Soil amendments change bacterial functional genes more than taxonomic structure in a cadmium-contaminated soil

Xu, Min; Hao, Xiuli; Xiong, Zhenqian; Liao, Hao; Wang, Li; Zhang, Tianyuan; Luo, Xuesong; Chen, Wenli; Huang, Qiaoyun

doi:10.1016/j.soilbio.2020.108126

Cited by 26 publications

(10 citation statements)

References 46 publications

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“…The concentration of Cd in each fraction was measured using an atomic absorption spectrophotometer (AAS) (AA240FS; Varian, Australia). Details on changes of soil physicochemical properties and Cd speciation in different treatments have been described previously ( 60 ). The main changes included a significant increase of soil pH in CL1, L3, CL3, and SL3 treatments compared to that of the control ( P < 0.05), a notable decrease of water-soluble Cd observed in CL1, SL1, L3, and CL3 treatments ( P < 0.05), and a significant decline of carbonate-bound Cd in all treatments ( P < 0.05).…”

Section: Methodsmentioning

confidence: 99%

“…Detailed methods on PAO and enzyme activities were described in Text S1 in the supplemental material. The abundances of functional genes involved in carbon fixation, carbon degradation, nitrification, denitrification, phosphorus, and sulfur cycling were measured by GeoChip5.0 ( 60 ). The values of 18 ecosystem functions and ecosystem multifunctionality were present in Table S4 in the supplemental material.…”

Section: Methodsmentioning

confidence: 99%

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Distinct Responses of Rare and Abundant Microbial Taxa to In Situ Chemical Stabilization of Cadmium-Contaminated Soil

Huang

Xiong

et al. 2021

mSystems

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Understanding the ecological roles of rare and abundant species in the restoration of soil ecosystem functions is crucial to remediation of heavy metal-polluted soil. Our study assessed the efficiencies of five commonly used soil amendments on recovery of ecosystem multifunctionality and emphasized the relative contributions of rare and abundant microbial communities to ecosystem multifunctionality.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Distinct Responses of Rare and Abundant Microbial Taxa to In Situ Chemical Stabilization of Cadmium-Contaminated Soil

Huang

Xiong

et al. 2021

mSystems

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“…For example, many studies supposed that Gemmatimonas [ 46 ], Saccharimonadales [ 47 ], and Bradyrhizobium [ 48 ] were negatively correlated with soil pH. Additionally, the fixation of heavy metals by SRAs could affect soil bacterial communities by alleviating the toxicity of heavy metals and improving soil quality [ 49 ]. Contrary to previous studies that have found increased diversity and richness of soil bacterial communities by biochar [ 17 , 50 , 51 ] and HAP [ 8 ], our present study found negative effects of biochar and HAP on soil community diversity and richness.…”

Section: Discussionmentioning

confidence: 99%

Remediation Agents Drive Bacterial Community in a Cd-Contaminated Soil

Cui

Liu

et al. 2023

Toxics

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Soil remediation agents (SRAs) such as biochar and hydroxyapatite (HAP) have shown a promising prospect in in situ soil remediation programs and safe crop production. However, the effects of SRAs on soil microbial communities still remain unclear, particularly under field conditions. Here, a field case study was conducted to compare the effects of biochar and HAP on soil bacterial communities in a slightly Cd-contaminated farmland grown with sweet sorghum of different planting densities. We found that both biochar and HAP decreased the diversity and richness of soil bacteria, but they differently altered bacterial community structure. Biochar decreased Chao1 (−7.3%), Observed_species (−8.6%), and Shannon indexes (−1.3%), and HAP caused Shannon (−2.0%) and Simpson indexes (−0.1%) to decline. The relative abundance (RA) of some specific taxa and marker species was differently changed by biochar and HAP. Overall, sweet sorghum cultivation did not significantly alter soil bacterial diversity and richness but caused changes in the RA of some taxa. Some significant correlations were observed between soil properties and bacterial abundance. In conclusion, soil remediation with biochar and HAP caused alterations in soil bacterial communities. Our findings help to understand the ecological impacts of SRAs in soil remediation programs.

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“…In line with previous studies working on natural and human-related environments, − we found that changes in the MRG abundance were not always consistent with metal pollution level. A possible explanation is that MRG abundance could be influenced by a variety of biotic and abiotic factors, including metal concentration and speciation, pH, organic matter content, nutrient conditions, and microbial community composition. ,− Some studies also imply that nutrient availability could mitigate metal toxicity and the selective pressure on the microbial community, − which thereby would affect the distribution of MRGs.…”

Section: Discussionmentioning

confidence: 99%

MRG Chip: A High-Throughput qPCR-Based Tool for Assessment of the Heavy Metal(loid) Resistome

Zhu

Huang

et al. 2022

Environ. Sci. Technol.

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Bacterial metal detoxification mechanisms have been well studied for centuries in pure culture systems. However, profiling metal resistance determinants at the community level is still a challenge due to the lack of comprehensive and reliable quantification tools. Here, a novel high-throughput quantitative polymerase chain reaction (HT-qPCR) chip, termed the metal resistance gene (MRG) chip, has been developed for the quantification of genes involved in the homeostasis of 9 metals. The MRG chip contains 77 newly designed degenerate primer sets and 9 published primer sets covering 56 metal resistance genes. Computational evaluation of the taxonomic coverage indicated that the MRG chip had a broad coverage matching 2 kingdoms, 29 phyla, 64 classes, 130 orders, 226 families, and 382 genera. Temperature gradient PCR and HT-qPCR verified that 57 °C was the optimal annealing temperature, with amplification efficiencies of over 94% primer sets achieving 80−110%, with R 2 > 0.993. Both computational evaluation and the melting curve analysis of HT-qPCR validated a high specificity. The MRG chip has been successfully applied to characterize the distribution of diverse metal resistance determinants in natural and human-related environments, confirming its wide scope of application. Collectively, the MRG chip is a powerful and efficient high-throughput quantification tool for exploring the microbial metal resistome.

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Soil amendments change bacterial functional genes more than taxonomic structure in a cadmium-contaminated soil

Cited by 26 publications

References 46 publications

Distinct Responses of Rare and Abundant Microbial Taxa to In Situ Chemical Stabilization of Cadmium-Contaminated Soil

Distinct Responses of Rare and Abundant Microbial Taxa to In Situ Chemical Stabilization of Cadmium-Contaminated Soil

Remediation Agents Drive Bacterial Community in a Cd-Contaminated Soil

MRG Chip: A High-Throughput qPCR-Based Tool for Assessment of the Heavy Metal(loid) Resistome

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