Soil Microbial Community Activity Research Articles

Effects of reduced snowpack due to climate warming on abiotic and biotic soil properties in alpine and boreal forest systems

Reduction in snow cover, depth, onset, and duration of seasonal snow in mid-latitude regions due to climate warming has multiple global and local scale ecosystem impacts. These effects include modulations of the hydrological cycles and increases in land surface solar radiation absorption due to decreased albedo. Changes in snow cover characteristics also affect underlying soils. Snow has an insulating effect on soils by decoupling air and soil temperatures, thus seasonal snow cover reduction leads to overall lower soil temperatures and an increase in freeze-thaw cycles. This is especially prominent during the fall and spring thaw seasons when the snow cover is not as extensive. This in turn has downstream impacts on soil physical, chemical, and biological properties. Among these impacts are soil moisture reduction, temperature, frost regimes, soil pH shifts, and alteration in nutrient flux dynamics during winter, snowmelt period and the following summer growing season. These changes in soil physicochemical properties due to snowpack reduction can then impact the biological soil properties via increased plant root mortality, reduced abundance and diversity of soil arthropods, and shifts in composition, abundance and activity of soil microbial communities. All these soil biotic factors can in turn alter the dynamics of soil nutrient fluxes and future greenhouse gas emissions. Here, we integrate data on the effects of snow cover reduction on abiotic and biotic soil properties, with focus on temperate alpine and forest ecosystems and with an outlook on future impacts.

Sterile sentinels and MinION sequencing capture active soil microbial communities that differentiate crop rotations

BackgroundSoil microbial communities are difficult to measure and critical to soil processes. The bulk soil microbiome is highly diverse and spatially heterogeneous, which can make it difficult to detect and monitor the responses of microbial communities to differences or changes in management, such as different crop rotations in agricultural research. Sampling a subset of actively growing microbes should promote monitoring how soil microbial communities respond to management by reducing the variation contributed by high microbial spatial and temporal heterogeneity and less active microbes. We tested an in-growth bag method using sterilized soil in root-excluding mesh, “sterile sentinels,” for the capacity to differentiate between crop rotations. We assessed the utility of different incubation times and compared colonized sentinels to concurrently sampled bulk soils for the statistical power to differentiate microbial community composition in low and high diversity crop rotations. We paired this method with Oxford Nanopore MinION sequencing to assess sterile sentinels as a standardized, fast turn-around monitoring method.ResultsCompared to bulk soil, sentinels provided greater statistical power to distinguish between crop rotations for bacterial communities and equivalent power for fungal communities. The incubation time did not affect the statistical power to detect treatment differences in community composition, although longer incubation time increased total biomass. Bulk and sentinel soil samples contained shared and unique microbial taxa that were differentially abundant between crop rotations.ConclusionsOverall, compared to bulk soils, the sentinels captured taxa with copiotrophic or ruderal traits, and plant-associated taxa. The sentinels show promise as a sensitive, scalable method to monitor soil microbial communities and provide information complementary to traditional soil sampling.

Responses of soil microbial community activities and soil physicochemical properties to coal fly ash soil amendment

BackgroundHundreds of millions of tons coal fly ash are produced annually to support economic development and industrial production. However, directly applying coal fly ash to agricultural production can decrease the land productivity and pose a threat to the ecosystem due to the poor physicochemical properties and seriously heavy metal pollution.MethodsIn this study, a field experiment to investigate the effects of coal fly ash as a soil amendment was conducted in Hebei province, China. The coal fly ash (CFA) soil field was mixed with the carrier soil (CS, without containing coal fly ash) at different rates (0–40% mass content) in the 0–20 cm layer of top soil and then mixed with a rotovator. The soil was then amended with 0.45–1.80 kg·m− 2 of G1 soil amendment for planting corn.PurposeThe purpose of this study is to investigate the response mechanism of soil microbial community activities, and soil physicochemical properties to soil amendment and carrier soil in coal fly ash soil.Key resultsThe study found that the G1 amendment, which consisted of humic acid, polyacrylamide, zeolite powder, and FeSO4·7H2O, improved the soil chemical properties and physical structure by increasing soil bulk density and macroaggregates. The highest corn yield was observed in B5 (20% CS and 1.3500 kg·m− 2 G1). Meanwhile, the abundance of microorganisms that facilitate the circulation of soil nutrients such as Acidobacteria (77.05%), Sphingomonas (25.60%), Nitrospira (20.78%), Streptomyces (11.32%), and Gaiella (10.20%) was increased.ConclusionsOverall, our results indicate that the use of coal fly ash soil as a amendment can enhance soil sustainability by improving soil microbial functions. These findings provide a reference for the development and application of coal fly ash soil amendments.

Revealing soil microbial ecophysiological indicators in acidic environments laden with heavy metals via predictive modeling: Understanding the impacts of black diamond excavation

Appraising the activity of soil microbial community in relation to soil acidity and heavy metal (HM) content can help evaluate it's quality and health. Coal mining has been reported to mobilize locked HM in soil and induce acid mine drainage. In this study, agricultural soils around coal mining areas were studied and compared to baseline soils in order to comprehend the former's effect in downgrading soil quality. Acidity as well as HM fractions were significantly higher in the two contaminated zones as compared to baseline soils (p < 0.01). Moreover, self-organizing and geostatistical maps show a similar pattern of localization in metal availability and soil acidity thereby indicating a causal relationship. Sobol sensitivity, cluster, and principal component analyses were employed to enunciate the relationship between the various metal and acidity fractions with that of soil microbial properties. The results indicate a significant negative impact of metal bioavailability, and acidity on soil microbial activity. Lastly, Taylor diagrams were employed to predict soil microbial quality and health based on soil physicochemical inputs. The efficiency of several machine learning algorithms was tested to identify Random Forrest as the best model for prediction. Thus, the study imparts knowledge about soil pollution parameters, and acidity status thereby projecting soil quality which can be a pioneer in sustainable agricultural practices.

Mixing Compost and Biochar Can Enhance the Chemical and Biological Recovery of Soils Contaminated by Potentially Toxic Elements.

Biochar and compost are able to influence the mobility of potentially toxic elements (PTEs) in soil. As such, they can be useful in restoring the functionality of contaminated soils, albeit their effectiveness can vary substantially depending on the chemical and/or the (micro)biological endpoint that is targeted. To better explore the potential of the two amendments in the restoration of PTE-contaminated soils, biochar, compost (separately added at 3% w/w), and their mixtures (1:1, 3:1, and 1:3 biochar-to-compost ratios) were added to contaminated soil (i.e., 2362 mg kg-1 of Sb and 2801 mg kg-1 of Zn). Compost and its mixtures promoted an increase in soil fertility (e.g., total N; extractable P; and exchangeable K, Ca, and Mg), which was not found in the soil treated with biochar alone. All the tested amendments substantially reduced labile Zn in soil, while biochar alone was the most effective in reducing labile Sb in the treated soils (-11% vs. control), followed by compost (-4%) and biochar-compost mixtures (-8%). Compost (especially alone) increased soil biochemical activities (e.g., dehydrogenase, urease, and β-glucosidase), as well as soil respiration and the potential catabolic activity of soil microbial communities, while biochar alone (probably due to its high adsorptive capacity towards nutrients) mostly exhibited an inhibitory effect, which was partially mitigated in soils treated with both amendments. Overall, the biochar-compost combinations had a synergistic effect on both amendments, i.e., reducing PTE mobility and restoring soil biological functionality at the same time. This finding was supported by plant growth trials which showed increased Sb and Zn mineralomass values for rigid ryegrass (Lolium rigidum Gaud.) grown on biochar-compost mixtures, suggesting a potential use of rigid ryegrass in the compost-biochar-assisted phytoremediation of PTE-contaminated soils.

Diversity and composition of active and total bacteria in rhizospheric soil in response to continuous cropping years of Panax notoginseng.

The synchronous research and analysis of total and active soil microbial communities can provide insight into how these communities are impacted by continuous cropping years and pathogen infection. The diversity of total and active bacteria in rhizospheric soil of 2-year-old and 3-year-old healthy and diseased Panax notoginseng can comprehensively reveal the bacterial response characteristics in continuous cropping practice. The results showed that 4916 operational taxonomic units (OTUs) were found in the rhizospheric soil bacterial community of P. notoginseng at the DNA level, but only 2773 OTUs were found at the RNA level. The rhizospheric environment had significant effects on the active and bacterial communities, as indicated by the number of OTUs, Shannon, Chao1, Faith's phylogenetic diversity (Faith's PD), and Simpson's diversity indexes. The DNA level can better show the difference in diversity level before and after infection with root rot. The bacterial Chao1 and Faith's PD diversity indexes of 2-year-old root rot-diseased P. notoginseng rhizospheric soil (D2) were higher than that of healthy plants, while the bacterial Shannon diversity index of 3-year-old root rot-diseased P. notoginseng rhizospheric soil (D3) was the lowest in the total bacteria. Principal coordinate analysis (PCoA) illustrated that the total bacterial species composition changed markedly after root rot disease. There were significant differences in the composition of active bacterial species between the 2-year and 3-year rhizospheres. In conclusion, the total and active edaphic rhizospheric bacterial communities could provide important opportunities to understand the responses of bacteria to continuous cropping of P. notoginseng. Differential responses of total and active edaphic rhizosphere bacterial communities to continuous cropping of Panax notoginseng.

Active soil microbial composition and proliferation are directly affected by the presence of biocides from building materials

Combinations of biocides are commonly added to building materials to prevent microbial growth and thereby cause degradation of the façades. These biocides reach the environment by leaching from façades posing an environmental risk. Although ecotoxicity to the aquatic habitat is well established, there is hardly any data on the ecotoxicological effects of biocides on the soil habitat. This study aimed to characterize the effect of the biocides terbutryn, isoproturon, octhilinone, and combinations thereof on the total and metabolically active soil microbial community composition and functions. Total soil microbial community was retrieved directly from the nucleic acid extracts, while the DNA of the active soil microbial community was separated after bromodeoxyuridine labeling. Bacterial 16S rRNA gene and fungal internal transcribed spacer region gene-based amplicon sequencing was carried out for both active and total, while gene copy numbers were quantified only for the total soil microbial community. Additionally, soil respiration and physico-chemical parameters were analyzed to investigate overall soil microbial activity. The bacterial and fungal gene copy numbers were significantly affected by single biocides and combined biocide soil treatment but not soil respiration and physico-chemical parameters. While the total soil microbiome experienced only minor effects from single and combined biocide treatment, the active soil microbiome was significantly impacted in its diversity, richness, composition, and functional patterns. The active bacterial richness was more sensitive than fungal richness. However, the adverse effects of the biocide combination treatments on soil bacterial richness were highly dependent on the identities of the biocide combination. Our results demonstrate that the presence of biocides frequently used in building materials affects the active soil microbiome. Thereby, the approach described herein can be used as an ecotoxicological measure for the effect on complex soil environments in future studies.

Composition and activity of soil microbial communities in native and non-native vegetation of southern California

The proliferation of non-native plant species in novel habitats has altered plant community diversity, ecosystem carbon (C) and nutrient cycling, and disturbance regimes worldwide. However, the impacts of non-native plants on soil microbial community composition and activity are still poorly known, especially in semi-arid woodlands. Here we utilized next generation sequencing (16S rRNA sequencing of the V3-V4 regions) and measurements of microbial activity (respiration, net N mineralization, and enzyme assays) to determine how soil microbial composition and activity varied between native and non-native vegetation patches in coastal sage scrub (CSS) woodlands. We sampled eight CSS sites and collected topsoil (0–10 cm) samples from six paired native and non-native vegetation patches at each site. Native patches had significantly (p < 0.05) higher vegetation cover, dissolved organic C (DOC), and dissolved inorganic nitrogen (DIN) concentrations than non-native patches. β-glucosidase activity was significantly higher (ca. 10 nM g−2 h−1) and peroxidase activity was significantly lower (ca. 60 nM g−2 h−1) in non-native vegetation, while rates of net N mineralization and nitrification, phosphatase and NAGase activities, and respiration were not significantly different in native and non-native vegetation but were positively correlated with total soil C and N (r > 0.60; p < 0.05). Bacterial alpha- and beta-diversity were not significantly different (p > 0.05) between native and non-native patches; however, bacteria/archaea in the phyla Gemmatimonadota, Planctomycetota, Armatimonadota, Fibrobacterota, Thermoplasmatota, and Entotheonellaeota were over-expressed in non-native patches. Within these phyla there were 20 orders that were differentially expressed in native or non-native vegetation, and more than half (60 %) had significantly higher relative abundance in native vegetation. Our results indicate that the expansion of non-native vegetation in semi-arid woodlands significantly alters soil C and N, which feeds back on microbial activity and community composition.

Taxonomic and functional characteristics of xerotolerant culturable bacterial community of Negev desert soil

Despite the significant expansion of the geography of soil microorganisms studies in various, including extreme natural environments, research on the biodiversity and metabolic activity of soil microbial communities under conditions of moisture deficiency are few. Biodiversity of culturable bacteria isolated from the surface horizon of the Negev desert soil (Aridic Calcisol) after pre-incubation of soil samples under the conditions of low water availability has been studied. An increase in the diversity of culturable bacteria after pre-incubation was revealed in comparison with the community isolated from the native soil. From the native and pre-incubated samples, 153 phenotypically unique pure cultures of bacteria from 22 genera belonging to the phyla Actinomycetota, Pseudomonadota, Bacillota, and Bacteroidota were isolated and identified. The taxonomic diversity of culturable bacteria isolated from the sample pre-incubated at a water activity (Aw) of 0.90 was two times higher than that obtained from the native soil. The strain of the genus Pedobacter has been identified, which may be a representative of a previously undescribed bacterial species. Bacteria of the genera Aerococcus, Bacillus, Brevibacterium, Staphylococcus, and Stenotrophomonas capable of growing at Aw 0.91 were found. One strain of the genus Microlunatus has been identified that is capable of growing on a nitrogen-free medium, exhibiting amylase and protease activity, and capable to growth on a medium with Aw down to 0.96. The obtained results confirm the hypothesis that arid ecosystems, in particular, desert soils and sediments, are a depository of a previously unexplored taxonomic diversity of bacteria with unique physiological properties that are promising for study and potential implementation in biotechnological processes.

Effects of Fungi on Soil Organic Carbon and Soil Enzyme Activity under Agricultural and Pasture Land of Eastern Türkiye

Soil organic matter (SOM) is a heterogeneous mixture of materials ranging from fresh plant tissues to highly decomposed humus at different stages of decomposition. Soil organic carbon (SOC) status is directly related to the amount of organic matter in soil and therefore is generally used to measure it. Soil carbon sequestration refers to the removal of carbon (C) containing substances from the atmosphere and its storage in soil C pools. The soil microbial community (SMC) plays an important role in the C cycle, and its activity is considered to be the main driver of differences in C storage potential in soil. The composition of SMC is crucial for maintaining soil ecosystem services, as the structure and activity of SMC also regulate the turnover and distribution of nutrients, as well as the rate of soil organic matter (SOM) decomposition. Here, we applied fungi on the soils taken from two fields, one used as a pasture and one for agriculture (wheat cultivation), in a histosol in the eastern part of Türkiye and investigated the changes in the organic carbon and enzyme activity contents of the soils at the end of the 41-day incubation period. In the study, four different fungal species (Verticillium dahliae (SOR-8), Rhizoctonia solani (S-TR-6), Fusarium oxysporum (HMK2-6), and Trichoderma sp.) were used and catalase, urease, and alkaline phosphatase activities were examined. Results showed that the values of SOC were V. dahliae (7.46%), Trichoderma sp. (7.27%), R. solani (7.03%), Control (6.97%), and F. oxysporum (6.7%) in pastureland and were V. dahlia (4.72%), control (4.69%), F. oxysporum (4.65%), R. solani (4.37%), and Trichoderma sp. (4.14%) in agricultural land, respectively. SOC and soil enzyme activities were significantly affected by land use types (p &lt; 0.05). The higher SOC and enzyme activities were observed in pastureland. Finally, it was determined that soil organic carbon and soil enzyme activities were affected by fungi. This study is important in terms of revealing that the effects of fungi on soil organic carbon and enzyme activities are different in various land types.

Biological activity of forest litters in Ukhta City’s Central Park soils (The Komi Republic)

Physicochemical properties and parameters of biological activity of forest litter horizons of illuvial-ferruginous podzols, formed the main part of soil cover of the largest recreational zone of Ukhta city, the G. A. Karchevsky Central Park, have been determined for the first time ever. In the park soils, a change in the basic agrochemical parameters (alkalinization and an increase in the content of available forms of the most important biogens with the exception of organic compounds carbon), the accumulation of heavy metals (up to moderately toxic level according to value of total pollution index) and petroleum hydrocarbons were indicated in comparison with background soils. An increase in soil enzymes (catalase, invertase) activity and a metabolic activity of soil microbial community was established. Based on the spectra of organic substrate consumption (multisubstrate testing method), a higher activity of all microbial functional (trophic) groups, with the exception of bacteria that consume alcohols, hexoses, and amino acids as an energy source, was revealed.

The interactions and hierarchical effects of long-term agricultural stressors on soil bacterial communities.

Soils are subjected to multiple anthropogenic modifications, but the synergistic impacts of simultaneous environmental stressors on below-ground communities are poorly understood. We used a large-scale (1152 plots), long-term (26 years), multi-factorial grassland experiment to assess the impact of five common agricultural practises (pesticides, herbicide, liming, fertilizers and grazing exclusion) and their interactive effects on the composition and activity of soil microbial communities. We confirmed that pH strongly impacts belowground communities, but further demonstrate that pH strongly mediates the impacts of other management factors. Notably, there was a significant interaction between liming and the effect of pesticide application, with only half of the taxa responding to pesticide being shared in both limed and unlimed treatments. Likewise, nutrient amendments significantly altered bacterial community structure in acidic soils. Not only do these results highlight an hierarchy of effect of commonly used agricultural practices but also the widespread interactions between treatments: many taxa were significantly affected by interactions between treatments, even in the absence of significant main effects. Furthermore, the results demonstrated that chemical amendments may not percolate deeply into physically unperturbed soils with effects concentrated between 0 and 30 cm, despite 20+ years of treatment. The research shows that future changes to agricultural practices will need to consider interactions among multiple factors.

Unearthing Shifts in Microbial Communities Across a Soil Disturbance Gradient.

Permafrost, an important source of soil disturbance, is particularly vulnerable to climate change in Alaska where 85% of the land is underlained with discontinuous permafrost. Boreal forests, home to plants integral to subsistence diets of many Alaska Native communities, are not immune to the effects of climate change. Soil disturbance events, such as permafrost thaw, wildfires, and land use change can influence abiotic conditions, which can then affect active layer soil microbial communities. In a previous study, we found negative effects on boreal plants inoculated with microbes impacted by soil disturbance compared to plants inoculated with microbes from undisturbed soils. Here, we identify key shifts in microbial communities altered by soil disturbance using 16S rRNA gene sequencing and make connections between microbial community changes and previously observed plant growth. Additionally, we identify further community shifts in potential functional mechanisms using long read metagenomics. Across a soil disturbance gradient, microbial communities differ significantly based on the level of soil disturbance. Consistent with the earlier study, the family Acidobacteriaceae, which consists of known plant growth promoters, was abundant in undisturbed soil, but practically absent in most disturbed soil. In contrast, Comamonadaceae, a family with known agricultural pathogens, was overrepresented in most disturbed soil communities compared to undisturbed. Within our metagenomic data, we found that soil disturbance level is associated with differences in microbial community function, including mechanisms potentially involved in plant pathogenicity. These results indicate that a decrease in plant growth can be linked to changes in the microbial community and functional composition driven by soil disturbance and climate change. Together, these results build a genomic understanding of how shifting soil microbiomes may affect plant productivity and ecosystem health as the Arctic warms.

Characterization of soil microbial community activity and structure for reducing available Cd by rice straw biochar and Bacillus cereus RC-1

The combination of biochar and specific bacteria has been widely applied to remediate Cadmium-contaminated soil. But little is known about how such composites affect the dynamic distribution of metal fractions. This process is accompanied by the alternations of soil properties and microbial community structures. Composite of rice straw biochar and Bacillus cereus RC-1 were applied to investigate its impacts on Cd alleviation and soil microbial diversity and structure. The bacterial/biochar composite treatment decreased the fraction of HOAc-extractable Cd by 38.82%, and increased residual Cd by 23.95% compared to the untreated control. Moreover, compared with the untreated control, the composite treatment significantly increased the soil pH by about 1.5 units, and the activities of catalase, urease and invertase enzymes were increased by 42.39%, 30.50% and 31.20%, respectively. Composite treatment increased soil bacterial and fungal alpha diversity, the relative abundance of Bacillus, Streptomyces, Arthrobacter, and Aspergillus species were also increased. Mantel test and correlation analysis indicated that the effects associated with fungal communities in influencing soil properties were lower than that those of bacterial communities by different treatment. Aggregated boosted tree (ABT) models analysis showed that soil chemical proprieties (as determined by SOM, CEC, AN, etc.,) contributed over 50% of the changes in bacterial and fungal communities by the composite treatment. The co-occurrence network results showed that all treatments enhanced the correlation between OUT groups and improved the possible relationships in the bacterial and fungal communities, especially the interrelationships between bacteria and fungi after the Cd fractions stabilized. These findings provide a new insight to optimal strategies for the remediation of Cd-contaminated soil.

Soil management and compost amendment are the main drivers of carbon sequestration in rainfed olive trees agroecosystems: An evaluation of chemical and biological markers

Traditional olive groves are considered at high risk of erosion and desertification due to low organic matter inputs and scarce vegetation cover coupled to highly intensity tillage, leading to a further decrease in soil organic carbon contents. In a context of climate change, carbon sequestration through waste management in the framework of a circular economy becomes of primary importance for rainfed Mediterranean agricultural soils. To unveil the mechanisms of carbon sequestration in those agroecosystems, we evaluated the effect of the application of two composts (olive waste “alperujo” and biosolid) at two different doses coupled to the sustainable soil management allowing spontaneous vegetation growing on the soil surface.With this aim, solid state nuclear magnetic resonance was used to trace the evolution of the chemical composition of compost-derived and soil-derived organic matter. Successively, the activity of soil microbial community after the compost addition was monitored by measuring two enzymatic activities (β-glucosidase and dehydrogenase) and soil CO2 respiration. Lastly, the adaptation of microbial communities was quantified using the genes encoding soil enzymes associated with C cycling -glucosidase and laccase-like multicopper oxidases. The results of this study show that biosolid compost has a higher potential for C storage at mid-term (24 to 30 months after first application) than alperujo compost, yielding up to 50% net C sequestration in the topsoil in addition to the compost-derived C applied. We attribute these results to biosolid compost chemical composition, closer to that of the native organic matter, which led to a less abrupt adaptation of soil microbial functioning (lower flushes of water soluble C, lower number of copies of genes encoding enzymatic activities) to the new C source, if compared to alperujo compost. The results encourage the reduction of soil perturbation and the use of organic amendments instead of mineral fertilizers to increase carbon storage and improve sustainability of olive groves in the Mediterranean agroecosystems.

Comprehensive evaluation of metal(loid)s pollution risk and microbial activity characteristics in non-ferrous metal smelting contaminated site

Large amounts of metal(loid)s in abandoned non-ferrous metal smelting site are released to the surrounding environment, causing serious harm to the environment. A weighted comprehensive pollution risk score (CRS), combining two typical metal(loid)s pollution and risk index evaluation methods (speciation and total content indices), and two microbial activity evaluation methods (microcalorimetry and enzyme activities), is proposed to evaluate the pollution degree and environmental risk of metal(loid)s. In the surface soil (Site SS) of contaminated site, the CRS identified seven metal(loid)s (CRSAs (20) > CRSCd (19) > CRSSb (18) > CRSZn (13) = CRSCu (13) > CRSNi (10) > CRSPb (8)) with higher risks, and six (CRSCr (7) > CRSMn (4) = CRSV (4) > CRSAl (3) = CRSMg (3) > CRSTi (2)) with lower risks. Different areas were sorted by the potential ecological risk index (RI) and CRS index from large to small: the deep soil (Site SD) > Site SS > the surrounding wasteland (Site Y), indicating that smelting site was heavily polluted by metal(loid)s. In Site SS, microbial activities were low confirming the inhibition effect of metal(loid)s on soil microbial community activities. Microbial activity characteristics were correlated to metal(loid)s concentration and mobility, indicating that microbial activity represents a potential indicator of pollution. Particularly, FDA activity and TMA are sensitive indicators to estimate soil metal(loid)s pollution level. Our study provides a comprehensive assessment of the metal(loid)s pollution risk, including microbial activity, in non-ferrous metal smelting sites, useful information for the management and remediation of metal(loid)s polluted sites.

Effects of slag and biochar amendments on microorganisms and fractions of soil organic carbon during flooding in a paddy field after two years in southeastern China

Incorporating amendments of industrial waste such as biochar and steel slag in cropland has been used to enhance the storage of soil organic carbon (SOC) while sustaining crop production. Short-term laboratory and field studies have identified important influences of biochar on active SOC fractions associated with soil microbial activity in paddy soils, but the long-term effects remain poorly understood. To address these knowledge gaps, we examined the effects of slag, biochar, and slag+biochar treatments on total SOC concentration, active SOC fractions and soil microbial communities in a paddy field two years after incorporation. Across both two seasons, the addition of slag, biochar, slag+biochar increased soil salinity by 26–80%, 1.3–37% and 42–79%, and also increased soil pH by 0.8–5.7%, 2.1–2.4% and 4.0–6.3%, respectively, relative to the control. SOC concentration was higher in the slag, biochar, and slag+biochar treatments across both rice seasons by 4.3–5%, 0.5–17% and 4.3–7%, respectively. Soil C-pool activity and C-pool management indices in the late paddy season were significantly lower in the slag+biochar treatment than the control by 26.3 and 21.3%, respectively, indicating that the amendments contributed to the stability of SOC. The C concentrations of the biochar and slag amendments affected bacterial abundance more than fungal abundance and affected C cycling. Our study suggests that combined slag and biochar amendments may increase bacterial abundance that may maintain SOC storage and reduce the abundances of potential SOC decomposers in key functional genera, indicating strong coupling relationships with changes of soil properties such as salinity, pH, and SOC concentration. These outcomes due to the amendments (e.g. slag+biochar) may increase microbial C-use efficiency and support the stability of active SOC fractions, with opportunities for long-term C sequestration.

Roots alter soil microbial diversity and interkingdom interactions in diversified agricultural landscapes

The complex interactions between plant roots and soil microorganisms are, broadly, well described. Yet the patterns of microbe–microbe interaction and their association with the root functional traits are less known especially in plant communities at the edges of agricultural landscapes. To address this gap, we measured the active soil microbial communities with and without the presence of plant roots, using in situ root exclusions, in four plant communities at the edges of agricultural fields: undisturbed natural deciduous forests (FOREST1), coniferous forests (FOREST2), rehabilitated agroforests (AGROFOREST) and perennial herbaceous grass buffers (GRASS). Amplicon‐based analysis of 16S rRNA and ITS transcripts was used to evaluate soil bacterial, archaeal and fungal communities, and their interactions, with ‘roots' and with ‘no roots'. Plants roots were measured for a suite of functional traits and explored in association with microbial community composition. Significant differences in bacterial and archaeal but not fungal diversity were observed between soil plots with ‘roots' and with ‘no roots'. Network analysis illustrated intra and inter kingdoms co‐occurrence patterns respond to the presence of plant roots, with GRASS exhibiting distinct patterns in comparison to tree‐dominated soils. A shift in microbial hub from bacterial to fungal was observed with the exclusion of roots; Planctomycetes (OM190)_10 was replaced by Archaeorhizomyces in AGROFOREST site. Microbial taxa strongly correlate with root traits especially specific root length, root diameter and root tissue density indicating root traits are predictors of microbial community composition. This study validates the vital role of root traits in predicting plant–microbe interactions and highlights the key role of fungi in microbial interkingdom interactions when roots are absent. These findings have significant ecosystem level implications, with the rising interest in associated biodiversity in and at the edges of agricultural landscapes, this work suggests that plant community selection for specific root traits may drive microbial community structure and ecosystem services.

Changes in soil microbial community activity and composition following substrate amendment within the MicroResp™ system

Changes in soil microbial community activity and composition following substrate amendment within the MicroResp™ system

Fertilization and Soil Microbial Community: A Review

The present paper reviews the most recent advances regarding the effects of chemical and organic fertilizers on soil microbial communities. Based on the results from the articles considered, some details are presented on how the use of various types of fertilizers affects the composition and activity of soil microbial communities. Soil microbes have different responses to fertilization based on differences in the total carbon (C), nitrogen (N) and phosphorus (P) contents in the soil, along with soil moisture and the presence of plant species. These articles show that the use of chemical fertilizers changes the abundance of microbial populations and stimulates their growth thanks to the nutrient supply added. Overall, however, the data revealed that chemical fertilizers have no significant influence on the richness and diversity of the bacteria and fungi. Instead, the abundance of individual bacterial or fungal species was sensitive to fertilization and was mainly attributed to the changes in the soil chemical properties induced by chemical or organic fertilization. Among the negative effects of chemical fertilization, the decrease in enzymatic activity has been highlighted by several papers, especially in soils that have received the largest amounts of fertilizers together with losses in organic matter.