Soil Microbial Abundance Research Articles

Impacts of Land Use Intensification Level on Fluvo-aquic Cropland Soil Microbial Community Abundance and Necromass Accumulation in North China

Despite the essential role of soil microorganisms in nutrient turnover in soil ecological systems and the recognized paramount significance of microbial necromass to soil organic carbon accumulation, how microbial community abundance and necromass respond to land use intensification level regulation remains poorly understood. To address this knowledge gap, based on the land use intensification level, three treatments were set up[annual wheat-maize rotation (CC), alternating temporary grassland with wheat planting (TG), and perennial grassland (PG)], and a long-term fixed filed experiment was established to investigate the influences of the regulation of land use intensification level on bacterial and fungal community abundances; the accumulation of bacterial, fungal, and total microbial necromass; and their contributions to SOC sequestration using droplet digital PCR and amino sugar detection technologies. We further sought to determine the key factors driving the bacterial, fungal, and total microbial necromass C accumulation. Our results demonstrated that fungal community abundance was strongly affected by land use intensification level regulation compared to that of the bacterial community, which increased with decreasing land use intensification level. The total microbial necromass C predominated the SOC accumulation across all three land use intensification levels, which contributed 52.78%, 58.36%, and 68.87% to SOC, respectively, exhibiting an increasing trend with the decline in land use intensification level. Fungal necromass C accounted for more than 80% of the total microbial necromass C, indicating its predominance in the accumulation of the total microbial necromass C and active variation via the reduction in land use intensification level. There was no significant difference in bacterial necromass C (MurA) content, with the trend of CC<PG<TG, whereas fungal necromass C (GluN) was observed to be significantly shifted by the modulation of land use intensification level, with contents in the TG and PG treatments being higher than that in the CC treatment, especially for the PG treatment (with an increase of 66.10%). The increase in bacterial necromass C accumulation was associated with microbial demand for N and was affected by the balance between soil C and N; however, the accumulation of fungal necromass C was jointly manipulated by a wide variety of biotic and abiotic factors. Altogether, our work provides evidence that agricultural land use intensification level regulation can enhance soil extracellular enzyme activity and accelerate nutrient transformation through changing edaphic properties, thus improving fungal amount and necromass C accumulation, with active contribution to total microbial necromass C and even SOC.

Earthworm activity effectively mitigated the negative impact of microplastics on maize growth

Microplastic pollution can have detrimental effects on soil environments and inhibit crop growth. Earthworms, known as soil engineers, promote crop growth, but their role and impact on the amelioration of microplastic-polluted soil is not yet clear. In this study, we investigated the impact and pathways of earthworm activity on microplastic-contaminated soil by introducing varying densities (without earthworm:0, low-density: 1, medium-density: 2, high-density: 5 ind column−1) of earthworms (epi-endogeic) into soil contaminated with two types of microplastics: polyethylene and polyvinyl chloride. Our results showed that earthworms all survived in soil polluted with two types of microplastics. Meanwhile, earthworm activity increased nutrient content and enzyme activity by 0.2–36.1% and 2.9–34.3%, respectively, and significantly increased soil microbial biomass and community diversity index. Earthworm activity also decreased antioxidant enzyme activity and promoted maize plant growth, including agronomic traits such as plant height, biomass, root length, and root surface area. Furthermore, the nutrient content of maize organs increased by 1.1–29.7%. Partial least squares models confirmed that earthworm activity alleviated the stress effect of microplastic pollution on plant growth by improving soil structure, fertility, and microbial abundance and diversity. The greatest effect on maize growth was observed with the improvement of soil physical-chemical properties. Our results suggest that medium densities of earthworms have the greatest soil improvement effect and provide an important basis for bioremediation of farmland contaminated by microplastics and promoting green and efficient development in agriculture.

Revisiting the relationships between soil nitrous oxide emissions and microbial functional gene abundances.

A conceptual framework proposes that soil N2 O emissions are more likely related to microbial functional gene abundances based on laboratory experiments than in-situ observations. This framework has largely contributed to reconciling the disputation on linking soil N2 O emissions with functional gene abundances, but the direct evidence is lacking. Wei et al. (2023) provided new evidence to support this framework, showing that O2 dynamics were a better predictor of in-situ soil N2 O emissions than were functional gene abundances. Before the observations can inform N2 O modeling and support sustainable nitrogen management, however, some additional efforts are needed to revisit the relationships between in-situ soil N2 O emissions and functional gene abundances.

Effects of long-term herbaceous plant restoration on microbial communities and metabolic profiles in coal gangue-contaminated soil

The soil microbial diversity in the gangue accumulation area is severely stressed by a variety of heavy metals, while the influence of long-term recovery of herbaceous plants on the ecological structure of gangue-contaminated soil is to be explored. Therefore, we analysed the differences in physicochemical properties, elemental changes, microbial community structure, metabolites and expression of related pathways in soils in the 10- and 20-year herbaceous remediation areas of coal gangue. Our results showed that phosphatase, soil urease, and sucrase activities of gangue soils significantly increased in the shallow layer after herbaceous remediation. However, in zone T1 (10-year remediation zone), the contents of harmful elements, such as Thorium (Th; 1.08-fold), Arsenic (As; 0.78-fold), lead (Pb; 0.99-fold), and uranium (U; 0.77-fold), increased significantly, whereas the soil microbial abundance and diversity also showed a significant decreasing trend. Conversely, in zone T2 (20-year restoration zone), the soil pH significantly increased by 1.03- to 1.06-fold and soil acidity significantly improved. Moreover, the abundance and diversity of soil microorganisms increased significantly, the expression of carbohydrates in soil was significantly downregulated, and sucrose content was significantly negatively correlated with the abundance of microorganisms, such as Streptomyces. A significant decrease in heavy metals was observed in the soil, such as U (1.01- to 1.09-fold) and Pb (1.13- to 1.25-fold). Additionally, the thiamin synthesis pathway was inhibited in the soil of the T1 zone; the expression level of sulfur (S)-containing histidine derivatives (Ergothioneine) was significantly up-regulated by 0.56-fold in the shallow soil of the T2 zone; and the S content in the soil significantly reduced. Aromatic compounds were significantly up-regulated in the soil after 20 years of herbaceous plant remediation in coal gangue soil, and microorganisms (Sphingomonas) with significant positive correlations with benzene ring-containing metabolites, such as Sulfaphenazole, were identified.

Composite sampling method for soil microbiome and microbial abundance analysis

Composite sampling method for soil microbiome and microbial abundance analysis

Composite sampling method for soil microbiome and microbial abundance analysis

Composite sampling method for soil microbiome and microbial abundance analysis

Soil microbial community composition along chronosequence of the introduction of Phragmites australis at Suncheon Bay

Vegetations of coastal wetlands play a vital role in providing numerous ecological services to the coastal ecosystem and are also key factors affecting the biogeochemical processes in the soil. The acreage of Phragmites australis is expanding and gradually replacing the Suaeda japonica at Suncheon Bay, Republic of Korea. However, the changes in soil microbial community composition caused by Phragmites introduction is poorly characterized. In the present study, soil cores were collected to a depth of 1m (divided into 10 segments of 10 cm) from Suaeda-vegetated, the boundary of Suaeda- and Phragmites-vegetated, Phragmites-vegetated marshes (after 5 and 10 years of the introduction). These samples were analyzed for physico-chemical characteristics, enzyme activities, soil microbial community (phospholipid fatty acids profiling) and abundance of functional genes related to the methane cycle (mcrA, pmoA and dsrA). Results showed that introduction the of Phragmites increased the water content, pH and dissolved organic carbon content in the soil. The contents of total PLFA and microbial group biomarkers of PLFA were observed to be higher in the surface soil and decreased with soil depth. Early introduction of Phragmites (10 yr) sediments had the significantly highest concentrations of total as well as other microbial biomarkers PLFAs compared with other salt marshes. The relative abundance of biomarker PLFAs of Gram-negative bacteria was significantly higher in Phragmites compared to other salt marshes. The abundance of mcrA was significantly highest in Phragmites salt marshes (10 yr) and mixed salt marshes while the abundance of mcrA, pmoA and dsrA were lowest in Suaeda marshes. Our results reflect the chronological effects of the introduction of Phragmites on the physicochemical and microbial community composition which contribute to establishing the relationship between the plant introduction and soil biogeochemical processes in coastal salt marshes.

Effect of two broad-spectrum fungicides on the microbial communities of a soil subjected to different degrees of water erosion

The impact of both fungicide and water erosion on soil microbial communities has been little studied, and far less in subhumid-dry climates. To help fill this knowledge gap, we evaluated the influence of two broad-spectrum fungicides applied to soil subjected to different degrees of water erosion on microbial population and function. Soil samples were taken from an experimental site under three water erosion levels: an agricultural land subjected to minimum water erosion by terrace farming (MIN), an agricultural land subjected to moderate water erosion without terrace farming (MOD), and a land with no water erosion control treatment (non-eroded, NON). Three dosages of both carbendazim and iprodione were applied to microcosms, and the responses of microbial community and function were examined after 30-day exposure. Phospholipid fatty acid (PLFA) analysis, soil enzyme activities, and microbial abundances estimated by quantitative real-time PCR (qPCR) were used to evaluate the impact of carbendazim and iprodione fungicides applied at three dosages on microbial community structure and enzyme activities. The lowest values of fluorescein diacetate hydrolase (FDA), dehydrogenase, urease, and glucosidase activities were registered in soil under moderate erosion, while the highest ones were observed in non-eroded soils. Both carbendazim and iprodione decreased C- and P-related activities, even when those fungicides were applied at field rate doses. Thus, phosphomonoesterase, glucosidase, and xylosidase in soil treated with fungicides applied at recommended field rate decreased by 46 %, 61 %, and 34 % compared to soil without fungicide application. The lowest values of PLFA biomarkers for Gram-positive bacteria, Gram-negative bacteria, and arbuscular mycorrhizal fungi were registered in soils treated with the highest dose of both carbendazim and iprodione. Thus, Gram-positive bacteria, Gram-negative bacteria, arbuscular mycorrhizal fungi, and fungal PLFA biomarkers in soils without fungicide application were about 36 %, 3 %, 47 %, and 82 % higher than those soils treated with the highest doses of fungicides, respectively. In addition, the highest doses of fungicide application tended to greater decrease total PLFAs in both non-eroded and minimum eroded compared to moderate eroded soils. Similarly, the response of bacterial and fungal populations to fungicide treatment was more pronounced in non-eroded soils than in eroded soils. This study illustrates how the interactions between fungicides and water erosion levels affect soil enzyme activities, microbial abundances, and microbial community structure in agroecosystems.

Single-cell Raman and functional gene analyses reveal microbial P solubilization in agriculture waste-modified soils.

Application of agricultural waste such as rapeseed meal (RM) is regarded as a sustainable way to improve soil phosphorus (P) availability by direct nutrient supply and stimulation of native phosphate-solubilizing microorganisms (PSMs) in soils. However, exploration of the in situ microbial P solubilizing function in soils remains a challenge. Here, by applying both phenotype-based single-cell Raman with D2O labeling (Raman-D2O) and genotype-based high-throughput chips targeting carbon, nitrogen and P (CNP) functional genes, the effect of RM application on microbial P solubilization in three typical farmland soils was investigated. The abundances of PSMs increased in two alkaline soils after RM application identified by single-cell Raman D2O. RM application reduced the diversity of bacterial communities and increased the abundance of a few bacteria with reported P solubilization function. Genotypic analysis indicated that RM addition generally increased the relative abundance of CNP functional genes. A correlation analysis of the abundance of active PSMs with the abundance of soil microbes or functional genes was carried out to decipher the linkage between the phenotype and genotype of PSMs. Myxococcota and C degradation genes were found to potentially contribute to the enhanced microbial P release following RM application. This work provides important new insights into the in situ function of soil PSMs. It will lead to better harnessing of agricultural waste to mobilize soil legacy P and mitigate the P crisis.

Elevated [CO2] enhances soil respiration and AMF abundance in a semiarid peanut agroecosystem

Rising atmospheric carbon dioxide [CO2] is a main climate change driver, and soil respiration is the most relevant contributor to ecosystem respiration. However, the soil microbiome and respiration responses of semiarid agroecosystems under elevated [CO2] (eCO2) conditions must be better understood. In particular, peanut agroecosystems host rhizobia and arbuscular mycorrhizal fungi (AMF) associations. Here, we sought to address the following questions: a) Does eCO2 conditions (650 µmol CO2 m−2 s−1, +250 µmol CO2 m−2 s−1, aCO2, control) alter soil chemical properties, soil microbial community size and composition, soil respiration, and β-Glucosidase activity? b) Are these responses influenced by transient water deficit periods? We conducted this study in a typical West Texas semiarid region (no well-watered treatment and drought was not an experimental factor) during two consecutive growing seasons (May-Oct). We induced the atmospheric CO2 enrichment using field-installed Canopy Evapotranspiration and Assimilation (CETA) systems. Our results showed no consistent significant changes in soil moisture, C: N ratio, total soil microbial EL-FAME abundance, or β-Glucosidase activity. However, we found that eCO2 increased soil temperature (+1 °C), AMF abundance (EL-FAME marker, +49%), and soil respiration (+82%). Our findings suggest that in future semiarid climates, peanut agroecosystems may experience: 1) increased soil metabolic activity as a result of increased autotrophic respiration; 2) increased AMF, which could further facilitate plant nutrient and water uptake; and 3) minimal change in the total size of the microbial community and C cycling enzyme activity during the growing season. In this manuscript, we demonstrated that soil respiration and temperature could be indicators of ecosystem productivity and climate feedback. Furthermore, soil organic carbon and AMF were good indicators of poor nutrient soil ecosystem transitional health across well-watered and water-deficit cycles. This study will increase our understanding of how these changes will affect soil ecology and climate feedback and will provide new insight into the peanut agroecosystem carbon source/sink functioning and productivity in future climates.

Exploring community dynamics: Cultivable and uncultivable for the microbial-mediated bioremediation of oil-based paints polluted soil from aqueous media by Plackett-Burman statistically designed conditions

Oil-based paint seriously threatens biodiversity due to its complex composition and biocide toxicity. Therefore, it alters the microbial diversity abundance and in modern approaches like metagenomic, a powerful tool to get insight into pollutants effect on soil microbial community abundance. Thus, present study aimed at “exploring community dynamics: cultivable and uncultivable for the microbial-mediated bioremediation of oil-based paints polluted soil from aqueous media by Plackett-Burman statistical designed conditions”. The total DNA from oil-based paints polluted soil was extracted by PowerSoil DNA Isolation Kit. The 16S rDNA genes were amplified using universal primers and PCR amplicons were sequenced for analysis of metagenomes to determine the bacterial microbiome abundance. A total 133,140 sequence reads, 2857 Operational Taxonomic Units (OTUs) of 16S rRNA genes, and 30 bacterial phyla were retrieved from all the oil-based paints polluted samples (C, R498, B698 and G492) with the significant increase in Firmicutes (18.90 %, 52.39 %, 49.75 %, 44.36 %) and Actinobacteria (26.66 %, 28.93 %, 28.17 %, 14.68 %) whereas a decrease in Proteobacteria (19.53 %, 6.32 %, 9.37 %, 16.21 %), Chloroflexi (16.93 %, 8.71 %, 9.78 %, 18.17 %), and Bacteroidetes (8.96 %, 0.36 %, 0.41 %, 0.11 %) was recorded respectively. Additionally, the 100 % removal of oil-based paints (R498, B698 and G492) was achieved by the cultivable microbial consortia in laboratory settings. On the other hand for the R498 single cultivable pure isolates exhibited biodegradation potential as “PDB20, 91 %”, “PDB14, 81 %”, and “PDB16, 87 %” while for the blue B698, “PDB4, 86 %”, “PDB20, 89 %”, “PDB5, and PDB2, 80%”. Moreover, in case of G492, maximum % removal was achieved with “PDB20, 93 %”, “PDB5, 90 %”, “PDB6, 90 %”, “PDB16, 88 %”, “PDB2, and PDB4, 89%”. Conclusively, in comparison to R498 and B698, maximum percent removal was displayed by G492 and this might be attributed due to difference in pigment. Cultivable consortia and individual pure isolates demonstrated >80 % contribution in the % removal of oil-based paints.

Dairy Manure-Derived Biochar in Soil Enhances Nutrient Metabolism and Soil Fertility, Altering the Soil Prokaryote Community

Although various studies have investigated biochar (BC) soil amendments for improving soil microbial abundance, functions, and community structure, a comparison of dairy manure biochar (MBC) to wood biochar (WBC) is warranted given the large volume of manure produced in high-intensity dairy production. Additionally, the synergistic effects of different BC sources and loading percentages on microbial functions and community composition using massively parallel 16S DNA sequencing in BC-amended soils with different types of crops are limited. In this study, the synergistic effects of BC type, BC loading percentage, and crop types on soil fertility, prokaryote community diversity, and functions were investigated in a greenhouse study. The MBC and WBC were used to amend sandy loam soils at increasing BC loading percentages (0, 5, and 10%) to grow the cool-season forages crimson clover (Trifolium incarnatum; an annual legume) and Italian ryegrass (Lolium multiflorum Lam.; an annual forage grass) for 120 days. High nutrient concentrations in MBC shifted microbial communities towards r-strategists and alkaliphiles, potentially increasing the rate of nutrient bioremediation from high nitrogen- and phosphorus-containing soil amendments. This study enables emerging biochar agronomic use recommendations with different crops.

Biochar alleviated the toxic effects of PVC microplastic in a soil-plant system by upregulating soil enzyme activities and microbial abundance

Plastics have become an emerging pollutant threatening the sustainability of agroecosystems and global food security. Biochar, a pro-ecosystem/negative carbon emission technology can be exploited as a circular approach for the conservation of plastics contaminated agricultural soils. However, relatively few studies have focused on the effects of biochar on plant growth and soil biochemical properties in a microplastic contaminated soil. This study investigated the effects of a cotton stalk (Gossypium hirsutum L.) biochar on plant growth, soil microbes, and enzyme activity in PVC microplastic (PVC-MPs) contaminated soil. Biochar amendment increased shoot dry matter production in PVC-MPs contaminated soil. However, PVC-MPs alone significantly reduced the soil urease and dehydrogenase activity, soil organic and microbial biomass carbon, bacterial/fungal community percentage, and their abundance (16S rRNA and 18S rRNA genes, respectively). Interestingly, biochar amendment with PVC-MPs significantly alleviated the hazardous effects. Principal component and redundancy analysis of the soil properties, bacterial 16S rRNA genes, and fungal ITS in the biochar-amended PVC-MPs treatments revealed that the observed traits formed an obvious cluster compared to non-biochar treatments. To sum up, this study indicated that PVC-MPs contamination was not benign, while biochar shielded the hazardous effects and sustained soil microbial functionality.

Reforestation substantially changed the soil antibiotic resistome and its relationships with metal resistance genes, mobile genetic elements, and pathogens

Revealing the effects of reforestation on soil antibiotic resistome is essential for assessing ecosystem health, yet related studies remain scarce. Here, to determine the responses of the soil antibiotic resistome to reforestation, 30 pairs of cropland and forest soil samples were collected from southwestern China, a region with high environmental heterogeneity. All the forests had been derived from croplands more than one decade ago. The diversity and abundance of soil antibiotic resistance genes (ARGs), metal resistance genes (MRGs), mobile genetic elements (MGEs), and pathogens were determined by metagenomic sequencing and real-time PCR. The results showed that reforestation significantly increased soil microbial abundance and the contents of Cu, total carbon, total nitrogen, total organic carbon, and ammonium nitrogen. Nevertheless, it decreased the contents of soil Zn, Ba, nitrate nitrogen, and available phosphorus. The main soil ARGs identified in this region were vancomycin, multidrug, and bacitracin resistance genes. Reforestation significantly increased the soil ARG abundance by 62.58%, while it decreased the ARG richness by 16.50%. Reforestation exerted no significant effects on the abundance of heavy metal resistance genes and pathogens, but it doubled the abundance of MGEs. Additionally, reforestation substantially decreased the co-occurrence frequencies of ARGs with MRGs and pathogens. In contrast, the correlation between ARGs and MGEs was greatly enhanced by reforestation. Similarly, the correlations between soil ARG abundance and environmental factors were also strengthened by reforestation. These findings suggest that reforestation can substantially affect the soil antibiotic resistome and exerts overall positive effects on soil health by decreasing ARG richness, providing critical information for assessing the effects of “grain for green” project on soil health.

Inoculations of phosphate-solubilizing bacteria alter soil microbial community and improve phosphorus bioavailability for moso bamboo (Phyllostachys edulis) growth

Moso bamboo plantations suffer from phosphorus (P) limitations. A better understanding of soil P cycling contributes to the sustainable management and development of the bamboo forests. In this study, different phosphate-solubilizing bacteria (PSB) were applied to soils to stimulate bamboo growth, and the metagenomics method was employed to investigate the changes in soil microbial communities and relative abundances of functional genes. Meanwhile, soil properties and bamboo biomass and physiological indices were also quantitatively analyzed. The PSB inoculations changed soil P fractions and significantly elevated available P (AP) content by stimulating phosphatase activity and functional genes involved in P-transformation. The PSB inoculations significantly stimulated soil acid phosphatase activities and enhanced the relative abundances of functional genes associated with inorganic P-solubilization and organic P-mineralization. Moreover, increased soil available nutrients were beneficial to the moso bamboo growth, and the bamboo biomass in the different treatments increased by from 32.43 % to 69.04 % compared with the control treatment. Significant increases in root activity, carotenoid, chlorophyll a and total chlorophyll contents after the PSB inoculations also contributed to moso bamboo growth. The PSB strain inoculations shaped soil microbial communities and increased microbial connections. Besides adjusting soil P supplies and functional genes, the PSB also promoted the moso bamboo growth by increasing soil mineral N, AK and bamboo chlorophyll contents and stimulating functional microorganisms. Our study could provide a theoretical basis to improve soil nutrient utilization for moso bamboo with the PSB inoculations.

Vegetation restoration of abandoned cropland improves soil phosphorus availability and microbial activities in the Danxia degraded region

Phosphorus is a limiting nutrient in subtropical region soils. The Danxia degraded region (DDR) is a typical ecologically degraded area in the south subtropical region of China, and mitigation measures for reconverting farmland to forest have been implemented to prevent further land degradation. However, whether vegetation restoration can alter soil P fractions (SPF) and P availability in the DDR remains unclear, and the mechanisms influencing P availability require further study. In this study, we collected soil samples from the main vegetation cover types, namely arbor forest, shrubland, and abandoned cropland, in the DDR to explore the characteristics of SPF, acid phosphatase (ACP), microbial community and their influencing factors. Results showed that vegetation restoration significantly affected soil P availability by modifying the SPF. Labile, moderately labile, and aggregate-occluded P content in the soil increased, whereas the proportion of stable P decreased. Vegetation restoration promoted the secretion of soil ACP and significantly increased the abundance of soil bacteria, fungi, actinomycetes, arbuscular mycorrhizal fungi, and the overall microbial abundance. Arbor forest soils presented higher SPF content and microbial activity than the soils from abandoned croplands and shrublands. This increases in soil microbial abundance was significantly correlated with soil microbial biomass and dissolved organic carbon. The results of redundancy and variance partitioning analyses indicated that soil nutrients and soil properties jointly drove SPF transformation in the DDR. Soil nutrient supply significantly affected soil microbial activity and SPF transformation. Vegetation restoration increased microbial activity by increasing the soil nutrient supply, and the resulting synergistic effect altered the SPF distribution and availability. This study provides a theoretical basis for the sustainable use of soil P resources in the DDR.

Distinct climatic regions drive antibiotic resistance genes dynamics across public parks and pristine soil ecosystems

To address the global concern of antibiotic resistance, a one-health concept is considered necessary that recognizes the interdependency between humans, animals and the environment, and acknowledges that each of these factors contributes to the evolution and rapid bloom of antibiotic resistance genes (ARGs). We implemented a GeoChip 5.0 strategy to examine the wide-spectrum profile of ARGs in the soil of urban parks and reference forests across three distinct climatic regions: Boreal (Lathi, Finland), Temperate (Baltimore, USA), and Tropical (Singapore). ARGs encoding multidrug resistance (MRGs) were among the most abundant, accounting for 90% of all ARGs detected. MRGs include MFS, MATE, Mex, SMR and ABC, which are involved in the transportation/efflux of multiple antibiotics. Multivariate analysis revealed that the ARG profile tends to be partitioned separately in urban parks and climatic regions. In addition, we opted to examine the impact of plant functional type (recalcitrant and labile tree litter, lawn) on ARGs. There was no significant influence of vegetation type on ARGs except in the tropical region, where its impact was evident as compared with boreal and temperate regions. More interestingly, the majority of ARGs were detected to have a higher relative abundance in the tropical region as compared to the boreal and temperate regions. Regional characteristics of the tropical area likely affects ARGs and the ARG-host profile, thereby boosting soil microbial abundances. Additionally, MFS, Mex, B_lactamase_A, vgb, ABC, Van, fosb, ABC_ multi, Tet and Mate_antibiotic were considerably more abundant in old parks as compared with young parks across the three climatic regions. Nevertheless, urban parks harboured a significantly higher abundance of ARGs than forests. Our study presents evidence of ARGs in varied climatic regions and provides valuable new insights in our understanding of ARGs in human-dominated environments as well as their prevalence in pristine ecosystems.

Urban land uses shape soil microbial abundance and diversity

Soil microbial biodiversity provides many useful services in cities. However, the ecology of microbial communities in urban soils remains poorly documented, and studies are required to better predict the impact of urban land use. We characterized microbial communities (archea/bacteria and fungi) in urban soils in Dijon (Burgundy, France). Three main land uses were considered – public leisure, traffic, and urban agriculture – sub-categorized in sub-land uses according to urban indexes and management practices. Microbial biomass and diversity were determined by quantifying and high-throughput sequencing of soil DNA. Variation partitioning analysis was used to rank soil physicochemical characteristics and land uses according to their relative contribution to the variation of soil microbial communities. Urban soils in Dijon harbored high levels of microbial biomass and diversity that varied according to land uses. Microbial biomass was 1.8 times higher in public leisure and traffic sites than in urban agriculture sites. Fungal richness increased by 25 % in urban agriculture soils, and bacterial richness was lower (by 20 %) in public leisure soils. Partitioning models explained 25.7 %, 46.2 % and 75.6 % of the variance of fungal richness, bacterial richness and microbial biomass, respectively. The organic carbon content and the C/N ratio were the best predictors of microbial biomass, whereas soil bacterial diversity was mainly explained by soil texture and land use. Neither metal trace elements nor polycyclic aromatic hydrocarbons contents explained variations of microbial communities, probably due to their very low concentration in the soils. The microbial composition results highlighted that leisure sites represented a stabilized habitat favoring specialized microbial groups and microbial plant symbionts, as opposed to urban agriculture sites that stimulated opportunistic populations able to face the impact of agricultural practices. Altogether, our results provide evidence that there is scope for urban planners to drive soil microbial diversity through sustainable urban land use and associated management practices.

Assessment of CuO NPs on soil microbial community structure based on phospholipid fatty acid techniques and phytotoxicity of bok choy seedlings

In this study, a soil culture and a hydroponic experiment were conducted to assess the toxicology effects of copper oxide nanoparticles (CuO NPs) on soil microbial community structure and the growth of bok choy. Results showed CuO NPs had an inhibitory effect on soil microbial abundance, diversity, and activity, as well as the bok choy seedling growth, whereas CuO NPs at low concentrations did not significantly affect the soil microbial biomass or plant growth. In soil, CuO NPs at high dose (80 mg kg−1) significantly reduced the indexes of Simpson diversity, Shannon–Wiener diversity and Pielou evenness by 3.7%, 4.9% and 4.5%, respectively. In addition, CuO NPs at 20 and 80 mg kg−1 treatment significantly reduced soil enzymes (urease, alkaline phosphatase, dehydrogenase, and catalase) activities by 25.5%–58.9%. Further, CuO NPs at 20 mg L−1 significantly inhibited the growth of plant root by 33.8%, and catalase (CAT) activity by 17.9% in bok choy seedlings. The present study can provide a basis for a comprehensive evaluation of the toxicity effect of CuO NPs on soil microorganisms and phytotoxicity to bok choy seedlings.

Dual indicators link geochemistry to microbiota in blue carbon soils

In blue carbon ecosystems, biomarkers and indicators have been developed to assess soil biogeochemical processes and history. In this study, we investigate blue carbon soils to determine if geochemical characteristics can predict soil microbial characteristics, and secondly to investigate if these two indicators can reveal novel information about processes about soil formation and alteration. First, phospholipid fatty acids (PLFAs) identified soil microbial functional groups and abundances. Microbes varied strongly among the three blue carbon ecosystems – seagrass, mangrove and saltmarsh – and to a lesser extent with soil age/depth. Then, x-ray fluorescence using a core scanner (ITRAX) was used to identify geochemical traits of the soil. Lastly, statistical procedures were carried out to test the ability of ITRAX-derived geochemical characteristics to explain the variation in PLFA composition. The soil geochemical indicators for organic matter (OM) source and turnover explained most of the variability in PLFAs, followed by indicators for redox and grain size. For both indicators the saltmarsh soils were associated with relatively higher OM availability and reactivity and microbial abundance. High OM samples also supported a range of microbial functional groups, including fungi and the co-existence of prokaryotic aerobic and anaerobic metabolisms. In contrast, increased depths representing older soil ages showed decreases in OM reactivity and shifts in OM processing through reduced active microbial abundance. We suggest that x-ray fluorescence data used as an indicator in conjunction with other biomarkers can be used to assess multiple aspects of blue carbon soils (biology, provenance, physicochemistry), while also possessing opportunity for future development as rapid field technique.