Soil Microbial Profiles Research Articles

Repercussions of Prolonged Pesticide Use on Natural Soil Microbiome Dynamics Using Metagenomics Approach.

The residual pesticides in soil can affect the natural microbiome composition and genetic profile that drive nutrient cycling and soil fertility. In the present study, metagenomic approach was leveraged to determine modulations in nutrient cycling and microbial composition along with connected nexus of pesticide, antibiotic, and heavy metal resistance in selected crop and fallow soils having history of consistent pesticide applications. GC-MS analysis estimated residuals of chlorpyrifos, hexachlorbenzene, and dieldrin showing persistent nature of pesticides that pose selective pressure for microbial adaptation. Taxonomic profiling showed increased abundance of pesticide degrading Streptomyces, Xanthomonas, Cupriavidus, and Pseudomonas across the selected soils. Genes encoding for pesticide degrading cytochrome p450, organophosphorus hydrolase, aldehyde dehydrogenase, and oxidase were predominant and positively correlated with Bacillus, Sphingobium, and Burkholderia. Nitrogen-fixing genes (nifH, narB, and nir) were relatively less abundant in crop soils, correlating to the decrease in nitrogen-fixing bacteria (Anabaena, Pantoea, and Azotobacter). Microbial enzymes involved in carbon (pfkA, gap, pgi, and tpiA) and phosphorus cycle (gmbh and phnJ) were significantly higher in crop soils indicating extensive utilization of pesticide residuals as a nutrient source by the indigenous soil microbiota. Additionally, presence of antibiotic and heavy metal resistance genes suggested potential cross-resistance under pressure from pesticide residues. The results implied selective increase in pesticide degrading microbes with decrease in beneficial bacteria that resulted in reduced soil health and fertility. The assessment of agricultural soil microbial profile will provide a framework to develop sustainable agriculture practices to conserve soil health and fertility.

Scope, Distribution, and Cause of the Peanut Kernel Shrivel (PKS) Syndrome: An Emerging Threat to Australia’s Peanut Industry

The cause of peanut kernel shrivel (PKS) syndrome, affecting peanut crops in Australia’s growing regions, is currently unknown. It is estimated that PKS is costing the peanut industry more than AUD 5 M p.a. and is a potential threat to the industry. Previous investigations have ruled out all abiotic factors and most biotic factors as the cause of PKS. This research aimed at investigating the scope, distribution, and cause of the PKS syndrome. The survey showed PKS symptoms to be present in peanut crops in all the growing regions surveyed. Based on our study of culturable microorganisms, there appears to be no clear-cut involvement of plant pathogenic bacteria and fungi; however, Fusarium spp. were revealed as the most prevalent fungi in affected plants. Moreover, the soil metagenomics study revealed Fusarium spp. as the most abundant fungal communities in the soil microbial profile, and they could contribute to the PKS syndrome. The consistent presence observed of the identified Fusarium oxysporum in PKS-affected samples could indicate a role for this pathogen in the syndrome, especially in conjunction with abiotic stressors. The pathogenicity testing of F. oxysporum resulted in very mild PKS symptoms. A separate report suggesting the involvement of phytoplasma in the PKS syndrome raises the possibility of an interplay of biotic factors in the development of this disease. Further investigation is warranted to determine the true cause or causes of this disease.

Synergistic Effects of Salicylic Acid and Bacillus butanolivorans KJ40 for Enhancing Napa Cabbage (Brassica napa subsp. pekinensis) Resilience to Water-Deficit Stress

Climate change exacerbates drought, globally impacting crop production and necessitating the adoption of sustainable strategies. This study investigates the potential synergistic effects of salicylic acid (SA) and Bacillus butanolivorans KJ40 (KJ40) on napa cabbage (Brassica rapa subsp. pekinensis) under water-deficit stress conditions by watering withheld for five days. Results demonstrate that the combined application of KJ40 and SA, particularly at concentrations of 0.5 mM and 1 mM, significantly enhances plant growth and mitigates the negative impacts of water deficit. Moreover, the combination treatment with SA (0.5 mM) and KJ40 (1 × 108 cells/mL) reduces lipid oxidation and enhances antioxidant enzyme activity, indicating improved plant stress tolerance. Analysis of soil microbial profiles reveals alterations in metabolic activity and substrate utilization patterns, suggesting potential changes in rhizosphere dynamics. Additionally, this study examines the impact of SA on KJ40 population dynamics in soil, revealing concentration-dependent effects on bacterial survival. Overall, the combination of KJ40 and SA was effective in mitigating water-deficit stress in napa cabbage. These findings highlight the combination as a novel synergistic strategy to enhance plant resilience to water-deficit stress, offering insights into plant–microbe interactions and soil ecosystem dynamics.

Leaf carbon chemistry effectively manipulated soil microbial profiles and induced metabolic adjustments under different revegetation types in the loess Plateau, China

Microorganisms are essential components of underground life systems and drive elemental cycling between plants and soil. Yet, in the ecologically fragile Loess Plateau, scant attention has been paid to the response of microbial communities to organic carbon (C) chemistry of both leaves and soils under different revegetation conditions, as well as subsequent alternation in their C metabolic functions. Here, Fourier transform infrared (FTIR) spectrum, amplicon sequencing of 16S rRNA and ITS, and temporal incubation with Biolog-Eco 96 plates were combined to explore the vegetative heterogeneity of microbial community properties and metabolic functions, as well as their regulatory mechanisms in three typical revegetation types including Robinia pseudoacacia L. (RF), Caragana korshinskii KOM. (SL), and abandoned grassland (AG). We observed higher bacterial-to-fungal ratios (B: F = 270.18) and richer copiotrophic bacteria (Proteobacteria = 33.08%) in RF soil than those in AG soil, suggesting that microbes were dominated by r-strategists in soil under RF treatment, which is mainly related to long-term priming of highly bioavailable leaf C (higher proportion of aromatic and hydrophilic functional groups and lower hydrophobicity). Conversely, microbial taxa in AG soil, which was characterized by higher leaf organic C hydrophobicity (1.39), were dominated by relatively more abundant fungi (lower B: F ratio = 149.49) and oligotrophic bacteria (Actinobacteria = 29.30%). The co-occurrence network analysis showed that microbial interactive associations in RF and AG soil were more complex and connective than in SL soil. Furthermore, Biolog-Eco plate experiments revealed that microorganisms tended to utilize labile C compounds (carbohydrates and amino acids) in RF soil and resistant C compounds (polymers) in AG soil, which were consistent with the substrate adaptation strategies of predominant microbial trophic groups in different revegetation environments. Meanwhile, we observed greater microbial metabolic activity and diversity advantages in RF vegetation. Collectively, we suggest that besides the nutrient variables in the leaf-soil system, the long-term regulation of the microbial community by the C chemistry of the leaf sequentially alters the microbial metabolic profiles in a domino-like manner. RF afforestation is more conducive to restoring soil microbial fertility (including microbial abundance, diversity, interactive association, and metabolic capacity). Our study potentially paves the way for achieving well-managed soil health and accurate prediction of C pool dynamics in areas undergoing ecological restoration of the Loess Plateau.

Spatial and Temporal Changes of Soil Microbial Communities in Field Tomato Production as Affected by Anaerobic Soil Disinfestation

Anaerobic soil disinfestation (ASD) has been demonstrated as an effective alternative to pre-plant chemical soil fumigation (CSF) commonly used to control soilborne pathogens. However, the ASD effects on spatial and temporal changes in soil microbial communities remain poorly understood in production systems with low soilborne disease pressure. The objective of this study was to assess the influence of ASD treatments on soil microbial community composition at different soil depths during the spring tomato production season in Florida. Soil treatments included ASD using 6.9 m3 ha−1 of molasses with 11 Mg ha−1 of composted poultry litter (CPL) (ASD0.5), ASD with 13.9 m3 ha−1 of molasses and 22 Mg ha−1 CPL (ASD1.0), and chemical soil fumigation (CSF) using a mixture of 1,3-dichloropropene and chloropicrin. Soil microbial community composition was measured at soil depths of 0–15 and 15–30 cm using phospholipid fatty acid (PLFA) analysis at 0, 36, 76, and 99 days after transplanting (DAT). Fatty acid methyl esters were categorized into biomarker groups including total microbial biomass (TMB), G+ bacteria (G+), G− bacteria (G−), actinomycetes (Actino), arbuscular mycorrhizal fungi (AMF), protozoa, and general fungi (F). Soil concentrations of G+, Actino, F, AMF, and the ratio of F:bacteria (B) were significantly impacted by a soil treatment × soil depth × sampling time three-way interaction. All the microbial biomarkers were significantly affected by soil treatment × sampling depth two-way interactions except for protozoa and F:B ratio. Concentrations of TMB, Actino, AMF, F, G+, and G− bacteria were significantly increased in ASD treated soils at both 0–15 and 15–30 cm soil depths across different sampling times compared with CSF. In addition, the concentrations of G+ and G− bacteria, AMF, F, and TMB were higher at 0–15 vs. 15–30 cm soil depth under ASD treatments, whereas no soil depth differences were observed in CSF. Discriminant analysis further confirmed that soil microbial community composition was distinctly different in CSF compared with ASD treatments. The soil microbial profile was well-differentiated between the two soil depths under ASD treatments but not in CSF, while the enhancement of PLFA biomarkers by ASD decreased with increasing soil depth.

Toxicological effects of WS2 nanomaterials on rice plants and associated soil microbes

As an important member of transition-metal dichalcogenides family, tungsten disulfides nanomaterials (WS2 NMs) have a wide range of applications. To date, their environmental risks remain largely unknown. In this study, rice plants were grown in soil amended with different concentrations (0, 10, and 100 mg/kg) of WS2 NMs for 4 weeks. WS2 NMs at 100 mg/kg significantly increased MDA (malondialdehyde) content and decreased total antioxidant capacities of leaves, indicating the oxidative response induced by WS2 NMs. Meanwhile, WS2 NMs at 100 mg/kg significantly decreased root biomass compared to control, indicating the negative impacts of WS2 NMs on plant growth. While exposure to 100 mg/kg WS2 NMs significantly increased soil bioavailable Cu, Fe, Zn, and Olsen-P, and increased the content of Cu, Fe, Zn, and P in rice leaves. Inductively coupled plasma-optical emission spectroscopy (ICP-OES) analysis showed that W was taken up by rice roots and translocated into leaves. The impact of WS2 on soil microbial communities was evaluated by 16S rRNA gene sequencing. WS2 NMs at 100 mg/kg significantly decreased soil microbial diversity, as indicated by decreased Shannon index. In addition, 100 mg/kg WS2 shifted the soil microbial profile, the relative abundance of the phylum Acidobacteriota decreased, and Actinobacteriota increased. Taken together, the soil microbial community's diversity and composition have been altered upon exposure to 100 mg/kg WS2 NMs. The results of this study provide some basic information regarding the environmental behavior and phytotoxicity of WS2 NMs, which is valuable for safe use of WS2 NMs.

Wheat Production Alters Soil Microbial Profiles and Enhances Beneficial Microbes in Double-Cropping Soybean

Plant-parasitic nematodes represent a substantial constraint on global food security by reducing the yield potential of all major crops. The soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is widely distributed across important soybean production areas of the U.S., being the major soybean yield-limiting factor, especially in the Midwestern U.S. Double cropped (DC) soybean is commonly planted following winter wheat. We previously reported double-cropping soybean fields with reduced SCN counts compared to fallow at both R1 growth stage (beginning of flowering) (−31.8%) and after soybean harvest (−32.7%). To test if higher counts of beneficial and SCN antagonistic microorganisms could be correlated with the suppression of SCN in fields previously planted with wheat, three field locations with noted SCN suppression were selected for a metagenomics study. Ten subplots were selected (5 wheat and 5 fallow pre-soybean) from each location. A total of 90 soil samples were selected: 3 fields ×2 treatments × 3 timepoints × 5 replications. Three DNA markers targeted distinct microbial groups: bacteria (16S V4-V5), fungi (ITS2), and Fusarium (tef1). Amplicons were sequenced using an Illumina MiSeq platform (300 bp paired-end). Sequencing datasets were processed in R using the DADA2 pipeline. Fungal populations were affected by location in all sampling periods and differed significantly between DC and fallow plots at soybean planting and after harvest (P < 0.001). Several enriched fungal and bacterial taxa in wheat plots, including Mortierella, Exophiala, Conocybe, Rhizobacter spp., and others, were previously reported to parasitize SCN and other plant-parasitic nematodes, suggesting a potential role of beneficial microbes in suppression of SCN in soybean fields double-cropped with wheat.

Exploiting the Innate Potential of Sorghum/Sorghum-Sudangrass Cover Crops to Improve Soil Microbial Profile That Can Lead to Suppression of Plant-Parasitic Nematodes.

Sorghum/sorghum–sudangrass hybrids (SSgH) have been used as a cover crop to improve soil health by adding soil organic matter, enhancing microbial activities, and suppressing soil-borne pathogens in various cropping systems. A series of SSgH were screened for (1) allelopathic suppression and (2) improvement of soil edaphic factors and soil microbial profile against plant-parasitic nematode (PPNs). The allelopathic potential of SSgH against PPNs is hypothesized to vary by variety and age. In two greenhouse bioassays, ‘NX-D-61′ sorghum and the ‘Latte’ SSgH amendment provided the most suppressive allelopathic effect against the female formation of Meloidogyne incognita on mustard green seedlings when using 1-, 2-, or 3-month-old SSgH tissue, though most varieties showed a decrease in allelopathic effect as SSgH mature. A field trial was conducted where seven SSgH varieties were grown for 2.5 months and terminated using a flail mower, and eggplant was planted in a no-till system. Multivariate analysis of measured parameters revealed that increase in soil moisture, microbial biomass, respiration rate, nematode enrichment index, and sorghum biomass were negatively related to the initial abundance of PPNs and the root-gall index at 5 months after planting eggplant in a no-till system. These results suggested that improvement of soil health by SSgH could lead to suppression of PPN infection.

Denaturing gradient gel electrophoresis and multi-SIR profiles of soil microbial communities from a karst doline at Aggtelek National Park, Hungary

Soils play an important role in the ecosystem of karstic landscapes both as a buffer zone and as a source of acidity to belowground water. Although the microbiota of karstic soils is known to have a great effect on karstification processes, the activity and composition of these communities are largely unknown. This study gives a comparative analysis of soil microbial profiles from different parts of a doline located at Aggtelek, Hungary. The aim was to reveal the relationships between the vegetation type and genetic fingerprints and substrate utilisation (multi-SIR) profiles of the soil microbiota. Soil samples were collected in early and late springs along a transect in a doline covered with different types of vegetation. Genetic fingerprints of bacterial communities were examined by denaturing gradient gel electrophoresis (DGGE) based on the 16S rRNA gene, along with multi-SIR profiles of the microbial communities measured by the MicroResp method using 15 different carbon sources. Genetic fingerprinting indicated that vegetation cover had a strong effect on the composition of soil bacterial communities. Procrustean analysis showed only a weak connection between DGGE and multi-SIR profiles, probably due to the high functional redundancy of the communities. Seasonality had a significant effect on substrate usage, which can be an important factor to consider in future studies.

Sediment Microbial Diversity in Urban Piedmont North Carolina Watersheds Receiving Wastewater Input

Urban streams are heavily influenced by human activity. One way that this occurs is through the reintroduction of treated effluent from wastewater treatment plants. We measured the microbial community composition of water, sediment, and soil at sites upstream and downstream from two Charlotte treatment facilities. We performed 16S rRNA gene sequencing to assay the microbial community composition at each site at four time points between the late winter and mid-summer of 2016. Despite the location of these streams in an urban area with many influences and disruptions, the streams maintain distinct water, sediment, and soil microbial profiles. While there is an overlap of microbial species in upstream and downstream sites, there are several taxa that differentiate these sites. Some taxa characteristics of human-associated microbial communities appear elevated in the downstream sediment communities. In the wastewater treatment plant and to a lesser extent in the downstream community, there are high abundance amplicon sequence variants (ASVs) which are less than 97% similar to any sequence in reference databases, suggesting that these environments contain an unexplored biological novelty. Taken together, these results suggest a need to more fully characterize the microbial communities associated with urban streams, and to integrate information about microbial community composition with mechanistic models.

An outlook on microbial behavior: Mimicking a biodiesel (B100) spill in sandy loam soil

Although different types of biodiesel are marketed worldwide, studies on their environmental impact are scarce. Therefore, we selected pure biodiesels (B100) from rapeseed (BR), sunflower (BF), and soybean (BS) to mimic their contamination of sandy loam soil and then studied their biodegradation by the soil microcosms. All the biodiesel samples presented significant values (p < 0.05) of CO2 release. The fatty acid profiles revealed that they all had high rates of degradation. After 56 days of study, the BR- and BF-contaminated samples had the most altered microbial profile, presenting a similarity of 75% with the uncontaminated sample. The results showed the high biodegradable potential of these three types of biodiesel, indicating that their compositions favored the degradation process. However, the high CO2 level released by the mineralization of these biocomposites and the alteration in the soil microbial profile can be worrying factors. This is the first work to evaluate the biodegradability of these three types of biodiesel, the microbial profile of soil contaminated by each type, and their emission of greenhouse gases.

Mitigating temporal mismatches in forensic soil microbial profiles

ABSTRACTForensic implementation of soil bacterial DNA profiling is limited by the potential for temporal mismatch of DNA profiles, e.g. after storage or seasonal changes. We compared profiles of samples retrieved at one location over 14 years after air-drying, freeze-drying and –80 °C freezing storage. Sample mismatch in freeze-dried and air-dried samples was significant after two years and continued to increase yearly, whereas profiles after –80 °C freezing remained unchanged for many years. In an attempt to mitigate inter-seasonal temporal mismatches, e.g. when months pass between crime and seizure of evidence, soils sampled in winter and summer were exposed to artificial ‘summer’ and ‘winter’ conditions, respectively, and their DNA profiles were compared. Differences were small between soil types, larger between seasons and largest between ‘natural’ and ‘artificial’ seasons. Understanding sources of temporal variations is critical for storage of forensics samples and for developing mitigation procedures that could help overcome these time-induced limitations.

The restoration age of Robinia pseudoacacia plantation impacts soil microbial biomass and microbial community structure in the Loess Plateau

Black locust (Robinia pseudoacacia, RP) has been widely grown for soil and water conservation in erosion regions. However, the effect on soil microbial profiles after long-term implementation of vegetation plantation was still unclear. In this study, soil samples from RP plantations of 10-, 15-, 30- and 38-year-old in a typical vegetation-recovering region on the Chinese Loess Plateau were investigated for microbial biomass carbon (MBC), nitrogen (MBN), phosphorous (MBP) and microbial community-profiles (revealed by phospholipid fatty acids, PLFAs).The results showed SOC, total N, MBC and MBP were significant (P < 0.05) higher in the older RP (30- and 38-year-old) than those in other younger plantations (10 and 15-year-old). Total viable microbial biomass (indicated by total PLFAs), bacterial PLFAs and MBP increased significantly (P < 0.05) with increasing plantation age. Soil microbial communities were distinctly differed in soils of younger- than in older- plantation plots. Redundancy analysis showed that the sampling site with various RP plantations (P < 0.05) was the most important factors in structuring various soil microbial communities. Soil C:N ratio, MBP and available P were also significant factors affecting soil microbial communities.These findings indicate that RP plantation has the potential to transform soil microbial biomass and microbial communities in the direction of improving soil P content in loess soil.

Effects of forest conversion on soil microbial communities depend on soil layer on the eastern Tibetan Plateau of China.

Forest land-use changes have long been suggested to profoundly affect soil microbial communities. However, how forest type conversion influences soil microbial properties remains unclear in Tibetan boreal forests. The aim of this study was to explore variations of soil microbial profiles in the surface organic layer and subsurface mineral soil among three contrasting forests (natural coniferous forest, NF; secondary birch forest, SF and spruce plantation, PT). Soil microbial biomass, activity and community structure of the two layers were investigated by chloroform fumigation, substrate respiration and phospholipid fatty acid analysis (PLFA), respectively. In the organic layer, both NF and SF exhibited higher soil nutrient levels (carbon, nitrogen and phosphorus), microbial biomass carbon and nitrogen, microbial respiration, PLFA contents as compared to PT. However, the measured parameters in the mineral soils often did not differ following forest type conversion. Irrespective of forest types, the microbial indexes generally were greater in the organic layer than in the mineral soil. PLFAs biomarkers were significantly correlated with soil substrate pools. Taken together, forest land-use change remarkably altered microbial community in the organic layer but often did not affect them in the mineral soil. The microbial responses to forest land-use change depend on soil layer, with organic horizons being more sensitive to forest conversion.

RisaAligner software for aligning fluorescence data between Agilent 2100 Bioanalyzer chips: Application to soil microbial community analysis.

Ribosomal Intergenic Spacer Analysis (RISA) is a high-resolution and highly reproducible fingerprinting technique for discriminating between microbial communities. The community profiles can be visualized using the Agilent 2100 Bioanalyzer. Comparison between fingerprints relies upon precise estimation of all amplified DNA fragment lengths; however, size standard computation can vary between gel runs. For complex samples such as soil microbial communities, discrimination by fragment size is not always sufficient. In such cases, the comparison of whole fluorescence data as a function of time (electrophoregrams) is more appropriate. When electrophoregrams [fluorescence = f (time)] are used, and more than one chip is involved, electrophoregram comparisons are challenging due to experimental variations between chips and the lack of correction by the Agilent software in such situations. Here we present RisaAligner software for analyzing and comparing electrophoregrams from Agilent chips using a nonlinear ladder-alignment algorithm. We demonstrate the robustness and substantial improvement of data analysis by analyzing soil microbial profiles obtained with Agilent DNA 1000 and High Sensitivity chips.