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Agronomy
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Innovations and Obstacles: Microbial Communities in the Journey of Soil...
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Innovations and Obstacles: Microbial Communities in the Journey of Soil Remediation

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Soil and Plant Nutrition".

Deadline for manuscript submissions: closed (15 October 2024) | Viewed by 3627

Special Issue Editor

Dr. Dong Liu

E-Mail Website
Guest Editor
The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
Interests: macrofungi-mediated carbon sequestration; soil microbiome; soil–plantmicrobe interaction; functional microbes dominated composting; bioresource utilization

Special Issue Information

Dear Colleagues,

With an increasing pressure on shifting to sustainable means of agriculture and food demand, agricultural soils are facing strong human-induced stresses such as exceeding chemical inputs, improper application of pesticides, etc. Such activities have caused an imbalance in soil microbiome, further disturbed microbe-mediated C, N and P cycles. Thus, it is time to modify soil properties and the microbiome, in the direction of accelerating soil nutrient recovery and disease resistance. With increasing pressure on agriculture soils, microbiome-based strategies have exhibited tremendous potential. The emphasis has now shifted from the storage of potent individual strains to the preservation of beneficial microorganisms and further establishing a healthy soil microbiome. Papers relevant to the following topics are welcomed to this Special Issue, including, but not limited to:

  1. Soil remediation in terms of fertility increase, abating hazardous substances and crop growth enhancement;
  2. Beneficial microbe-protecting techniques, and their transplantation and subsequent application.

Dr. Dong Liu
Guest Editor

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • microbiome transplantation
  • microbiome storage and efficient application
  • soil remediation
  • safety biofertilizers
  • soil nutrient enhancement

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Published Papers (6 papers)

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Research

22 pages, 2884 KiB  
Article
Leguminous Plants and Microbial Inoculation: An Approach for Biocatalytic Phytoremediation of Tebuthiuron in Agricultural Soil
by Victor Hugo Cruz, Bruno Rafael de Almeida Moreira, Thalia Silva Valério, Yanca Araujo Frias, Vinícius Luiz da Silva, Eduardo Beraldo de Morais, Leonardo Gomes de Vasconcelos, Leandro Tropaldi, Evandro Pereira Prado, Renato Nallin Montagnolli and Paulo Renato Matos Lopes
Agronomy 2024, 14(12), 2805; https://doi.org/10.3390/agronomy14122805 - 26 Nov 2024
Viewed by 130
Abstract
Herbicides are important for weed control but can severely impact ecosystems, causing soil and water contamination, biodiversity loss, and harm to non-target organisms. Tebuthiuron, widely used in sugarcane cultivation, is highly soluble and persistent, posing significant environmental risks. Microbial inoculation has emerged as [...] Read more.
Herbicides are important for weed control but can severely impact ecosystems, causing soil and water contamination, biodiversity loss, and harm to non-target organisms. Tebuthiuron, widely used in sugarcane cultivation, is highly soluble and persistent, posing significant environmental risks. Microbial inoculation has emerged as a sustainable strategy to mitigate such damage. This study investigated the phytoremediation potential of Mucuna pruriens and Canavalia ensiformis in tebuthiuron-contaminated soils, enhanced by fungal and bacterial inoculants. Crotalaria juncea served as a bioindicator plant, and Lactuca sativa was used in ecotoxicological bioassays. During a 140-day greenhouse experiment from September 2021 to March 2022, M. pruriens showed faster growth than C. ensiformis in uncontaminated soils but was more affected by tebuthiuron. Bacterial inoculants improved M. pruriens growth under stress, while fungal inoculants mitigated tebuthiuron’s effects on C. ensiformis. C. juncea exhibited high sensitivity to tebuthiuron but grew beyond 100 cm with bacterial inoculants. Ecotoxicological assays showed that bacterial bioaugmentation significantly reduced soil toxicity. Natural attenuation further decreased tebuthiuron toxicity, and prior cultivation of M. pruriens enhanced soil detoxification. This integrated approach combining phytoremediation and bioaugmentation offers a sustainable method to degrade tebuthiuron, foster safer agriculture, and reduce environmental and health risks. Full article
(This article belongs to the Special Issue Innovations and Obstacles: Microbial Communities in the Journey of Soil Remediation)
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14 pages, 7595 KiB  
Article
Environmental Constraints Mitigation Directly Drove the Diversifications of Fungal Community and Functional Profile in Amended Coastal Salt-Affected Soils
by Yunlong Li, Weifeng Chen, Yiwei Xu, Jie Yu, Wengang Zuo, Yuhua Shan and Yanchao Bai
Agronomy 2024, 14(12), 2772; https://doi.org/10.3390/agronomy14122772 - 22 Nov 2024
Viewed by 312
Abstract
Although organic amendment has been widely demonstrated to be capable of reassembling soil microbiomes in coastal salt-affected soils, quantitative characterization in respect to how abiotic and biotic components drive the diversifications of soil microbial community and function remains rudimentary. We investigated the effects [...] Read more.
Although organic amendment has been widely demonstrated to be capable of reassembling soil microbiomes in coastal salt-affected soils, quantitative characterization in respect to how abiotic and biotic components drive the diversifications of soil microbial community and function remains rudimentary. We investigated the effects of types and application rates of different exogenous organic ameliorants (sewage sludge, S; vermicompost, V) on the physicochemical properties, fungal community diversity, and fungal functional traits in coastal salt-affected soils. Results revealed that both S and V amendments exhibited significantly positive impacts on the alleviation of environmental constraints and the reassembly of fungal community and functional profile. Of note, efficacy of the two exogenous organic ameliorants was significantly influenced by the types of carbon sources utilized and the rates at which they are applied. More pronounced variations in soil physicochemical and microbiological properties were observed in soils amended by S and V at the application rate of 200 t ha−1. Both S and V treatments positively boosted soil fungal community diversification with higher compositional diversities found in the majority of amended soils when compared to unamended soils. In addition, S and V applications favored the flourishment of functions linked to saprotrophic strategy with soil saprotrophs and wood saprotrophs predominating the functional profiles in soils amended by S and V, respectively. Results obtained from redundancy analysis and structural equation modeling revealed that pH, salinity, and SOC were the principle edaphic factors that significantly and directly affected the reassembly of fungal community. In addition, fluctuations in the prevalence of specific fungal genera, including Stachybotrys, Trichoderma, Mortierella, and Acremonium, emerged as a decisive biotic factor influencing diversifications of fungal communities and functional profiles. Taken together, this study not only highlighted the efficacy of S and V application on environmental constraints alleviation in coastal mudflats, but also qualitatively identified and quantitatively illustrated potential pathways and effectiveness of edaphic and biotic components driving the diversification of soil fungal microbiomes and functional profiles. These findings would enhance our understanding in respect to the microbial-mediated amelioration process of salt-affected soils within coastal mudflat ecosystem. Full article
(This article belongs to the Special Issue Innovations and Obstacles: Microbial Communities in the Journey of Soil Remediation)
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14 pages, 1958 KiB  
Article
Arbuscular Mycorrhizae Affect Soil Nitrogen Fertilizer Utilization, Denitrification Functional Genes, and N2O Emissions During Biochar Amendment
by Yanfang Wang, Jing Liu, Xuxian Deng, Yuyang Li, Jiakai Gao and Ling Liu
Agronomy 2024, 14(11), 2627; https://doi.org/10.3390/agronomy14112627 - 7 Nov 2024
Viewed by 444
Abstract
Arbuscular mycorrhizal fungi (AMF) can form symbionts with plant roots, acquire soil nitrogen, and affect nitrous oxide (N2O) production. Biochar, as a soil additive for the management of agricultural soil, affects soil nitrogen (N) utilization and plant growth. However, how AMF [...] Read more.
Arbuscular mycorrhizal fungi (AMF) can form symbionts with plant roots, acquire soil nitrogen, and affect nitrous oxide (N2O) production. Biochar, as a soil additive for the management of agricultural soil, affects soil nitrogen (N) utilization and plant growth. However, how AMF regulates soil N unitization, the denitrification process, and N2O emissions in plant–soil systems remains largely unknown, particularly under the biochar amendment. In this study, a microcosm experiment was conducted to investigate the impacts of different mycorrhizal treatments (CK: neither AMF hyphae nor plant roots; AMF: only AMF hyphae; AMF + R: AMF hyphae and plant roots) on plant growth, soil N fertilizer utilization, N2O production and consumption, functional gene abundance, and N2O emission at two biochar addition levels (B0: no biochar; B1: biochar addition rate of 10 g·kg−1 soil) in a maize planting soil system. The results revealed that AMF alone and AMF with plant root treatments enhanced the fresh weight of maize plants by 10.15% and 19.23% and decreased soil inorganic N contents by 33.28% and 75.56%, respectively. The combination of biochar, AMF, and plant roots showed the largest increase in maize plant biomass. The AMF and AMF with root treatments all significantly decreased the nirS + nirK/nosZ ratio and N2O emissions at two biochar levels. The presence of AMF and plant roots during biochar amendment showed the smallest nirS + nirK/nosZ ratio and N2O emissions. The AMF combined with biochar and AMF and plant roots combined with biochar treatments increased nirS + nirK/nosZ by 24.32% and 26.90% and decreased N2O accumulation emission by 21.12% and 38.13%, respectively. The results imply that biochar, AMF, and plant roots reduced N2O emissions directly by reducing soil N and increasing soil N unitization efficiency and indirectly by shifting the N2O production and consumption gene abundance in agroecosystems. These findings suggest that the addition of biochar and AMF and/or the presence of plant roots can interact to alleviate soil N2O emissions by manipulating plant inorganic N acquisition and the soil denitrification process. Full article
(This article belongs to the Special Issue Innovations and Obstacles: Microbial Communities in the Journey of Soil Remediation)
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18 pages, 3820 KiB  
Article
Isolation, Characterization, and Optimization of Culture Medium for Local Straw-Degrading Bacteria from Northeastern Black Soils of China
by Lei Zhang, Tianyu Liu, Chengzhao Yan, Jinpeng Zhang, Rui Yu, Nana Luo and Yong Yu
Agronomy 2024, 14(11), 2591; https://doi.org/10.3390/agronomy14112591 - 3 Nov 2024
Viewed by 813
Abstract
In order to solve the problem of low and poor straw degradation in typical black soil areas of Northeast China, the present study was carried out to screen the potential of in situ strains with cellulose degradation ability from black soils of Northeast [...] Read more.
In order to solve the problem of low and poor straw degradation in typical black soil areas of Northeast China, the present study was carried out to screen the potential of in situ strains with cellulose degradation ability from black soils of Northeast China to play a role in the resourceful utilization of straw and the development of sustainable agriculture. The straw degradation potential of the strains was evaluated by combining sodium carboxymethyl cellulose plate screening and cellulase viability assay; the species identification of the strains was carried out by morphology, physiology, biochemistry, and molecular biology; and the basic medium formulation of the strains was optimized by Box–Behnken response surface methodology. Ten cellulose-degrading strains were identified: ZL-5, ZL-69, ZL-88, ZL-95, ZL-111, ZL-137, ZL-139, ZL-140, ZL-187, and ZL-216, of which ZL-139 had the highest cellulase production capacity, with a cellulase secretion of 7.8781 U/mL in the enzyme-producing medium. ZL-139 was identified as Bacillus cereus; the optimized best formulation was glucose—4.284 g/L, yeast extract—1.454 g/L, MgSO4—0.417 g/L, KH2PO4—0.5 g/L, KH2PO4—0.5 g/L, K2HPO4—1.5 g/L, and NaCl—1.0 g/L. In conclusion, strain ZL-139 has good potential for crop straw degradation and can be a candidate strain for a straw-rotting agent in northeast China, with promising prospects for development and utilization. Full article
(This article belongs to the Special Issue Innovations and Obstacles: Microbial Communities in the Journey of Soil Remediation)
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21 pages, 5308 KiB  
Article
Combined Application of High-Throughput Sequencing and Metabolomics to Evaluate the Microbial Mechanisms of Plant-Growth-Promoting Bacteria in Enhancing the Remediation of Cd-Contaminated Soil by Hybrid Pennisetum
by Shan-Shan Gao, Ying-Jun Zhang, Yang Shao, B. Larry Li, Han Liu, Yu-Ying Li, Xue-Min Ren and Zhao-Jin Chen
Agronomy 2024, 14(10), 2348; https://doi.org/10.3390/agronomy14102348 - 11 Oct 2024
Viewed by 645
Abstract
The contamination of soil with the heavy metal cadmium (Cd) is increasingly prominent and severely threatens food security in China. Owing to its low cost, suitable efficacy, and ability to address the shortcomings of plant remediation by enhancing the ability of plants to [...] Read more.
The contamination of soil with the heavy metal cadmium (Cd) is increasingly prominent and severely threatens food security in China. Owing to its low cost, suitable efficacy, and ability to address the shortcomings of plant remediation by enhancing the ability of plants to take up Cd, plant–microbe combination remediation technology has become a research hotspot in heavy metal pollution remediation. A pot experiment was performed to examine the effects of inoculation with the plant-growth-promoting bacterium Brevibacillus sp. SR-9 on the biomass, Cd accumulation, and soil nutrients of hybrid Pennisetum. The purpose of this study was to determine how Brevibacillus sp. SR-9 alleviates stress caused by heavy metal contamination. High-throughput sequencing and metabolomics were used to determine the effects of inoculation on the soil bacterial community composition and microbial metabolic functions associated with hybrid Pennisetum. The results suggest that mutation of Brevibacillus sp. SR-9 effectively alleviates Cd pollution stress, leading to increased biomass and accumulation of Cd in hybrid Pennisetum. The aboveground biomass and the root weight increased by 12.08% and 27.03%, respectively. Additionally, the accumulation of Cd in the aboveground sections and roots increased by 21.16% and 15.50%, respectively. Measurements of the physicochemical properties of the soil revealed that the strain Brevibacillus sp. SR-9 slightly increased the levels of available phosphorus, total nitrogen, total phosphorus, and available potassium. High-throughput DNA sequencing revealed that Brevibacillus sp. SR-9 implantation modified the composition of the soil bacterial community by increasing the average number of Actinobacteria and Bacillus. The total nitrogen content of the soil was positively correlated with the Actinobacteria abundance, total phosphorus level, and available phosphorus level. Metabolomic analysis revealed that inoculation affected the abundance of soil metabolites, and 59 differentially abundant metabolites were identified (p < 0.05). Among these, 14 metabolites presented increased abundance, whereas 45 metabolites presented decreased abundance. Fourteen metabolic pathways were enriched in these metabolites: the folate resistance pathway, the ABC transporter pathway, D-glutamine and D-glutamic acid metabolism, purine metabolism, and pyrimidine metabolism. The abundance of the metabolites was positively correlated with the levels of available phosphorus, total potassium, total phosphorus, and total nitrogen. According to correlation analyses, the development of hybrid Pennisetum and the accumulation of Cd are strongly associated with differentially abundant metabolites, which also impact the abundance of certain bacterial populations. This work revealed that by altering the makeup of microbial communities and their metabolic processes, bacteria that promote plant development can mitigate the stress caused by Cd. These findings reveal the microbiological mechanisms through which these bacteria increase the ability of hybrid Pennisetum to take up the Cd present in contaminated soils. Full article
(This article belongs to the Special Issue Innovations and Obstacles: Microbial Communities in the Journey of Soil Remediation)
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17 pages, 3600 KiB  
Article
Responses of Methane Emission and Bacterial Community to Fertilizer Reduction Plus Organic Materials over the Course of an 85-Day Leaching Experiment
by Jiakai Gao, Zhenyi Ma, Ling Liu, Zhaoyong Shi and Jialong Lv
Agronomy 2024, 14(9), 1972; https://doi.org/10.3390/agronomy14091972 - 1 Sep 2024
Viewed by 865
Abstract
Methane produced from paddy fields has a negative impact on global climate change. However, the role of soil bacterial community composition in mediating methane (CH4) emission from waterlogged paddy soil using the column experiment is poorly known. In the present study, [...] Read more.
Methane produced from paddy fields has a negative impact on global climate change. However, the role of soil bacterial community composition in mediating methane (CH4) emission from waterlogged paddy soil using the column experiment is poorly known. In the present study, various fertilization treatments were adopted to investigate the effects of fertilizer reduction combined with organic materials (CK: control; CF: conventional fertilization; RF: 20% fertilizer reduction; RFWS: RF plus wheat straw amendment; RFRS: RF plus rapeseed shell amendment; RFAS: RF plus astragalus smicus amendment) on CH4 emission and soil bacterial community during an 85-day leaching experiment. We hypothesized that the fertilizer reduction plus the organic materials could enrich the bacterial communities and increase CH4 emission. The average CH4 flux varied from 0.03 μg m−2 h−1 to 76.19 μg m−2 h−1 among all treatments in the nine sampling times, which may account for the experimental conditions such as air temperature, moisture, and anthropogenic factors. In addition, high-throughput sequencing was utilized to investigate the alteration of the soil bacterial community structure. It was revealed that the diversity and composition of the bacterial community in the topsoil amended with organic materials underwent significant shifts after the 85-day leaching experiment. Proteobacteria was identified as the dominant phylum of the soil bacteria, with an average proportion of 35.2%. For Firmicutes, the proportion of RFRS (11%) was higher than that in the CK (8%), RF (8%), RFWS (7%), RFAS (6%), and CF (5%) treatments. Additionally, Gammaproteobacteria and Alphaproteobateria were supposed to be the major class bacterial communities, with average proportions of 12.8% and 12.2%, respectively. For the RFWS treatment, the contribution of Alphaproteobateria was the highest among all the bacterial relative abundance. According to the correlation heatmap analysis, the top ten bacterial communities were positively related to soil microbial biomass carbon (MBC) and ammonia nitrogen (NH4+-N) (p < 0.01). The findings also indicated that the RFRS treatment was the favorable management to alleviate CH4 emission during an 85-day leaching experiment or possibly in paddy production. Collectively, these results predict that the impacts of different treatments on CH4 production are strongly driven by soil microbial communities and soil properties, with soil bacteria being more prone to the crop residue degradation stage and more sensitive to soil properties. The discoveries presented in this study will be useful for assessing the efficacy and mechanisms of organic material amendments on CH4 emissions in paddy soil. Full article
(This article belongs to the Special Issue Innovations and Obstacles: Microbial Communities in the Journey of Soil Remediation)
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