Effect of Commercial Amendments on Immobilization of Arsenic, Copper, and Zinc in Contaminated Soil: Comprehensive Assessing to Plant Uptake Combined with a Microbial Community Approach

Identifying the proper chemical and biological materials as soil amendments is a great concern because they replace soil properties and subsequently change the soil quality. Hence, this study was conducted to evaluate the effects of a diverse range of soil amendments including bentonite (B), talc (T), activated carbon (AC), and cornstarch (CS) in form of sole and composite on the immobilization and bioavailability of As, Cu, and Zn. The amendments were characterized by SEM, FT-IR, and XRF, and applied at 2% (w/w) in the experimental pots with an Asteraceae (i.e., lettuce) for 45 days to monitor plant growth parameters and soil microbial community. Soil pH from 6.1 ± 0.02 significantly increased in the amended soils with the maximum value found for TAC (7.4 ± 0.04). The results showed that soil amendments reduced easily in an exchangeable fractionation of As, Cu, and Zn with the maximum values found for BAC by 66.4%, AC by 84.2%, and T by 89.7% respectively. Adding B, T, AC, and their composites induced dry biomass of lettuce >40 wt.%, while CS and its composites did not affect the dry biomass of the plant. The average content of Cu and Zn in plant tissues decreased >45 wt% in B, AC, and their composites amended soils; meanwhile, AC and its composites mitigated As uptake by >30 wt.% in lettuce. The results of Biolog Ecoplate showed that the amending soils improved the microbial community, especially for composites (e.g., TCS). The results demonstrated that adding composites amendments provided an efficient method for the immobilization of metals and metalloids, and also induced plant growth parameters and microbial community.

Assessment of Carbon Substrate Catabolism Pattern and Functional Metabolic Pathway for Microbiota of Limestone Caves

Carbon utilization of bacterial communities is a key factor of the biomineralization process in limestone-rich curst areas. An efficient carbon catabolism of the microbial community is associated with the availability of carbon sources in such an ecological niche. As cave environments promote oligotrophic (carbon source stress) situations, the present study investigated the variations of different carbon substrate utilization patterns of soil and rock microbial communities between outside and inside cave environments in limestone-rich crust topography by Biolog EcoPlate™ assay and categorized their taxonomical structure and predicted functional metabolic pathways based on 16S rRNA amplicon sequencing. Community level physiological profiling (CLPP) analysis by Biolog EcoPlate™ assay revealed that microbes from outside of the cave were metabolically active and had higher carbon source utilization rate than the microbial community inside the cave. 16S rRNA amplicon sequence analysis demonstrated, among eight predominant bacterial phylum Planctomycetes, Proteobacteria, Cyanobacteria, and Nitrospirae were predominantly associated with outside-cave samples, whereas Acidobacteria, Actinobacteria, Chloroflexi, and Gemmatimonadetes were associated with inside-cave samples. Functional prediction showed bacterial communities both inside and outside of the cave were functionally involved in the metabolism of carbohydrates, amino acids, lipids, xenobiotic compounds, energy metabolism, and environmental information processing. However, the amino acid and carbohydrate metabolic pathways were predominantly linked to the outside-cave samples, while xenobiotic compounds, lipids, other amino acids, and energy metabolism were associated with inside-cave samples. Overall, a positive correlation was observed between Biolog EcoPlate™ assay carbon utilization and the abundance of functional metabolic pathways in this study.

Assessment of the Short-Term Fertilizer Potential of Mealworm Frass Using a Pot Experiment

The forecasted growth of insect production in the next few years will generate high quantities of frass (insect excreta). Although frass is increasingly considered a potential fertilizer, the dynamics of nutrient supply by frass is still poorly understood. Here, we aimed at gaining insight into the short-term fertilizer value of frass from mealworm (Tenebrio molitor L.) in order to optimize its sustainable use in agroecosystems. Using a short-term pot experiment, we showed that, even though frass has a great potential to be used as a substitute of mineral NPK fertilizer, its N fertilizer potential is mediated by its rate of application. At 10 t ha−1, due to its fast mineralization coupled with improvement in microbial activity (assessed using Biolog EcoPlate), frass was as effective as mineral fertilizer to supply N to plant. By contrast, at 5 t ha−1, the lower frass mineralization induced a reduced N uptake compared to its mineral control. Unlike N, frass was as effective as mineral fertilizer to supply P and K to plants irrespective of its application rate. This was attributed to the presence of P and K in a readily available form in frass. Taken together, our results indicate that mealworm frass supplies very rapidly N, P and K to plants but its effects on N dynamics should be better investigated to warrant its sustainable use as an alternative fertilizer for managing NPK nutrition in cropping systems.

The Biolog EcoPlate™ Technique for Assessing the Effect of Metal Oxide Nanoparticles on Freshwater Microbial Communities

The application of Biolog EcoPlate™ for community-level physiological profiling of soils is well documented; however, the functional diversity of aquatic bacterial communities has been hardly studied. The objective of this study was to investigate the applicability of the Biolog EcoPlate™ technique and evaluate comparatively the applied endpoints, for the characterisation of the effects of metal oxide nanoparticles (MONPs) on freshwater microbial communities. Microcosm experiments were run to assess the effect of nano ZnO and nano TiO2 in freshwater at 0.8–100 mg/L concentration range. The average well colour development, substrate average well colour development, substrate richness, Shannon index and evenness, Simpson index, McIntosh index and Gini coefficient were determined to quantify the metabolic capabilities and functional diversity. Comprehensive analysis of the experimental data demonstrated that short-term exposure to TiO2 and ZnO NPs affected the metabolic activity at different extent and through different mechanisms of action. TiO2 NPs displayed lower impact on the metabolic profile showing up to 30% inhibition. However, the inhibitory effect of ZnO NPs reached 99% with clearly concentration-dependent responses. This study demonstrated that the McIntosh and Gini coefficients were well applicable and sensitive diversity indices. The parallel use of general metabolic capabilities and functional diversity indices may improve the output information of the ecological studies on microbial communities.

Assessment of Carbon Substrate Catabolism Pattern and Functional Metabolic Pathway for Microbiota of Limestone Caves

Microbially induced calcium carbonate precipitation (MICP), a widespread biochemical process involving heterotopic bacterial communities, generally occurs in organic matter-rich environments. Limestone caves, whose oligotrophic conditions result from the absence of sunlight, are considered an extreme environment. In such environments, bacteria have the potential to form calcium carbonate. In this study, the microbial community diversity and taxonomical structure outside and inside a limestone cave was investigated with their community-level carbon source by fingerprinting and functional metabolic pathway prediction using 16S rRNA amplicon sequencing analysis. The Biolog EcoPlate™ assay revealed that microbes from outside the cave were metabolically highly active, resulting in a rising carbon source utilization rate curve. Conversely, the microbial community within the cave was not very active in consuming the carbon substrates of Biolog EcoPlate™. Although major carbon sources were found to be used by microbial communities both inside and outside the cave, the microbial utilization rate of carbon bacteria inside was much lower than for bacteria outside the cave. The taxonomic classification of microbial diversity using 16S rRNA metagenomic analysis revealed eight predominant bacterial phyla associated with both sampling areas: Proteobacteria, Acidobacteria, Actinobacteria, Planctomycetes, Nitrospirae, Chloroflexi, Gemmatimonadetes, and Cyanobacteria. Among these, Planctomycetes, Proteobacteria, Cyanobacteria, and Nitrospirae were predominantly associated with external cave samples, whereas Acidobacteria, Actinobacteria, Chloroflexi, and Gemmatimonadetes were associated with internal cave samples. Functional prediction analysis showed that bacterial communities both inside and outside the cave were functionally involved in the metabolism of carbohydrates, amino acids, other amino acid, lipids, xenobiotic compounds, energy metabolism, and environmental information processing. However, the amino acid and carbohydrate metabolic pathways were predominantly linked to the external cave samples, while xenobiotic compounds, lipids, other amino acids, and energy metabolism were associated with internal cave samples. Overall, a positive correlation was observed between Biolog EcoPlate™ assay carbon utilization and metagenomically observed metabolic function.

Dynamics of Bacterial Community Structure in the Rhizosphere and Root Nodule of Soybean: Impacts of Growth Stages and Varieties

Bacterial communities in rhizosphere and root nodules have significant contributions to the growth and productivity of the soybean (Glycine max (L.) Merr.). In this report, we analyzed the physiological properties and dynamics of bacterial community structure in rhizosphere and root nodules at different growth stages using BioLog EcoPlate and high-throughput sequencing technology, respectively. The BioLog assay found that the metabolic capability of rhizosphere is in increasing trend in the growth of soybeans as compared to the bulk soil. As a result of the Illumina sequencing analysis, the microbial community structure of rhizosphere and root nodules was found to be influenced by the variety and growth stage of the soybean. At the phylum level, Actinobacteria were the most abundant in rhizosphere at all growth stages, followed by Alphaproteobacteria and Acidobacteria, and the phylum Bacteroidetes showed the greatest change. But, in the root nodules Alphaproteobacteria were dominant. The results of the OTU analysis exhibited the dominance of Bradyrhizobium during the entire stage of growth, but the ratio of non-rhizobial bacteria showed an increasing trend as the soybean growth progressed. These findings revealed that bacterial community in the rhizosphere and root nodules changed according to both the variety and growth stages of soybean in the field.

Dynamics of Bacterial Community Structure in the Rhizosphere and Root Nodule of Soybean: Impacts of Growth Stages and Varieties

Bacterial communities in rhizosphere and root nodules have significant contributions to the growth and productivity of the soybean (Glycine max L.). In this report, we analyzed the physiological properties and dynamics of bacterial community structure in rhizosphere and root nodules at different growth stages using BioLog EcoPlate and high-throughput sequencing technology, respectively. The BioLog assay found that the metabolic capability of rhizosphere is in increasing trend in the growth of soybeans as compared to the bulk soil. As a result of the Illumina sequencing analysis, the microbial community structure of rhizosphere and root nodules was found to be influenced by the variety and growth stage of the soybean. At the phylum level, Actinobacteria were the most abundant in rhizosphere at all growth stages, followed by Alphaproteobacteria and Acidobacteria and the phylum Bacteroidetes showed the greatest change. But, in the root nodules Alphaproteobacteria were dominant. The results of the OTU analysis exhibited the dominance of Bradyrhizobium during the entire stage of growth, but the ratio of non-rhizobial bacteria showed an increasing trend as the soybean growth progressed. These findings revealed that bacterial community in the rhizosphere and root nodules changed according to both the variety and growth stages of soybean in the field.