient cycling in soil aggregates and associated microbial functional genes. Moreover, the environmental characteristics of microhabitats (e.g., soil pH) altered the soil microbiome and strongly contributed to C sequestration. Our findings reveal new evidence from soil microbiology for optimizing grazing exclusion duration to maintain multiple belowground ecosystem functions, providing promising suggestions for climate‐smart and resource‐efficient grasslands.

The Microbiomes of Various Types of Abandoned Fallow Soils of South Taiga (Novgorod Region, Russian North-West)

More than 30 years have passed after the collapse of the Soviet Union, and huge areas of soil were left in a fallow state. The study of the microbiological status of fallow soils is an extremely urgent task because fallow soils represent the “hidden” food basket of Eurasia. In this context, we studied the influence of land use type (pasture, vegetable garden, hayfield, or secondary afforestation) on key agrochemical parameters and parameters of soil microbial biodiversity. All anthropogenically transformed soils included in the analysis showed increased humus content and pH shift to a more neutral side compared to the mature soil; the same seemed to be the case for all nutrient elements. It was established that the key factor regulating soil microbiome composition shift was the duration and degree of irreversibility of an agrogenic impact. The key phyla of soil microorganisms were Pseudomonadota, Acidobacteriota, Verrucomicrobiota, Bacteroidota, and Actinobacteriota. The proportion of other phyla was quite variative in soils of different land use. At the same time, all the 30-year-old abandoned soils were more similar to each other than to mature reference soil and 130-year-old soils of monoculture vegetable gardens. Thus, the first factor, regulating soil microbiome composition, is a continuation of soil agrogenic transformation. The second factor is the type of land use if the soil age was equal for fallow territory in the case of one initial podzol soil and one type of landscape. Thus, 30-year-old abandoned soils are intermediate in terms of microbial biodiversity between pristine natural podzols and plaggic podzol. It could be suggested that in the case of secondary involvement of soils in agriculture, the composition of the microbiome may turn to mature soil or to plaggic soil under intensive amelioration.

Shifts of the soil microbiome composition induced by plant–plant interactions under increasing cover crop densities and diversities

Interspecific and intraspecific competition and facilitation have been a focus of study in plant-plant interactions, but their influence on plant recruitment of soil microbes is unknown. In this greenhouse microcosm experiment, three cover crops (alfalfa, brassica, and fescue) were grown alone, in paired mixtures, and all together under different densities. For all monoculture trials, total pot biomass increased as density increased. Monoculture plantings of brassica were associated with the bacteria Azospirillum spp., fescue with Ensifer adhaerens, and alfalfa with both bacterial taxa. In the polycultures of cover crops, for all plant mixtures, total above-ground alfalfa biomass increased with density, and total above ground brassica biomass remained unchanged. For each plant mixture, differential abundances highlighted bacterial taxa which had not been previously identified in monocultures. For instance, mixtures of all three plants showed an increase in abundance of Planctomyces sp. SH-PL14 and Sandaracinus amylolyticus which were not represented in the monocultures. Facilitation was best supported for the alfalfa-fescue interaction as the total above ground biomass was the highest of any mixture. Additionally, the bulk soil microbiome that correlated with increasing plant densities showed increases in plant growth-promoting rhizobacteria such as Achromobacter xylosoxidans, Stentotrophomonas spp., and Azospirillum sp. In contrast, Agrobacterium tumefaciens, a previously known generalist phytopathogen, also increased with alfalfa-fescue plant densities. This could suggest a strategy by which, after facilitation, a plant neighbor could culture a pathogen that could be more detrimental to the other.

Crop rotation-driven changes in rhizosphere metabolite profiles regulate soil microbial diversity and functional capacity

Plants are increasingly revealed to have the ability to shape microbiome composition and function by triggering rhizosphere metabolites. Rotation, a model of crop diversification, promotes crop production by influencing rhizosphere microbiome. However, the rhizosphere metabolites of different rice rotations are rarely reported and, in particular, the regulation of key metabolites on rhizosphere microbiome is unclear. To address this gap, we collected the bulk and rhizosphere soils of four crop rotations (rice-rice, tobacco-rice, rice-oilseed rape, and rice-rice-oilseed rape) to assess rhizosphere metabolites, soil bacterial and fungal diversity, as well as functional microbial populations from a long-term (more than 20 years) field experiment. Compared with the rice-rice system, rhizosphere metabolites, such as deazaflavin, 10-Deacetylbaccatin III, and paclobutrazol, significantly increased in the rice rotation systems with tobacco and oilseed rape. Metabolite components (e.g., azelaic acid, soyasapogenol B, and canrenone) and microbial taxa (Xanthobacteraceae, Bradyrhizobium, and Mortierella) were the keystones regulating the co-occurring correlations of rhizosphere metabolites and soil microorganisms. Compared with the rice-rice, the bulk and rhizosphere soil of rice rotations with oilseed rape or tobacco showed higher abundance of the microbial populations related to C degradation and fixation, N fixation, nitrification, nitrate reduction, inorganic P (Pi) solubilization, and organic P (Po) mineralization. Metabolites, such as 7-chloro-norlichexanthone, daidzein, and soyasapogenol B, were the keystones regulating the co-occurrence relationships of rhizosphere metabolites and functional microbial populations. Rhizosphere metabolite composition was positively related to the populations associated with C fixation and degradation, nitrification, and P solubilization, and negatively related to those associated with methane metabolism, nitrate reduction, denitrification, and anammox (P ≤ 0.05). Soyasapogenol B, daidzei, and [1,1'-biphenyl]− 2,2'-dicarboxylic acid enriched in rotation systems were negatively correlated with dominant microbial taxa such as phylum Bacteroidetes and Chytridiomycota, and positively correlated with phylum Zoopagomycota and the populations associated with key soil functions such as C degradation, nitrate reduction, and P solubilization (P ≤ 0.05). These results demonstrated the importance of rhizosphere metabolites in regulating soil microbiome composition and functional capacity, which deepens understanding of rotations improving rice production via rhizosphere effect.

Glyphosate and terbuthylazine effects on soil functions, microbiome composition and crop performance

Herbicides are widely used for weed control in agriculture, though their fate and impact on non-target organisms like soil microbes and their function remain relatively unknown. A further complication is that herbicide effects vary depending on how they are applied and due to varying soil moisture conditions. In this study we tested the hypothesis that spraying glyphosate or terbuthylazine directly onto bare soil and when soil moisture is high would impact the soil microbial communities and their function most strongly. We measured similar amounts of glyphosate and terbuthylazine in soil whether the herbicides were directly applied to soil or first sprayed on the weed Chenopodium album and we found evidence for more rapid metabolization at high soil moisture. We found that the soil bacterial rather than the fungal community was mainly affected by a single application of the two tested herbicides. The identified shifts in community composition were independent of the modes of herbicide application but strongly dependent on soil moisture. We further found that herbicide applications only had a small impact on soil microbial function, which was approximated with analyses of the activities of N-β-acetylglucosaminidase, acid phosphatase and β-glucosidase enzymes in soil. Finally, we also assessed the post-application performance of the subsequent crop and found that the herbicides did not affect maize height, chlorophyll content and biomass. Overall, our study revealed that a single application of herbicides in recommended doses had minor effects on the soil microbiome with a temporal and soil moisture dependency. The latter finding points out that to avoid repercussions on non-target organisms and soil function, key research needs to solve the context-dependency of rapid herbicide degradation in soil.

Recovery of the soil fungal microbiome after steam disinfection to manage the plant pathogen Fusarium solani.

Soil disinfection using high temperatures via steam is a promising approach to manage plant pathogens, pests, and weeds. Soil steaming is a viable option for growers who are moving away from dependence on chemical soil fumigants, especially in plant nursery or high tunnel environments. However, there are few studies that investigate how soil steaming causes substantial disturbance to the soil by killing both target pathogens and other soil biota. Steaming treatments also change the trajectory of the soil microbiome as it reassembles over time. Growers are interested in the health of soils after using steam-disinfection, especially if a virulent pathogen colonizes the soil and then flourishes in a situation where there are very few microbes to suppress its growth. Should recruitment of a virulent pathogen occur in the soil, this could have devasting effects on seed germination, seedling establishment and survival. Beneficial microbes are often used to prevent the colonization of plant pathogens, especially after a soil-steaming event. Here, we experimentally test how soil fungal communities assemble after steaming disinfection. We introduce to steam-treated soil Fusarium solani, an important fungal pathogen of soybean and Trichoderma harzianum, a known beneficial fungus used for soilborne pathogen suppression. Results show that F. solani significantly affects the relative abundance and diversity of the soil fungal microbiome, however, T. harzianum does not mitigate the amount of F. solani in the steam treated soil. Within the T. harzianum microbial addition, the soil fungal communities were similar to the control (steaming only). This result suggests inoculating the soil with T. harzianum does not drastically alter the assembly trajectory of the soil fungal microbiome. Other soil amendments such as a combination of Trichoderma spp. or other genera could suppress F. solani growth and shift soil microbiome composition and function post-steaming, however, more experimental research is needed.

Immobilization of Klebsiella jilinsis strain 2N3 by corn straw biochar enhanced the degradation of nicosulfuron and restores the soil microbiome function and composition

Investigations on the bioremediation of nicosulfuron-contaminated soil environments based on biochar-immobilized bacteria are sparse. In this study, we characterized the degradation of nicosulfuron by Klebsiella jilinsis strain 2N3 with the highest degradation rate (92.62 %) and the optimal degrading conditions identified. Then, the strain 2N3 was further immobilized with corn straw biochar (BC 2N3) to enhance its degrading of nicosulfuron. The results of liquid chromatography showed that the treatment of BC 2N3 significantly shortened the half-life of nicosulfuron in non-sterilized soil from 22.8 to 5.1 days and recovered the enzymatic activities of urease, sucrase, dehydrogenase, and catalase involved in the degradation of soil pollutants. Surprisingly, results of 16S rRNA sequencing showed that BC 2N3 efficiently recovered the bacterial taxa with decreased relative abundances under the nicosulfuron stress, and significantly enhanced the degradation and metabolic pathways of nicosulfuron in soil. The vegetative growth of two nicosulfuron-sensitive crops (i.e., oilseed rape and wheat) was significantly increased in soil remediated by BC 2N3. Our results demonstrated that BC 2N3 efficiently degraded the nicosulfuron residues, providing a potentially promising bioremediation approach for improving the biological properties of herbicide-contaminated soil.

Seasonal variations in the composition and diversity of rhizosphere soil microbiome of bamboo plants as infected by soil-borne pathogen and screening of associated antagonistic strains

As the occurrence and severity of soil-borne diseases are strongly season-dependent, the ecological processes that shift plant microbiome compositions and functions upon pathogen infection in different seasons are rarely studied. In this study, we compared the differences in fungal and bacterial communities in rhizosphere soil between healthy and diseased bamboo plants throughout the four seasons at the main bamboo production site in China and investigated how basal rot disease caused by Fusarium proliferatum affected the composition, structure and ecological functions of rhizosphere-associated microorganisms. The results showed that diseased bamboo plants enriched the highest abundance of Fusarium genus in rhizosphere soil while receiving largely increased stem lesion area in summer. Microbiome analysis further proved that healthy bamboo plants harbored more ecologically beneficial microbial taxa that might function as biological protectants in their rhizosphere soil than diseased plants at the same season. Three individual strains with biocontrol potentials were further isolated and identified as Trichoderma spirale, Bacillus velezensis and Streptomyces mirabilis. The antagonistic tests further demonstrated their inhibition effects on the growth and pathogenicity of the pathogenic fungus F. proliferatum in vitro and in vivo. This study advances our understanding of soil-borne pathogen mediated changes in microbiome structure and function in plant rhizosphere soil and provides potential biocontrol strains for increasing plant resistance against basal rot disease.

Interactive effects of depth and differential irrigation on soil microbiome composition and functioning

Two factors that are well-known to influence soil microbiomes are the depth of the soil as well as the level of moisture. Previous works have demonstrated that climate change will increase the incidence of drought in soils, but it is unknown how fluctuations in moisture availability affect soil microbiome composition and functioning down the depth profile. Here, we investigated soil and wheatgrass rhizosphere microbiomes in a single common field setting under four different levels of irrigation (100%, 75%, 50%, and 25%) and three depths (0-5 cm, 5-15 cm, and 15-25 cm from the surface). We demonstrated that there is a significant interactive effect between depth and irrigation, where changes in soil moisture more strongly affect soil microbiomes at the surface layer than at deeper layers. This was true for not only microbiome community composition and diversity metrics, but also for functional profiles (transcriptomic and metabolomic datasets). Meanwhile, in rhizosphere communities the influence of irrigation was similar across the different depths. However, for the ‘Alkar’ wheatgrass cultivar, the rhizosphere microbial communities responded more strongly to changes in irrigation level than did the communities for the ‘Jose’ cultivar rhizosphere. The lessened response of deeper soil microbiomes to changes in irrigation may be due to higher incidence of slow-growing, stress-resistant microbes. These results demonstrate that the soil microbiome response to moisture content is depth-dependent. As such, it will be optimal for soil microbiome studies to incorporate deeper as well as surface soils, to get a more accurate picture of the soil microbiome response to stress.

Composition and biodiversity of soil and root-associated microbiome in Vitis vinifera cultivar Lambrusco distinguish the microbial terroir of the Lambrusco DOC protected designation of origin area on a local scale.

Wines produced from the same grape cultivars but in different locations possess distinctive qualities leading to different consumer's appreciation, preferences, and thus purchase choices. Here, we explore the possible importance of microbiomes at the soil-plant interface as a determinant of the terroir properties in grapevine production, which confer specific growth performances and wine chemo-sensory properties at the local scale. In particular, we investigated the variation in microbial communities associated with the roots of Vitis vinifera cultivar Lambrusco, as well as with surrounding bulk soils, in different vineyards across the "Consorzio Tutela Lambrusco DOC" protected designation of origin area (PDO, Emilia Romagna, Italy), considering viticultural sites located both inside and outside the consortium in two different seasons (June and November 2021). According to our findings, rhizospheric and soil microbiomes show significant structural differences in relation to the sampling site, regardless of seasonality, while endophytic microbiomes seem to be completely unaffected by such variables. Furthermore, a deeper insight into the microbial terroir of PDO areas highlighted the presence of some rhizospheric microorganisms enriched inside the consortium and characterizing the PDO regardless of both sampling season and farming strategy. These include Bacillus, Paenibacillus, and Azospirillum, which are all well-known plant growth-promoting bacteria. Taken together, our results suggest a connection between soil and root microbiomes of V. vinifera cultivar Lambrusco and the local designation of origin, emphasizing the potential role of PDO-enriched plant growth-promoting bacteria in vine growing and final quality of the Lambrusco DOC wine.

Soil water extract and bacteriome determine N2O emission potential in soils

Soil chemical properties and microbiome composition impact N2O emission potential, but the relative importance of these factors as determinants of N2O emission in denitrifying systems is rarely tested. In addition, previous linkages between microbiome composition and N2O emission potential rarely demonstrate causality. Here, we determined the relative impact of bacteriome composition (i.e., soil extracted bacterial cells) and soil water extract (i.e., water extractable chemicals and particles below 0.22 µm) on N2O emission potential utilizing an anoxic cell-based assay system. Cells and water extract for assays were sourced from soils with contrasting N2O/N2O + N2 ratios, combined in various combinations and denitrification gas production was measured in response to nitrate addition. Analysis of 16S amplicon sequencing data revealed similarity in composition between extracted and parent soil bacteriomes. Average directionless effects of cell and water extract on N2O/N2O + N2 (Cell: ∆0.17, soil water extract: ∆0.22) and total N2O hypothetically emitted (Cell: ∆2.62 µmol-N, soil water extract: ∆4.14 µmol-N) across two assays indicated water extract is the most important determinant of N2O emissions. Independent pH differences of just 0.6 points impacted N2O/N2O + N2 on par with independent water extract differences, supporting the dominance of this variable in previous studies. However, impacts on overall N2O hypothetically emitted were smaller, suggesting that soil pH manipulation may not necessarily be a successful approach to mitigate emissions. In addition, we observed increased N2O accumulation and emission potential at the end of incubations concomitant with predicted decreases in carbon (C) availability, suggesting that C limitation increases N2O emission transiently with the magnitude of emission dependent on both chemical and bacteriome controls.

Pasture management intensification shifts the soil microbiome composition and ecosystem functions

Natural grasslands are important reservoirs of animal and plant biodiversity and provide several ecosystem services, through the action of soil microorganisms. The increased demand for food, energy, and cattle activity has led to the conversion of natural grasslands to cultivated systems. However, the consequences of this conversion for soil microbial diversity and ecosystem functioning are yet to be discovered. Here, we used the 16 S rRNA amplicon sequencing and a large set of soil and environmental variables to understand the possible effects of natural grasslands to cultivated pasture conversion on the soil microbial structure, composition, diversity, and functions. The study areas followed a gradient of increasing soil disturbance intensity, as follows: Natural grassland (NG), Improved-natural grassland (IG), Perennial-cultivated pasture (PP), and Annual-cultivated pasture (AP). Natural grassland conversion to managed and cultivated pastures decreased the abundances of Acidobacteria and Verrucomicrobia, while increased α-, γ-, and δ-Proteobacteria, Gemmatimonadetes, Bacteroidetes, Patescibacteria, and Latescibacteria. The predicted functional profiles have also changed, as functions like ‘cellulolytic and symbionts/parasites’ decreased after natural to cultivated pastures conversion, while ‘nitrogen respiration’, ‘sulfur respiration’, and ‘aromatic compound degradation’ functions increased. Aboveground plant diversity decrease influenced belowground microbial diversity. The main drivers of diversity, composition, and functional potential are associated with soil attributes affected by liming, like aluminum complexation. In conclusion, we have found taxonomic and functional differences between natural and managed grasslands (NG and IG, respectively) and cultivated pastures (PP and AP), with consequences for management strategies and biodiversity conservation priorities.

Grazing lowers soil multifunctionality but boosts soil microbial network complexity and stability in a subtropical grassland of China.

Long-term grazing profoundly affects grassland ecosystems, whereas how the soil microbiome and multiple soil ecosystem functions alter in response to two-decades of grazing, especially how soil microbiome (diversity, composition, network complexity, and stability) forms soil multifunctionality is rarely addressed. We used a long-term buffalo grazing grassland to measure the responses of soil physicochemical attributes, stoichiometry, enzyme activities, soil microbial niche width, structure, functions, and networks to grazing in a subtropical grassland of Guizhou Plateau, China. The evidence from this work suggested that grazing elevated the soil hardness, available calcium content, and available magnesium content by 6.5, 1.9, and 1.9 times (p = 0.00015-0.0160) and acid phosphatase activity, bulk density, pH by 59, 8, and 0.5 unit (p = 0.0014-0.0370), but decreased the soil water content, available phosphorus content, and multifunctionality by 47, 73, and 9-21% (p = 0.0250-0.0460), respectively. Grazing intensified the soil microbial carbon limitation (+78%, p = 0.0260) as indicated by the increased investment in the soil β-glucosidase activity (+90%, p = 0.0120). Grazing enhanced the complexity and stability of the bacterial and fungal networks but reduced the bacterial Simpson diversity (p < 0.05). The bacterial diversity, network complexity, and stability had positive effects, while bacterial and fungal compositions had negative effects on multifunctionality. This work is an original attempt to show that grazing lowered multifunctionality via the reduced bacterial diversity and shifted soil bacterial and fungal compositions rather than the enhanced bacterial and fungal network complexities and stability by grazing. Protecting the bacterial diversity from decreasing, optimizing the composition of bacteria and fungi, and enhancing the complexity and stability of bacterial network may be conducive to improving the soil multifunction of grazing grassland, on a subtropical grassland.

A shift from inorganic to organic nitrogen-dominance shapes soil microbiome composition and co-occurrence networks.

Soil microbiomes are characterized by their composition and networks, which are linked to soil nitrogen (N) availability. In nature, inorganic N dominates at one end and organic N dominates at the other end along soil N gradients; however, little is known about how this shift influences soil microbiome composition and co-occurrence networks, as well as their controls. To this end, we conducted an experiment with the host plant Solidago canadensis, which was subject to three N regimes: inorganic N-dominated, co-dominated by inorganic and organic N (CIO), and organic N-dominated. Organic N dominance exhibited stronger effects on the composition and co-occurrence networks of soil microbiomes than inorganic N dominance. The predominant control was plant traits for bacterial and fungal richness, and soil pH for keystone species. Relative to the CIO regime, inorganic N dominance did not affect fungal richness and increased keystone species; organic N dominance decreased fungal richness and keystone species. Pathogenic fungi and arbuscular mycorrhizal fungi were suppressed by organic N dominance but not by inorganic N dominance. These findings suggest that the shift from soil inorganic N-dominance to soil organic N-dominance could strongly shape soil microbiome composition and co-occurrence networks by altering species diversity and topological properties.

Microbiome analysis and biocontrol bacteria isolation from rhizosphere soils associated with different sugarcane root rot severity.

To explore the causal pathogen and the correlated rhizosphere soil microecology of sugarcane root rot, we sampled the sugarcane root materials displaying different disease severity, and the corresponding rhizosphere soil, for systematic root phenotype and microbial population analyses. We found that with increased level of disease severity reflected by above-ground parts of sugarcane, the total root length, total root surface area and total volume were significantly reduced, accompanied with changes in the microbial population diversity and structure in rhizosphere soil. Fungal community richness was significantly lower in the rhizosphere soil samples from mildly diseased plant than that from either healthy plant, or severely diseased plant. Particularly, we noticed that a peculiar decrease of potential pathogenic fungi in rhizosphere soil, including genera Fusarium, Talaromyces and Neocosmospora, with increased level of disease severity. As for bacterial community, Firmicutes was found to be of the highest level, while Acidobacteria and Chloroflexi of the lowest level, in rhizosphere soil from healthy plant compared to that from diseased plant of different severity. FUNGuild prediction showed that the proportion of saprophytic fungi was higher in the rhizosphere soil of healthy plants, while the proportion of pathogenic fungi was higher in the rhizosphere soil of diseased plants. By co-occurrence network analysis we demonstrated the Bacillus and Burkholderia were in a strong interaction with Fusarium pathogen(s). Consistently, the biocontrol and/or growth-promoting bacteria isolated from the rhizosphere soil were mostly (6 out of 7) belonging to Bacillus and Burkholderia species. By confrontation culture and pot experiments, we verified the biocontrol and/or growth-promoting property of the isolated bacterial strains. Overall, we demonstrated a clear correlation between sugarcane root rot severity and rhizosphere soil microbiome composition and function, and identified several promising biocontrol bacteria strains with strong disease suppression effect and growth-promoting properties.