Soil Microbial Composition Research Articles

Combined metagenomics and metabolomic analysis of microbial community structure and metabolic function in continuous soybean cropping soils of Songnen Plain, China

Continuous cropping has a negative effect on soybean yield. In this study, a positioning experiment was conducted starting in 2015, with three treatments: maize–soybean rotation (SMR), 2-year maize, 2-year soybean rotation cropping (SC2), and 8-year soybean continuous cropping (SC8). We determined soybean yields (2015–2022) and analyzed soil microbial communities, functions, and metabolites composition in the 0–20 cm tillage layer using metagenomics technology and GC–MS technology during soybean flowering in 2022. Results indicated that continuous cropping (SC8) significantly reduced soybean yield compared to crop rotation (SMR) during the experimental period, while SC8 showed higher yield than SC2 in 2022. Compared to SMR, SC8 significantly increased soil N content and significantly decreased pH and TP, AP, and AK content. However, the pH and AK contents of SC8 were significantly higher than those of SC2. LeFSe analysis showed that Friedmanniella, Microlunatus, Nitrososphaera, Rubrobacter, Geodermatophilus, Nitriliruptor were enriched in SC8. Gaiella, Sphaerobacter, Methyloceanibacter were enriched in SC2. Sphingomonas, Cryobacterium, Marmoricola, Haliangium, Arthrobacter, Ramlibacter, Rhizobacter, Pseudolabrys, Methylibium, Variovorax were enriched in SMR. And the relative abundance of Cryobacterium, Marmoricola, Haliangium, Arthrobacter, Ramlibacter, Rhizobacter, Methylibium, Variovorax was significantly positively correlated with yield, while the relative abundance of Gaiella and Sphaerobacter was significantly negatively correlated with yield. SC8 significantly increased the abundance of genes in nitrogen metabolism and significantly decreased the abundance of genes related to phosphorus and potassium metabolism compared with SMR. However, the abundance of genes in potassium metabolism was significantly higher in SC8 than in SC2. Metabolomic analysis showed that compared to SMR, SC8 decreased the abundance of carbohydrates, ketones, and lipid. However, the abundance of carbohydrates, ketones, and lipid was significantly higher in SC8 than in SC2. Mantel test showed that soil pH and AK significantly affected soil microbial community, function, and metabolite composition. Correlation analysis showed significant correlation between soil metabolites and microorganisms, metabolic functions.Graphical

Soil microbial diversity and composition response to degradation of the alpine meadow in the southeastern Qinghai-Tibet Plateau.

With the interaction between global climate change and unreasonable human utilization, the alpine meadows on the Qinghai-Tibet Plateau have suffered various weathering degrees. Uncovering the degradation mechanism and restoration strategies can be facilitated by gaining insights into the diversity of soil microflora during meadow degradation. Therefore, we used Illumina sequencing technology to investigate the patterns of soil microbial diversity, microbial community composition, and the driving factors of microbial change in all non-degraded (ND), lightly degraded (LD), moderately degraded (MD), and severely degraded (SD) alpine meadows in the southeastern Qinghai-Tibet Plateau. Our results pointed out that with the intensification of degradation, vegetation characteristics were significantly reduced, and soil parameters significantly varied among all degraded meadows. The contents of soil organic carbon (SOC), total nitrogen (TN), available phosphorus (AN), and total phosphorous (AK) in soils decreased with the increase of degradation. The dominant bacterial phyla were the same regardless of the meadow degradation level with Actinobacteria (37.67%) and Proteobacteria (20.62%) having the highest relative abundance. Meanwhile, the dominant fungi were Ascomycota (49.9%). Based on the linear discriminant analysis (LDA) and effect size (LEfSe) method, 38 bacterial and 49 fungal species were found to be affected in the degraded alpine meadow, most of which belonged to Actinobacteria and Ascomycota, respectively. Mantel test analysis illustrated that the bacterial community was mainly significantly dependent on below-ground biomass, pH, soil organic carbon, and total nitrogen, while the fungal community was significantly dependent on soil organic carbon, total nitrogen, available nitrogen, and available potassium. These results suggest that the degeneration of alpine meadows contributes to the variability of the diversity and composition of microflora on the Tibetan plateau. Yet this effect is mainly dependent on soil factors.

Effect of phenolics on soil microbe distribution, plant growth, and gall formation

Phenolic compounds, abundant secondary metabolites in plants, profoundly influence soil ecosystems, plant growth, and interactions with herbivores. In this study, we explore the intricate relationships between phenolics, soil microbes, and gall formation in Ageratina adenophora (A. adenophora), an invasive plant species in China known for its allelopathic traits. Using metabolomic and microbial profiling, significant differences in soil microbial composition and metabolite profiles were observed between bulk and rhizosphere soil samples. Phenolics influenced bacterial communities, with distinct microbial populations enriched in each soil type. Additionally, phenolics impacted soil metabolic processes, with variations observed in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis between different soil treatments. Analysis of phenolic content in plant and soil samples revealed considerable variations, with higher concentrations observed in certain plant tissues and soil types. Bioactive phenols extracted from plant and soil samples were identified using gas chromatography/mass spectrometry (GC–MS), providing insights into the diverse chemical composition of these compounds. Furthermore, the effects of phenolics on plant growth and gall formation were investigated. Phenols exhibited both stimulatory and inhibitory effects on plant growth, with optimal concentrations promoting emergence but higher concentrations hindering growth. Gall formation was influenced by phenolic concentrations, leading to structural alterations in stem tissue and gall morphology. Histochemical analysis revealed starch and lipid accumulation in gall tissues, indicating metabolic changes induced by phenolics. The presence of phenolics disrupted tissue structures and influenced vascular bundle orientation in gall tissues. Overall, our study highlights the multifaceted roles of phenolic compounds in soil ecosystems, plant development, and gall formation, facilitating the utilization of secondary metabolites in agriculture.

Soil, Plant, and Microorganism Interactions Drive Secondary Succession in Alpine Grassland Restoration.

Plant secondary succession has been explored extensively in restoring degraded grasslands in semiarid or dry environments. However, the dynamics of soil microbial communities and their interactions with plant succession following restoration efforts remain understudied, particularly in alpine ecosystems. This study investigates the interplay between soil properties, plant communities, and microbial populations across a chronosequence of grassland restoration on the Qinghai-Tibet Plateau in China. We examined five succession stages representing artificial grasslands of varying recovery durations from 0 to 19. We characterized soil microbial compositions using high-throughput sequencing, enzymatic activity assessments, and biomass analyses. Our findings reveal distinct plant and microbial secondary succession patterns, marked by increased soil organic carbon, total phosphorus, and NH4+-N contents. Soil microbial biomass, enzymatic activities, and microbial community diversity increased as recovery time progressed, attributed to increased plant aboveground biomass, cover, and diversity. The observed patterns in biomass and diversity dynamics of plant, bacterial, and fungal communities suggest parallel plant and fungal succession occurrences. Indicators of bacterial and fungal communities, including biomass, enzymatic activities, and community composition, exhibited sensitivity to variations in plant biomass and diversity. Fungal succession, in particular, exhibited susceptibility to changes in the soil C: N ratio. Our results underscore the significant roles of plant biomass, cover, and diversity in shaping microbial community composition attributed to vegetation-induced alterations in soil nutrients and soil microclimates. This study contributes valuable insights into the intricate relationships driving secondary succession in alpine grassland restoration.

Soil Microbial Community Structure and Functional Diversity Character of Abandoned Farmland in Minqin Oasis

To clarify the impact of the structure and function of soil microbial communities in the stage of abandoned farmland, three different stages of land abandoned in desert oasis areas were selected as the research objects. We used metagenomic sequencing technology to research soil microbial community structure and functional diversity characteristics of different stages of abandoned farmland. The results showed that there were significant differences in the relative abundance of the dominant phyla Actinobacteria, Proteobacteria, and Gemmatimonadetes in the soil of the three stages of returning farmland. Compared with that in the early stage of abandoned farmland, the later stage of abandoned farmland restoration increased the gene proportion involved in Quorum sensing, porphyrin and chlorophyll metabolism, pantothenate and CoA biosynthesis, and styrene degradation, and there was a significant difference in relative abundance (P<0.05), which indicated that different stages of abandoned farmland had changed the functional potential of the nutrient cycle and energy metabolism in soil microbial communities. The RDA results showed that EC, AK, and TN had a significant impact on the functional composition of soil microbes, and soil EC had the greatest impact on microbial functional composition. The results showed that different stages of abandoned farmland had a significant impact on the soil microbial community structure and functional composition. In the ecological restoration of abandoned farmland in Minqin Oasis, the sensitivity of microbial community structure and functional composition to soil restoration at different stages should be considered using comprehensive relevant indicators.

Effects of land-use patterns on soil microbial diversity and composition in the Loess Plateau, China

Effects of land-use patterns on soil microbial diversity and composition in the Loess Plateau, China

Properties and Fungal Communities of Different Soils for Growth of the Medicinal Asian Water Plantain, Alisma orientale, in Fujian, China.

The Asian water plantain, Alisma orientale (Sam.) Juzep, is a traditional Chinese medicinal plant. The dried tubers of the Alisma orientale, commonly referred to as Alismatis rhizome (AR), have long been used in traditional Chinese medicine to treat a variety of diseases. Soil properties and the soil microbial composition are known to affect the quality and bioactivity of plants. Here, we sought to identify variations in soil fungal communities and soil properties to determine which would be optimal for cultivation of A. orietale. Soil properties, heavy metal content, and pesticide residues were determined from soils derived from four different agricultural regions around Shaowu City, Fujian, China, that had previously been cultivated with various crops, namely, Shui Dao Tu (SDT, rice), Guo Shu Tu (GST, pecan), Cha Shu Tu (CST, tea trees), and Sang Shen Tu (SST, mulberry). As fungi can either positively or negatively impact plant growth, the fungal communities in the different soils were characterized using long-read PacBio sequencing. Finally, we examined the quality of A. orientale grown in the different soils. Our results show that fungal community diversity of the GST soil was the highest with saprotrophs the main functional modes in these and SDT soils. Our data show that GST and SDT soils were most suitable for A. orientale growth, with the quality of the AR tubers harvested from GST soil being the highest. These data provide a systematic approach at soil properties of agricultural lands in need of replacement and/or rotating crops. Based on our findings, GST was identified as the optimal soil for planting A. orientale, providing a new resource for local farmers.

The Characteristics of the Root-Zone Soil's Biological Properties and Microbial Community Structure in Grafted Star Anise Plantations.

Extensive management seriously affects the output, quality, and sustainable development of star anise, and grafting is commonly used to improve its production and quality. Although many studies have explored the effects of grafting on soil microorganisms for other plants, there is a lack of research on aromatic plants, especially on the soil ecosystems of star anise plantations. The effect of grafting star anise on the soil's biological characteristics and microbial composition remains unclear. The soil's enzyme activities, soil microbial biomass, and microbial community composition in grafted and non-grafted star anise plantations in Guangxi, China were studied using high-throughput sequencing technology. The results showed that the microbial biomass carbon and phosphorus contents in the soils of grafted star anise were significantly lower and the phosphatase activity was significantly higher than in the soils of non-grafted star anise. In comparison with the soils of non-grafted star anise plantations, the proportions of Proteobacteria, Acidobacteria, Actinobacteria, and WPS-2 decreased and the proportions of Chloroflexi, Planctomycetes, and Verrucomicrobia increased in the grafted star anise plantations. Meanwhile, Bacteroidetes was a dominant bacterial phylum unique to the soil of the grafted star anise plantations. Moreover, the proportions of Ascomycota and Basidiomycota increased and the proportions of Mortierellomycota and unclassified_k_Fungi decreased in the soils of the grafted star anise plantations. Furthermore, Basidiomycota and Rozellomycota had significant dominance in the grafted star anise plantations. In general, grafting can improve soil fertility and maintain soil health by promoting soil nutrient cycling and increasing the soil's microbial diversity.

Dynamics of the soil microbial community associated with Morchella cultivation: diversity, assembly mechanism and yield prediction.

The artificial cultivation of morels has been a global research focus owing to production variability. Understanding the microbial ecology in cultivated soil is essential to increase morel yield and alleviate pathogen harm. A total of nine Morchella cultivation experiments in four soil field types, forest, paddy, greenhouse, and orchard in Shanghai city were performed to determine the potential ecological relationship between Morchella growth and soil microbial ecology. Generally, significant variation was observed in the soil microbial diversity and composition between the different experimental field types. The niche width analysis indicated that the bacterial habitat niche breadth was significantly greater than the fungal community width, which was further confirmed by a null model that revealed that homogeneous selection could explain 46.26 and 53.64% of the variance in the bacterial and fungal assemblies, respectively. Moreover, the neutral community model revealed that stochastic processes dominate the bacterial community in forests and paddies and both the bacterial and fungal communities in orchard crops, whereas deterministic processes mostly govern the fungal community in forests and paddies and both the bacterial and the fungal communities in greenhouses. Furthermore, co-occurrence patterns were constructed, and the results demonstrated that the dynamics of the soil microbial community are related to fluctuations in soil physicochemical characteristics, especially soil potassium. Importantly, structural equation modeling further demonstrated that the experimental soil type significantly affects the potassium content of the soil, which can directly or indirectly promote Morchella yield by inhibiting soil fungal richness. This was the first study to predict morel yield through soil potassium fertilizer and soil fungal community richness, which provides new insights into deciphering the importance of microbial ecology in morel agroecosystems.

Soil microbial composition, diversity, and network stability in intercropping versus monoculture responded differently to drought

Drought alters the diversity, composition, and network stability of microbial communities. Natural resources benefit from intercropping, particularly cereal-legume intercropping, where soil microbes are important for biogeochemical cycles and plant growth. However, little is understood about how different cropping environments' soil microbial communities respond to drought. Here, we examined bulk and rhizospheric soil microbial communities in the cereal/legume monoculture versus intercropping in a three-year drought legacy field experiment. We found that drought treatment decreased the microbial alpha diversity compared to the control with no significant differences between monoculture and intercropping systems or bulk soil and rhizosphere soil. Moreover, drought was the main factor affecting microbial community compositions, thereby increasing the abundance of Actinobacteriota, Firmicutes, and Basidiomycota and decreasing the abundance of Proteobacteria, Acidobacteriota, and Ascomycota. Soil labile organic carbon and nitrogen, as well as enzyme activities, were the main environmental factors affecting the bacterial and fungal community compositions. The co-occurrence network analysis revealed that, in response to drought, the intercropping system produced larger, more complex, and more stable soil fungal networks and less stable bacterial networks compared to the monoculture system, even though the microbial diversity was unaffected by the cropping system used. Taken together, drought was the principal factor accounting for variations in microbial communities and changes in soil properties. Even though microbial diversity and structure did not vary significantly in response to drought legacy between monoculture and intercropping systems, the co-occurrence of bacterial and fungal taxa showed notable differences. These findings provided a new strategy to cope with drought stress by optimizing the cropping systems.

Enhanced phytoremediation of metal contaminated soils aimed at decreasing the risk of antibiotic resistance dissemination

The enhanced phytoremediation of metal contaminated soils holds great promise for the recovery of soil health and functionality, while providing a range of co-benefits, from an environmental and human health perspective, derived from the revegetation of the degraded sites and the concomitant delivery of ecosystem services. Due to diverse evolutionary co-selection mechanisms between metal resistance and antibiotic resistance in bacteria, metal contaminated soils are considered potential reservoirs of antibiotic resistant bacteria (ARB) which can contribute to the existing antibiotic resistance crisis. During the enhanced phytoremediation of metal contaminated soils, the application of organic wastes (e.g., manure, slurry, sewage sludge) as soil amendments can aggravate the risk of antibiotic resistance spread, because they often contain ARB which harbor antibiotic resistance genes (ARGs) that can then be propagated among soil bacterial populations through horizontal gene transfer (HGT). Due to the magnitude and criticality of the antibiotic resistance crisis, as well as the higher risk of spread and dispersal of ARB and ARGs (they make copies of themselves) compared to metals, it is proposed here to aim enhanced phytoremediation strategies towards decreasing the soil resistome (and, hence, the risk of its potential link with the human resistome), while reducing total and/or bioavailable metal concentrations and restoring soil health and the delivery of ecosystem services. To this purpose, a decalogue of practices is tentatively suggested. Finally, a proper management of plant and soil microbial compositions is a most crucial aspect, together with the selection of the right organic wastes and phytoremediation practices.

Microbial Community Response to Alpine Meadow Degradation and Its Impact on Soil Nutrient Cycling

The degradation of alpine meadows on the Qinghai–Tibet Plateau is a major issue affecting both the ecology and the economy. Microorganisms play an important role in soil nutrient cycling and the regulation of ecosystem function. This study aimed to investigate the species composition and diversity of microbial communities and understand the response of microbial communities to changes in physicochemical properties resulting from meadow degradation. In this study, the soil bacterial and fungal communities’ composition and diversity of alpine meadows of degradation gradient were sequenced by high-throughput sequencing. During the process of grassland degradation, there were 59 bacterial taxa and 29 fungal taxa showing significant differences. The relative abundance of meadow pathogenic fungi significantly increased (p &lt; 0.05). PICRUSt2 analysis showed a decrease in synthesis-related functional gene abundance and an increase in metabolism-related functional gene abundance. FUNGuild analysis showed that symbiotic and saprophytic nutrient fungi decreased significantly (p &lt; 0.05). The soil nutrient cycling was mainly influenced by the beta diversity of microbial communities. Grassland degradation affects soil structure, thereby affecting the diversity of soil microbial composition and functional soil nutrient content. This work reveals the response of microbial communities to the degradation of alpine meadows and their impact on nutrient cycling, providing theoretical support for the protection and sustainable development of alpine meadows.

Biochar regulates the functions of keystone taxa to reduce p-coumaric acid accumulation in soil.

Applying biochar (BC) to reduce toxic substance accumulation in soil, either through direct adsorption or modulation of the microbial community, has received considerable attention. However, a knowledge gap exists regarding how BC regulates microbial community structure and functions to mitigate toxic substance accumulation. We previously identified p-coumaric acid (p-CA) as a representative autotoxin in tobacco rhizosphere soil. On this basis, this study simulated a soil environment with p-CA accumulation to investigate the impacts of BC on p-CA, soil physicochemical properties, and microbial community structure and function. The results showed that p-CA could be directly adsorbed onto BC, which followed the pseudo-second-order kinetic model (R 2 = 0.996). A pot experiment revealed that BC significantly reduced soil p-CA, altered soil microbial composition, and enhanced bacterial community diversity. A weighted correlation network analysis showed a close association between taxon 1 in the microbial network and p-CA, suggesting a pivotal role for this taxon in reducing p-CA, with Devosia and Nocardioides identified as potential key contributors to this process. The prediction of possible keystone taxa functions showed that BC increased the relative abundances of aromatic compound degraders. Mantel tests indicated that soil organic matter exerted the greatest influence on keystone taxa functions and hub genera. These findings suggest that BC may either directly chemisorb p-CA or indirectly facilitate p-CA degradation by regulating the functioning of keystone taxa. The results of this study provide a novel perspective for further investigation of the mechanisms through which BC reduces the accumulation of toxic substances in soil.

Seasonal changes of soil microbiota and its association with environmental factors in coal mining subsidence area

As a special type of wetland, the new wetland in the coal mining subsidence area is highly sensitive to environmental changes. In recent years, more and more attention has been paid to the studies of soil microbial diversity in newly born wetlands in coal mining subsidence areas. However, there are few reports on the seasonal variation of soil microbial diversity and its relationship with soil physical and chemical properties. In this study, 16S rRNA gene sequencing technology was used to analyze the seasonal changes of soil microbial composition and functional diversity in newly formed wetlands in coal mining subsidence areas, and to determine the seasonal changes of soil nutrient elements and physical and chemical properties in coal mining subsidence areas, so as to analyze the correlation between soil microbial diversity and soil nutrient elements and physical and chemical properties in newly formed wetlands in coal mining subsidence areas. A total of 16,050 OTUs were obtained after sample gene noise reduction. Proteobacteria, Acidobacteriota and Bacteroidota were the highest abundance in the coal mining subsidence area of Jining. The two seasons gathered separately, and temperature (Temp), total phosphorus (TP), available phosphorus (AP), total organic carbon (TOC) and dry matter content (DMC) were the key factors for the seasonal change of soil microbial community in the wetland of the coal mining subsidence area of Jining. The contents of Temp, AP and TP were significantly correlated with the abundance of soil microorganisms in summer subsidence area, while the contents of DMC and TOC were significantly correlated with the abundance of soil microorganisms in winter subsidence area. Soil microbial diversity in coal mining subsidence area was correlated with the seasons. Temp, TP, AP, TOC and DMC were the key factors for the seasonal change of soil microbial community in the wetland of the coal mining subsidence area of Jining.

Mechanisms of microbial-driven changes in soil ecological stoichiometry around gold mines

In this study, we used soils with different pollution and nutrient levels (non-polluted S1, highly polluted low-nutrient S2, and highly polluted high nutrient S3) around the gold mine tailing ponds, and combined with metabolic limitation modeling and macro-genomics approaches, aiming to investigate the relationship between soil microbial composition and soil eco-chemometrics characteristics under heavy metal stress. The results showed that heavy pollution resulted in reduced SOC, TN, microbial biomass, and with C- and P- acquisition (BG, CBH, ALP) as well as nitrogen limitation of soil microbial metabolism in soils (S2, S3). Further analysis by macrogenomics showed that heavy metal contamination led to an increase in α-microbial diversity and altered the composition of microbial communities in the soil. The cycling of C, N, and P nutrients was altered by affecting the relative abundance of Anaeromyxobacter, Steroidobacter, Bradyrhizobium, Acidobacterium, Limnochorda (predominantly in the Ascomycetes and Acidobacteria phyla), with the most pronounced effect on the composition of microorganisms synthesizing C-acquiring enzymes, and heavy metals and pH were the main influences on ecological stoichiometry. The results of this study are useful for understanding the sustainability of ecological remediation in heavy metal contaminated areas and for developing ecological restoration strategies.

Changes in Nutrient-Regulated Soil Microbial Communities in Soils Concomitant with Grassland Restoration in the Alpine Mining Region of the Qilian Mountains

In response to the significant ecological damage caused by unsustainable mining practices in the Qilian Mountains, ecological restoration projects have been undertaken in recent years. Analyzing the changes in soil microbial communities during the restoration process of mine meadows helps to reveal the mechanism of the restoration process in alpine mining areas. To explore the characteristics of soil microbial community distribution and their relationships with soil environmental factors during the restoration of alpine grasslands in the Qilian Mountains, we conducted surveys and analyses in two restoration levels low restoration (LR) and high restoration (HR) in the eastern Qilian Mountains, along with an undisturbed natural grassland control (NG). We found that as the degree of high-altitude mining area recovery increases, there were significant increases in vegetation cover, vegetation height, above-ground biomass, vegetation Shannon–Wiener index, soil organic carbon (SOC), soil water content (SWC), total nitrogen (TN), total phosphorus (TP), total potassium (TK), available phosphorus (AP), and available nitrogen (AN). Conversely, soil pH and electrical conductivity (EC) significantly decreased, with soil pH decreasing from 6.93 to 4.13. Restoration of high-altitude mining area grasslands significantly alters the distribution and composition of soil bacteria and fungi, while the impact on soil microbial community changes was not significant. Notably, with increasing recovery level, the dominant bacterial phyla are Acidobacteria and Proteobacteria, while the dominant fungal phyla are Ascomycota and Basidiomycota. These results indicate that changes in vegetation and soil properties both affect the composition of soil microbial communities, with soil properties having a greater influence. Soil fertility and nutrient levels emerge as the primary drivers influencing soil microbial composition communities and the degree of high-altitude mining area grassland recovery.

Correlation between microbial communities and volatile organic compounds in an urban soil provides clues on soil quality towards sustainability of city flowerbeds

Soil functionality is critical to the biosphere as it provides ecosystem services relevant for a healthy planet. The soil microbial composition is significantly impacted by anthropogenic activities, including urbanization. In this context, the study of soil microorganisms associated to urban green spaces has started to be crucial toward sustainable city development. Microbes living in the soil produce and degrade volatile organic compounds (VOCs). The VOC profiles may be used to distinguish between soils with various characteristics and management practices, reflecting variations in the activity of soil microbes that use a variety of metabolic pathways. Here, a combined approach based on DNA metabarcoding and GC-MS analysis was used to evaluate the soil quality from urban flowerbeds in Prato (Tuscany, Italy) in terms of microbial biodiversity and VOC emission profiles, with the final aim of evaluating the possible correlation between composition of microbial community and VOC patterns. Results showed that VOCs in the considered soil originated from anthropic and biological activity, and significant correlations between specific microbial taxa and VOCs were detected. Overall, the study demonstrated the feasibility of the use of microbe-VOC correlation as a proxy for soil quality assessment in urban soils.

Pot experimental trial for assessing the role of different composts on decontamination and reclamation of a polluted soil from an illegal dump site in Southern Italy using Brassica juncea and Sorghum bicolor

A pot experiment was carried out to evaluate the remediation potential of Brassica juncea and Sorghum bicolor in the decontamination of soil polluted with heavy metals such as copper, lead, tin, and zinc along with polychlorinated biphenyls, polycyclic aromatic hydrocarbons, and heavy hydrocarbons. Two composts obtained from different composting processes were tested as biostimulating agents. At the end of the trial, the effect of plant/compost combinations on soil microbial composition, contaminant removal, biochemical indicators, and plant biomass production was determined. The results highlighted that compost addition improved plant biomass despite slowing down plants’ removal of organic and inorganic contaminants. In addition, compost partially enhanced the soil biochemical indicators and modified the relative abundance of the rhizosphere microorganisms. Sorghum showed better mitigation performance than Brassica due to its higher growth. The soil fertility level, the choice of plant species, and microbial richness were found fundamental to perform soil remediation. In contrast, compost was relevant for a higher crop biomass yield.Graphical abstract

The Impact and Determinants of Mountainous Topographical Factors on Soil Microbial Community Characteristics.

Soil bacterial and fungal community communities play significant ecological functions in mountain ecosystems. However, it is not clear how topographic factors and soil physicochemical properties influence changes in microbial community structure and diversity. This study aims to investigate how altitude and slope orientation affect soil physicochemical properties, soil microbial communities, and their contributing factors. The assessment was conducted using Illumina MiSeq sequencing in various altitude gradients and on slopes with different aspects (shady slopes and sunny slopes) in the subalpine meadow of Dongling Mountain, Beijing. Topographical factors had a significant effect on soil physicochemical properties: the primary factors determining the structure of microbial communities are total potassium (TK), ammonium nitrogen (NH4+-N), and soil organic carbon (SOC). There was no significant change in the diversity of the bacterial community, whereas the diversity of the fungal community displayed a single-peaked trend. The effect of slope orientation on microbial communities was not as significant as the effect of elevation on them. The number of bacterial communities with significant differences showed a unimodal trend, while the number of fungal communities showed a decreasing trend. The co-occurrence network of fungal communities exhibits greater intricacy than that of bacterial communities, and bacterial communities are more complex in soils with sunny slopes compared to soils with shady slopes, and the opposite is true for fungal communities. The identification of the main factors that control soil microbial diversity and composition in this study, provided the groundwork for investigating the soil microbial response and adaptation to environmental changes in subalpine meadows.

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.