Scaling down the analysis of environmental processes: monitoring enzyme activity in natural substrates on a millimeter resolution scale

Bioremediation system consisted with Leclercia adecarboxylata and nZVI@Carbon/Phosphate for lead immobilization: The passivation mechanisms of chemical reaction and biological metabolism in soil

Bioremediation is one of the most promising strategies for heavy metal immobilization. A new remediation system was demonstrated in this research, which combined phosphate solubilizing bacteria (PSB) with nZVI@Carbon/Phosphate (nZVI@C/P) composite to remediate lead contaminated soil. Experimental results indicated that the new system (nZVI@C/P + PSB) could effectively convert the labile Pb into the stable fraction after 30 days of incubation, which increased the maximum residual fraction percentage of Pb by 70.58%. The characterization results showed that lead may exist in the forms of Pb₅(PO₄)₃Cl, PbSO₄ and 3PbCO₃·2Pb(OH)₂·H₂O in the soil treated with nZVI@C/P + PSB. Meanwhile, soil enzyme activities and Leclercia abundance were enhanced in the treated soil compared with CK during the incubation time. In addition, the specialized functions (e.g. ABC transporters, siderophore metabolism, sulfur metabolism and phosphorus metabolism) in PSB and nZVI@C/P + PSB group were also enhanced. These phenomena proved that the key soil metabolic functions may be maintained and enhanced through the synergistic effect of incubated PSB and nZVI@C/P. The study demonstrated that this new bioremediation system provided feasible way to improve the efficacy for lead contaminated soil remediation.

Assessing the effects of elevated ozone on physiology, growth, yield and quality of soybean in the past 40 years: A meta-analysis

Soybean (Glycine max) production is seriously threatened by ground-level ozone (O3) pollution. The goal of our study is to summarize the impacts of O3 on physiology, growth, yield, and quality of soybean, as well as root parameters. We performed meta-analysis on the collated 48 peer-reviewed papers published between 1980 and 2019 to quantitatively summarize the response of soybean to elevated O3 concentrations ([O3]). Relative to charcoal-filtered air (CF), elevated [O3] significantly accelerated chlorophyll degradation, enhanced foliar injury, and inhibited growth of soybean, evidenced by great reductions in leaf area (-20.8%), biomass of leaves (-13.8%), shoot (-22.8%), and root (-16.9%). Shoot of soybean was more sensitive to O3 than root in case of biomass. Chronic ozone exposure of about 75.5 ppb posed pronounced decrease in seed yield of soybean (-28.3%). In addition, root environment in pot contributes to higher reduction in shoot biomass and yield of soybean. Negative linear relationships were observed between yield loss and intensity of O3 treatment, AOT40. The larger loss in seed yield was significantly associated with higher reduction in shoot biomass and other yield component. This meta-analysis demonstrates the effects of elevated O3 on soybean were pronounced, suggesting that O3 pollution is still a soaring threat to the productivity of soybean in regions with high ozone levels.

Effects of nitrogen fertilization and bioenergy crop species on central tendency and spatial heterogeneity of soil glycosidase activities

Extracellular glycosidases in soil, produced by microorganisms, act as major agents for decomposing labile soil organic carbon (e.g., cellulose). Soil extracellular glycosidases are significantly affected by nitrogen (N) fertilization but fertilization effects on spatial distributions of soil glycosidases have not been well addressed. Whether the effects of N fertilization vary with bioenergy crop species also remains unclear. Based on a 3-year fertilization experiment in Middle Tennessee, USA, a total of 288 soil samples in topsoil (0–15 cm) were collected from two 15 m² plots under three fertilization treatments in switchgrass (SG: Panicum virgatum L.) and gamagrass (GG: Tripsacum dactyloides L.) using a spatially explicit design. Four glycosidases, α-glucosidase (AG), β-glucosidase (BG), β-xylosidase (BX), cellobiohydrolase (CBH), and their sum associated with C acquisition (C_acq) were quantified. The three fertilization treatments were no N input (NN), low N input (LN: 84 kg N ha⁻¹ year⁻¹ in urea) and high N input (HN: 168 kg N ha⁻¹ year⁻¹ in urea). The descriptive and geostatistical approaches were used to evaluate their central tendency and spatial heterogeneity. Results showed significant interactive effects of N fertilization and crop type on BX such that LN and HN significantly enhanced BX by 14% and 44% in SG, respectively. The significant effect of crop type was identified and glycosidase activities were 15–39% higher in GG than those in SG except AG. Within-plot variances of glycosidases appeared higher in SG than GG but little differed with N fertilization due to large plot-plot variation. Spatial patterns were generally more evident in LN or HN plots than NN plots for BG in SG and CBH in GG. This study suggested that N fertilization elevated central tendency and spatial heterogeneity of glycosidase activities in surficial soil horizons and these effects however varied with crop and enzyme types. Future studies need to focus on specific enzyme in certain bioenergy cropland soil when N fertilization effect is evaluated.

Feeding on fungi: genomic and proteomic analysis of the enzymatic machinery of bacteria decomposing fungal biomass

Dead fungal biomass is an abundant source of nutrition in both litter and soil of temperate forests largely decomposed by bacteria. Here, we have examined the utilization of dead fungal biomass by the five dominant bacteria isolated from the in situ decomposition of fungal mycelia using a multiOMIC approach. The genomes of the isolates encoded a broad suite of carbohydrate-active enzymes, peptidases and transporters. In the extracellular proteome, only Ewingella americana expressed chitinases while the two Pseudomonas isolates attacked chitin by lytic chitin monooxygenase, deacetylation and deamination. Variovorax sp. expressed enzymes acting on the side-chains of various glucans and the chitin backbone. Surprisingly, despite its genomic potential, Pedobacter sp. did not produce extracellular proteins to decompose fungal mycelia but presumably feeds on simple substrates. The ecological roles of the five individual strains exhibited complementary features for a fast and efficient decomposition of dead fungal biomass by the entire bacterial community.

Amendment of Agricultural Soil with Metal Nanoparticles: Effects on Soil Enzyme Activity and Microbial Community Composition

Several types of engineered nanoparticles (ENPs) are being considered for direct application to soils to reduce the application and degradation of pesticides, provide micronutrients, control pathogens, and increase crop yields. This study examined the effects of different metal ENPs and their dissolved ions on the microbial community composition and enzyme activity of agricultural soil amended with biosolids. The activity of five extracellular nutrient-cycling enzymes was measured in biosolid-amended soils treated with different concentrations (1, 10, or 100 mg ENP/kg soil) of silver (nAg), zinc oxide (nZnO), copper oxide (nCuO), or titanium dioxide (nTiO₂) nanoparticles and their ions over a 30-day period. At 30 days, nZnO and nCuO either had no significant effect on soil enzyme activity or enhanced enzyme activity. In contrast, Ag inhibited selected enzymes when dosed in particulate or dissolved form (at 100 mg/kg). nTiO₂ either had no significant effect or slightly decreased enzyme activity. Illumina MiSeq sequencing of microbial communities indicated a shift in soil microbial community composition upon exposure to high doses of metal ions or nAg and negligible shift in the presence of nTiO₂. Some taxa responded differently to nAg and Ag⁺. This work shows how metal ENPs can impact soil enzyme activity and microbial community composition upon introduction into soils amended with biosolids, depending on their type, concentration, and dissolution behavior, hence providing much needed information for the sustainable application of nanotechnology in agriculture.

Small-scale spatial heterogeneity of ecosystem properties, microbial community composition and microbial activities in a temperate mountain forest soil

Forests are recognised as spatially heterogeneous ecosystems. However, knowledge of the small-scale spatial variation in microbial abundance, community composition and activity is limited. Here, we aimed to describe the heterogeneity of environmental properties, namely vegetation, soil chemical composition, fungal and bacterial abundance and community composition, and enzymatic activity, in the topsoil in a small area (36 m²) of a highly heterogeneous regenerating temperate natural forest, and to explore the relationships among these variables. The results demonstrated a high level of spatial heterogeneity in all properties and revealed differences between litter and soil. Fungal communities had substantially higher beta-diversity than bacterial communities, which were more uniform and less spatially autocorrelated. In litter, fungal communities were affected by vegetation and appeared to be more involved in decomposition. In the soil, chemical composition affected both microbial abundance and the rates of decomposition, whereas the effect of vegetation was small. Importantly, decomposition appeared to be concentrated in hotspots with increased activity of multiple enzymes. Overall, forest topsoil should be considered a spatially heterogeneous environment in which the mean estimates of ecosystem-level processes and microbial community composition may confound the existence of highly specific microenvironments.

Soil nutrient content influences the abundance of soil microbes but not plant biomass at the small-scale

Small-scale heterogeneity of abiotic and biotic factors is expected to play a crucial role in species coexistence. It is known that plants are able to concentrate their root biomass into areas with high nutrient content and also acquire nutrients via symbiotic microorganisms such as arbuscular mycorrhizal (AM) fungi. At the same time, little is known about the small-scale distribution of soil nutrients, microbes and plant biomass occurring in the same area. We examined small-scale temporal and spatial variation as well as covariation of soil nutrients, microbial biomass (using soil fatty acid biomarker content) and above- and belowground biomass of herbaceous plants in a natural herb-rich boreonemoral spruce forest. The abundance of AM fungi and bacteria decreased during the plant growing season while soil nutrient content rather increased. The abundance of all microbes studied also varied in space and was affected by soil nutrient content. In particular, the abundance of AM fungi was negatively related to soil phosphorus and positively influenced by soil nitrogen content. Neither shoot nor root biomass of herbaceous plants showed any significant relationship with variation in soil nutrient content or the abundance of soil microbes. Our study suggests that plants can compensate for low soil phosphorus concentration via interactions with soil microbes, most probably due to a more efficient symbiosis with AM fungi. This compensation results in relatively constant plant biomass despite variation in soil phosphorous content and in the abundance of AM fungi. Hence, it is crucial to consider both soil nutrient content and the abundance of soil microbes when exploring the mechanisms driving vegetation patterns.