Response of soil bacterial communities, antibiotic residuals, and crop yields to organic fertilizer substitution in North China under wheat–maize rotation

Heavy metal and pesticide pollution have become an inevitable part of the modern industrialized environment that find their way into all ecosystems. Because of their persistent nature, recalcitrance, high toxicity and biological enrichment, metal and pesticide pollution has threatened the stability of the environment as well as the health of living beings. Due to the environmental persistence of heavy metals and pesticides, they get accumulated in the environs and consequently lead to food chain contamination. Therefore, remediation of heavy metals and pesticide contaminations needs to be addressed as a high priority. Various physico-chemical approaches have been employed for this purpose, but they have significant drawbacks such as high expenses, high labor, alteration in soil properties, disruption of native soil microflora and generation of toxic by-products. Researchers worldwide are focusing on bioremediation strategies to overcome this multifaceted problem, i.e., the removal, immobilization and detoxification of pesticides and heavy metals, in the most efficient and cost-effective ways. For a period of millions of evolutionary years, microorganisms have become resistant to intoxicants and have developed the capability to remediate heavy metal ions and pesticides, and as a result, they have helped in the restoration of the natural state of degraded environs with long term environmental benefits. Keeping in view the environmental and health concerns imposed by heavy metals and pesticides in our society, we aimed to present a generalized picture of the bioremediation capacity of microorganisms. We explore the use of bacteria, fungi, algae and genetically engineered microbes for the remediation of both metals and pesticides. This review summarizes the major detoxification pathways and bioremediation technologies; in addition to that, a brief account is given of molecular approaches such as systemic biology, gene editing and omics that have enhanced the bioremediation process and widened its microbiological techniques toward the remediation of heavy metals and pesticides.

/pdf/microbial-remediation-a-promising-tool-for-reclamation-of-3a3rlzj4.pdf

Microbial Remediation: A Promising Tool for Reclamation of Contaminated Sites with Special Emphasis on Heavy Metal and Pesticide Pollution: A Review

Labile organic carbon fractions drive soil microbial communities after long-term fertilization

Reducing chemical fertilizers in combination with bio-organic fertilizers can limit the use of chemical fertilizers while maintaining soil fertility. However, the effects of combined fertilization on soil chemical properties, microbial community structure, and crop yield and quality are unknown. Using high-throughput sequencing, we conducted field experiments using lettuce plants subjected to five fertilization treatments: chemical fertilizer with conventional fertilization rate (CK), chemical fertilizer reduction by 30% + 6,000 kg ha–1 bio-organic fertilizer (T1), chemical fertilizer reduction by 30% + 9,000 kg ha–1 bio-organic fertilizer (T2), chemical fertilizer reduction by 40% + 6,000 kg ha–1 bio-organic fertilizer (T3), and chemical fertilizer reduction by 40% + 9,000 kg ha–1 bio-organic fertilizer (T4). Compared with CK, the T1–T4 had significantly higher soil pH and soil organic matter (SOM) and showed increased richness and diversity of the bacterial community, and decreased richness and diversity of the fungal community. Principal coordinate analysis evidenced that the bacterial and fungal communities of CK and T1–T4 were distinctly separated. The Kruskal-Wallis H-test demonstrated that the fungal community was more sensitive than the bacterial community to chemical fertilizer reduction combined with bio-organic fertilizer. Among the soil chemical parameters measured, only TN (total nitrogen) was significantly correlated with bacterial and fungal community composition. The T1 and T2 increased lettuce yield. Moreover, T1–T4 characterized reduced nitrate content and increased levels of soluble sugars and vitamin C in lettuce. Overall, the combined application of reduced chemical fertilizer and bio-organic fertilizer effectively improved soil fertility, microbial community structure, and lettuce yield and quality. These findings have valuable implications for vegetable safety and long-term environmental sustainability.

https://www.frontiersin.org/articles/10.3389/fmicb.2022.863325/pdf

Reduced Chemical Fertilizer Combined With Bio-Organic Fertilizer Affects the Soil Microbial Community and Yield and Quality of Lettuce

The global utilization of single-use, non-biodegradable plastics, such as bottles made of polyethylene terephthalate (PET), has contributed to catastrophic levels of plastic pollution. Fortunately, microbial communities are adapting to assimilate plastic waste. Previously, our work showed a full consortium of five bacteria capable of synergistically degrading PET. Using omics approaches, we identified the key genes implicated in PET degradation within the consortium’s pangenome and transcriptome. This analysis led to the discovery of a novel PETase, EstB, which has been observed to hydrolyze the oligomer BHET and the polymer PET. Besides the genes implicated in PET degradation, many other biodegradation genes were discovered. Over 200 plastic and plasticizer degradation-related genes were discovered through the Plastic Microbial Biodegradation Database (PMBD). Diverse carbon source utilization was observed by a microbial community-based assay, which, paired with an abundant number of plastic- and plasticizer-degrading enzymes, indicates a promising possibility for mixed plastic degradation. Using RNAseq differential analysis, several genes were predicted to be involved in PET degradation, including aldehyde dehydrogenases and several classes of hydrolases. Active transcription of PET monomer metabolism was also observed, including the generation of polyhydroxyalkanoate (PHA)/polyhydroxybutyrate (PHB) biopolymers. These results present an exciting opportunity for the bio-recycling of mixed plastic waste with upcycling potential.

/pdf/microbial-consortia-and-mixed-plastic-waste-pangenomic-1ir1ecgm.pdf

Microbial Consortia and Mixed Plastic Waste: Pangenomic Analysis Reveals Potential for Degradation of Multiple Plastic Types via Previously Identified PET Degrading Bacteria

Since 2015, China has implemented chemical fertilizer reduction, aiming to achieve zero growth in the application rate of chemical fertilizer. Therefore, it is of great significance to explore the effect of chemical fertilizer reduction combined with organic materials in a wheat-maize rotation system from fluvo-aquic soil in North China on soil microbial community. The field experiment included five fertilization treatments, i.e., chemical fertilizer with conventional application rate (F), chemical fertilizer reduction on the basis of conventional fertilization (FR), chemical fertilizer reduction plus straw (FRS), chemical fertilizer reduction combined with organic fertilizer (FRO), and chemical fertilizer reduction combined with organic fertilizer and straw (FROS). The abundance, composition, diversity, and structure of bacterial and fungal communities among treatments were evaluated using qPCR and Illumina high-throughput sequencing technology. The results showed that the concentrations of soil organic matter (SOM) and total nitrogen (TN) in all treatments with addition of organic materials were much higher than those in treatments applied with only chemical fertilizer. The SOM content in the FRS, FRO, and FROS treatments increased by 23.91%, 37.12%, 26.09%, and the TN content increased by 11.96%, 21.08%, 15.22% in comparison with the F treatment, respectively. The lowest contents of available phosphorus (AP) and nitrate nitrogen (NO3−-N) were observed in FR treatment. The AP content in FRO and FROS treatments were 2.44 times and 2.42 times greater than that in FR treatment, respectively. Compared with F treatment, the organic materials input significantly increased bacterial and fungal abundances. More significant effects on the α-diversity with organic fertilizer were observed in the fungal community compared with the bacterial community. The significant increase of Ascomycota and the decline of Mortierellomycota and Glomeromycota were observed in the combined with organic materials treated soils. The nonmetric multidimensional scaling (NMDS) analysis demonstrated that the bacterial community structure in the F treatment was clearly separated from the other treatments, and the other treatments clustered closely, while with respect to fungal community structure, the FRO and FROS treatments grouped together and were separated from the other three treatments. The redundancy analysis (RDA) results showed that the structure of the bacterial community was significantly correlated with SOM and TN, and the fungal community structure was strongly correlated with AP, SOM, and TN. The chemical fertilizer reduction combined with organic fertilizer and straw can effectively improve soil fertility and nutrient availability, altered the community structure of both bacteria and fungi, but only significantly reduced fungal biodiversity. The influence of chemical fertilizer reduction combined with organic materials on fungi was greater than that on bacteria in fluvo-aquic soil of North China.

Variation of Soil Bacterial and Fungal Communities from Fluvo-Aquic Soil Under Chemical Fertilizer Reduction Combined with Organic Materials in North China Plain

Soil pollution is one of the most serious environmental problems globally due to the weak self-purification ability, long degradation time, and high cost of cleaning soil pollution. The pollutants in the soil can be transported into the human body through water or dust, causing adverse effects on human health. The latest research has shown that the clean-up of soil pollutants through microbial consortium is a very promising method. This review provides an in-depth discussion on the efficient removal, bio-adsorption, or carbonated precipitation of organic and inorganic pollutants by the microbial consortium, including PAHs, BPS, BPF, crude oil, pyrene, DBP, DOP, TPHP, PHs, butane, DON, TC, Mn, and Cd. In view of the good degradation ability of the consortium compared to single strains, six different synergistic mechanisms and corresponding microorganisms are summarized. The microbial consortium obtains such activities through enhancing synergistic degradation, reducing the accumulation of intermediate products, generating the crude enzyme, and self-regulating, etc. Furthermore, the degradation efficiency of pollutants can be greatly improved by adding chemical materials such as the surfactants Tween 20, Tween 80, and SDS. This review provides insightful information regarding the application of microbial consortia for soil pollutant removal.

/pdf/microbial-consortia-are-needed-to-degrade-soil-pollutants-3nwqvamk.pdf

Ting Zhang

Papers

Variation of Soil Bacterial and Fungal Communities from Fluvo-Aquic Soil Under Chemical Fertilizer Reduction Combined with Organic Materials in North China Plain

Microbial Consortia Are Needed to Degrade Soil Pollutants

Crop yield estimation and irrigation scheduling optimization using a root-weighted soil water availability based water production function

Optimizing relative root-zone water depletion thresholds to maximize yield and water productivity of winter wheat using AquaCrop