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Liu J, Pei S, Zheng Q, Li J, Liu X, Ruan Y, Luo B, Ma L, Chen R, Hu W, Niu J, Tian T. Heavy metal contamination impacts the structure and co-occurrence patterns of bacterial communities in agricultural soils. J Basic Microbiol 2024; 64:e2300435. [PMID: 38150647 DOI: 10.1002/jobm.202300435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 11/12/2023] [Accepted: 12/12/2023] [Indexed: 12/29/2023]
Abstract
Heavy metal (HM) contamination caused by mining and smelting activities can be harmful to soil microbiota, which are highly sensitive to HM stress. Here, we explore the effects of HM contamination on the taxonomic composition, predicted function, and co-occurrence patterns of soil bacterial communities in two agricultural fields with contrasting levels of soil HMs (i.e., contaminated and uncontaminated natural areas). Our results indicate that HM contamination does not significantly influence soil bacterial α diversity but changes the bacterial community composition by enriching the phyla Gemmatimonadetes, Planctomycetes, and Parcubacteria and reducing the relative abundance of Actinobacteria. Our results further demonstrate that HM contamination can strengthen the complexity and modularity of the bacterial co-occurrence network but weaken positive interactions between keystone taxa, leading to the gradual disappearance of some taxa that originally played an important role in healthy soil, thereby possibly reducing the resistance of bacterial communities to HM toxicity. The predicted functions of bacterial communities are related to membrane transport, amino acid metabolism, energy metabolism, and carbohydrate metabolism. Among these, functions related to HM detoxification and antioxidation are enriched in uncontaminated soils, while HM contamination enriches functions related to metal resistance. This study demonstrated that microorganisms adapt to the stress of HM pollution by adjusting their composition and enhancing their network complexity and potential ecological functions.
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Affiliation(s)
- Jiangyun Liu
- School of Public Health, Lanzhou University, Lanzhou, Gansu, The People's Republic of China
| | - Shuwei Pei
- School of Public Health, Lanzhou University, Lanzhou, Gansu, The People's Republic of China
| | - Qiwen Zheng
- School of Public Health, Lanzhou University, Lanzhou, Gansu, The People's Republic of China
| | - Jia Li
- School of Public Health, Lanzhou University, Lanzhou, Gansu, The People's Republic of China
| | - Xingrong Liu
- School of Public Health, Lanzhou University, Lanzhou, Gansu, The People's Republic of China
| | - Ye Ruan
- School of Public Health, Lanzhou University, Lanzhou, Gansu, The People's Republic of China
| | - Bin Luo
- School of Public Health, Lanzhou University, Lanzhou, Gansu, The People's Republic of China
| | - Li Ma
- School of Public Health, Lanzhou University, Lanzhou, Gansu, The People's Republic of China
| | - Rentong Chen
- School of Public Health, Lanzhou University, Lanzhou, Gansu, The People's Republic of China
| | - Weigang Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, The People's Republic of China
| | - Jingping Niu
- School of Public Health, Lanzhou University, Lanzhou, Gansu, The People's Republic of China
| | - Tian Tian
- School of Public Health, Lanzhou University, Lanzhou, Gansu, The People's Republic of China
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Wentzien NM, Fernández-González AJ, Villadas PJ, Valverde-Corredor A, Mercado-Blanco J, Fernández-López M. Thriving beneath olive trees: The influence of organic farming on microbial communities. Comput Struct Biotechnol J 2023; 21:3575-3589. [PMID: 37520283 PMCID: PMC10372477 DOI: 10.1016/j.csbj.2023.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023] Open
Abstract
Soil health and root-associated microbiome are interconnected factors involved in plant health. The use of manure amendment on agricultural fields exerts a direct benefit on soil nutrient content and water retention, among others. However, little is known about the impact of manure amendment on the root-associated microbiome, particularly in woody species. In this study, we aimed to evaluate the effects of ovine manure on the microbial communities of the olive rhizosphere and root endosphere. Two adjacent orchards subjected to conventional (CM) and organic (OM) management were selected. We used metabarcoding sequencing to assess the bacterial and fungal communities. Our results point out a clear effect of manure amendment on the microbial community. Fungal richness and diversity were increased in the rhizosphere. The fungal biomass in the rhizosphere was more than doubled, ranging from 1.72 × 106 ± 1.62 × 105 (CM) to 4.54 × 106 ± 8.07 × 105 (OM) copies of the 18 S rRNA gene g-1 soil. Soil nutrient content was also enhanced in the OM orchard. Specifically, oxidable organic matter, total nitrogen, nitrate, phosphorous, potassium and sulfate concentrations were significantly increased in the OM orchard. Moreover, we predicted a higher abundance of bacteria in OM with metabolic functions involved in pollutant degradation and defence against pathogens. Lastly, microbial co-occurrence network showed more positive interactions, complexity and shorter geodesic distance in the OM orchard. According to our results, manure amendment on olive orchards represents a promising tool for positively modulating the microbial community in direct contact with the plant.
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Affiliation(s)
- Nuria M. Wentzien
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
| | - Antonio J. Fernández-González
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
| | - Pablo J. Villadas
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
| | | | - Jesús Mercado-Blanco
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
- Crop Protection Department, Instituto de Agricultura Sostenible (CSIC), 14004 Córdoba, Spain
| | - Manuel Fernández-López
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
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Lagunas B, Richards L, Sergaki C, Burgess J, Pardal AJ, Hussain RMF, Richmond BL, Baxter L, Roy P, Pakidi A, Stovold G, Vázquez S, Ott S, Schäfer P, Gifford ML. Rhizobial nitrogen fixation efficiency shapes endosphere bacterial communities and Medicago truncatula host growth. MICROBIOME 2023; 11:146. [PMID: 37394496 DOI: 10.1186/s40168-023-01592-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 06/05/2023] [Indexed: 07/04/2023]
Abstract
BACKGROUND Despite the knowledge that the soil-plant-microbiome nexus is shaped by interactions amongst its members, very little is known about how individual symbioses regulate this shaping. Even less is known about how the agriculturally important symbiosis of nitrogen-fixing rhizobia with legumes is impacted according to soil type, yet this knowledge is crucial if we are to harness or improve it. We asked how the plant, soil and microbiome are modulated by symbiosis between the model legume Medicago truncatula and different strains of Sinorhizobium meliloti or Sinorhizobium medicae whose nitrogen-fixing efficiency varies, in three distinct soil types that differ in nutrient fertility, to examine the role of the soil environment upon the plant-microbe interaction during nodulation. RESULTS The outcome of symbiosis results in installment of a potentially beneficial microbiome that leads to increased nutrient uptake that is not simply proportional to soil nutrient abundance. A number of soil edaphic factors including Zn and Mo, and not just the classical N/P/K nutrients, group with microbial community changes, and alterations in the microbiome can be seen across different soil fertility types. Root endosphere emerged as the plant microhabitat more affected by this rhizobial efficiency-driven community reshaping, manifested by the accumulation of members of the phylum Actinobacteria. The plant in turn plays an active role in regulating its root community, including sanctioning low nitrogen efficiency rhizobial strains, leading to nodule senescence in particular plant-soil-rhizobia strain combinations. CONCLUSIONS The microbiome-soil-rhizobial dynamic strongly influences plant nutrient uptake and growth, with the endosphere and rhizosphere shaped differentially according to plant-rhizobial interactions with strains that vary in nitrogen-fixing efficiency levels. These results open up the possibility to select inoculation partners best suited for plant, soil type and microbial community. Video Abstract.
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Affiliation(s)
- Beatriz Lagunas
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
| | - Luke Richards
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Chrysi Sergaki
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Jamie Burgess
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Rana M F Hussain
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Laura Baxter
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Proyash Roy
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Anastasia Pakidi
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Gina Stovold
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Saúl Vázquez
- University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Nottingham, LE12 5RD, UK
| | - Sascha Ott
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Patrick Schäfer
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
- Present Address: Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, 35392, Germany.
| | - Miriam L Gifford
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, CV47AL, UK.
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Shen Q, Fu W, Chen B, Zhang X, Xing S, Ji C, Zhang X. Community response of soil microorganisms to combined contamination of polycyclic aromatic hydrocarbons and potentially toxic elements in a typical coking plant. Front Microbiol 2023; 14:1143742. [PMID: 36950156 PMCID: PMC10025358 DOI: 10.3389/fmicb.2023.1143742] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/07/2023] [Indexed: 03/08/2023] Open
Abstract
Both polycyclic aromatic hydrocarbons (PAHs) and potentially toxic elements (PTEs) of coking industries impose negative effects on the stability of soil ecosystem. Soil microbes are regarded as an essential moderator of biochemical processes and soil remediation, while their responses to PAHs-PTEs combined contamination are largely unknown. In the present study, soil microbial diversity and community composition in the typical coking plant under the chronic co-exposure of PAHs and PTEs were investigated and microbial interaction networks were built to reveal microbial co-occurrence patterns. The results indicated that the concentrations of PAHs in the soil inside the coking plant were significantly higher than those outside the plant. The mean concentration of ∑16PAHs was 2894.4 ng·g-1, which is 5.58 times higher than that outside the plant. The average Hg concentration inside the coking plant was 22 times higher than the background value of Hebei province. The soil fungal community inside the coking plant showed lower richness compared with that of outside community, and there are significant difference in the bacterial and fungal community composition between inside and outside of coking plant (p < 0.01). Predicted contribution of different environmental factors to each dominant species based on random forest identified 20 and 25 biomarkers in bacteria and fungi, respectively, that were highly sensitive to coking plant soil in operation, such as Betaproteobacteria,Sordariomycetes and Dothideomycetes. Bacterial and fungal communities were shaped by the soil chemical properties (pH), PTEs (Hg), and PAHs together in the coking plant soils. Furthermore, the bacterial and fungal interaction patterns were investigated separately or jointly by intradomain and interdomain networks. Competition is the main strategy based on the co-exclusion pattern in fungal community, and the competitive relationship inside the coking plant is more complex than that outside the plant. In contrast, cooperation is the dominant strategy in bacterial networks based on the co-occurrence pattern. The present study provided insights into microbial response strategies and the interactions between bacteria and fungi under long-term combined contamination.
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Affiliation(s)
- Qihui Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Fu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Shuping Xing
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chuning Ji
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Xin Zhang,
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Ducret V, Gonzalez D, Perron K. Zinc homeostasis in Pseudomonas. Biometals 2022:10.1007/s10534-022-00475-5. [PMID: 36472780 PMCID: PMC10393844 DOI: 10.1007/s10534-022-00475-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022]
Abstract
AbstractIn the genus Pseudomonas, zinc homeostasis is mediated by a complete set of import and export systems, whose expression is precisely controlled by three transcriptional regulators: Zur, CzcR and CadR. In this review, we describe in detail our current knowledge of these systems, their regulation, and the biological significance of zinc homeostasis, taking Pseudomonas aeruginosa as our paradigm. Moreover, significant parts of this overview are dedicated to highlight interactions and cross-regulations between zinc and copper import/export systems, and to shed light, through a review of the literature and comparative genomics, on differences in gene complement and function across the whole Pseudomonas genus. The impact and importance of zinc homeostasis in Pseudomonas and beyond will be discussed throughout this review.
Graphical abstract
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Lv H, Ji C, Ding J, Yu L, Cai H. High Levels of Zinc Affect Nitrogen and Phosphorus Transformation in Rice Rhizosphere Soil by Modifying Microbial Communities. PLANTS 2022; 11:plants11172271. [PMID: 36079652 PMCID: PMC9460630 DOI: 10.3390/plants11172271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/24/2022] [Accepted: 08/28/2022] [Indexed: 11/16/2022]
Abstract
Due to global industrialization in recent decades, large areas have been threatened by heavy metal contamination. Research about the impact of excessive Zn on N and P transformation in farmland has received little attention, and its mechanism is still not completely known. In this study, we planted rice in soils with toxic levels of Zn, and analyzed the plant growth and nutrient uptake, the N and P transformation, enzyme activities and microbial communities in rhizosphere soil to reveal the underlying mechanism. Results showed high levels of Zn severely repressed the plant growth and uptake of N and P, but improved the N availability and promoted the conversion of organic P into inorganic forms in rice rhizosphere soil. Moreover, high levels of Zn significantly elevated the activities of hydrolases including urease, protease, acid phosphatase, sucrase and cellulose, and dehydrogenase, as well as the abundances of Flavisolibacter, Sphingomonas, Gemmatirosa, and subgroup_6, which contributed to the mineralization of organic matter in soil. Additionally, toxic level of Zn repressed the nitrifying process by decreasing the abundance of nitrosifying bacteria Ellin6067 and promoted denitrification by increasing the abundance of Noviherbaspirillum, which resulted in decreased NO3− concentration in rice rhizosphere soil under VHZn condition.
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Affiliation(s)
- Haihan Lv
- Microelement Research Center, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Chenchen Ji
- Microelement Research Center, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingli Ding
- Microelement Research Center, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Lu Yu
- Microelement Research Center, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongmei Cai
- Microelement Research Center, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence:
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Zhang X, Chen B, Yin R, Xing S, Fu W, Wu H, Hao Z, Ma Y, Zhang X. Long-term nickel contamination increased soil fungal diversity and altered fungal community structure and co-occurrence patterns in agricultural soils. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129113. [PMID: 35580502 DOI: 10.1016/j.jhazmat.2022.129113] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 04/23/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Nickel (Ni) contamination imposes deleterious effects on the stability of soil ecosystem. Soil fungal community as a crucial moderator of soil remediation and biochemical processes has attracted more and more research interests. In the present study, soil fungal community composition and diversity under long-term Ni contamination were investigated and fungal interaction networks were built to reveal fungal co-occurrence patterns. The results showed that moderate Ni contamination significantly increased fungal diversity and altered fungal community structure. Functional predictions based on FUNGuild suggested that the relative abundance of arbuscular mycorrhizal fungi (AMF) significantly increased at moderate Ni contamination level. Ni contamination strengthened fungal interactions. Keystone taxa at different Ni contamination levels, such as Penicillium at light contamination, were identified, which might have ecological significance in maintaining the stability of fungal community to Ni stress. The present study provided a deeper insight into the effect of long-term Ni contamination on fungal community composition and co-occurrence patterns, and was helpful to further explore ecological risk of Ni contamination in cultivated field.
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Affiliation(s)
- Xuemeng Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rongbin Yin
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuping Xing
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Fu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Wu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhipeng Hao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yibing Ma
- Macau Environmental Research Institute, Macau University of Science and Technology, Macau 999078, China
| | - Xin Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Suppressive Effect of Soil Microbiomes Associated with Tropical Fruit Trees on Meloidogyne enterolobii. Microorganisms 2022; 10:microorganisms10050894. [PMID: 35630339 PMCID: PMC9144879 DOI: 10.3390/microorganisms10050894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 11/16/2022] Open
Abstract
Plant-parasitic nematodes are one of the main biotic factors limiting agricultural production worldwide, with root-knot nematodes (Meloidogyne spp.) being the most damaging group. This study was conducted to evaluate the efficacy of soil microbiomes, associated with various subtropical fruit trees, on the management of a Meloidogyne enterolobii population. Of 14 soil microbiomes tested for nematode suppression, 9 samples in the first experiment and 10 samples in the repeat experiment had significantly (p ≤ 0.05) lower numbers of eggs and J2 compared to the untreated control. The highest nematode suppression was recorded for SA12 extracted from a papaya orchard with a 38% reduction in the nematode population density. In addition, the presence of some bacteria (Bacillus aryabhattai, B. funiculus and B. simplex) and fungi (Metarhizium marquandii, Acremonium sp. and Mortierella sp.) was correlated to a higher suppression potential in some samples. Substantial variations were observed for the diversity of bacterial and fungal isolates among the samples collected from various crop hosts and regions. This suggests that the nematode suppression potential of different soil microbiomes highly depends on the abundance and diversity of fungal and bacterial strains present in the soil. The study confirmed that among all variables, soil dryness, pH, Fe, Zn, organic matter, altitude, and crop cultivar strongly influenced the soil microbial composition.
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Huang X, Wu X, Tang X, Zhang Z, Ma J, Zhang J, Liu H. Distribution characteristics and risk of heavy metals and microbial community composition around the Wanshan mercury mine in Southwest China. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 227:112897. [PMID: 34655882 DOI: 10.1016/j.ecoenv.2021.112897] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/09/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
The Wanshan mercury (Hg) mine in Guizhou Province is one of the main Hg-producing mines in China, resulting in serious Hg pollution in soil and wastewater. Therefore, the present study is mainly aimed to investigate the current degree of heavy metal pollution and compared the microbial diversity in the Wanshan Hg mine and its surrounding environment. The results showed the distribution of the pollution load index values was low in the west and high in the east. The northwestern (Aozhai River), northern (Meizi Stream), and southwestern parts of the study area and the area surrounding Erkeng did not reach moderate pollution. Mercury accounted for the majority of the potential ecological risk index values, reaching 67.62%, while the proportions of Cd and As were 15.75% and 10.75%, respectively. Mercury was found mainly in a residual state, which had an average proportion of 71.09%. In the three regions, Proteobacteria and Actinobacteria had the highest relative abundances. According to linear discriminant analysis effect size, the indicator species in the Hg mining area, woodland and cultivated land was f__67-14 (belonging to a family of Solirubrobacterales), Reyranellales and Reyranellaceae, Intrasporangiaceae, respectively. In summary, this study for the very first time estimated that the higher Hg, Cd and As pollution existed in Wanshan Hg mine since their concentration in the all soil samples totally exceeded the standard value (GB15618-2018), while Cd and As pollution in soil was commonly ignored by the previous study. The cultivated land had higher community richness than the mercury mining district and woodland. Our results suggested that the relevant local departments need to take more active measures to solve the problem of high levels of Hg, Cd, and As in the local soil, and prevent their adverse effects on humans.
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Affiliation(s)
- Xianfei Huang
- Guizhou Provincial Key Laboratory for Environment, Guizhou Normal University, Guiyang 550001, Guizhou, PR China
| | - Xianliang Wu
- Guizhou Institute of Biology, Guiyang Guizhou, 550009, China
| | - Xiangchen Tang
- Guizhou Provincial Key Laboratory for Environment, Guizhou Normal University, Guiyang 550001, Guizhou, PR China
| | - Zhenming Zhang
- College of Resource and Environmental Engineering, Guizhou University, Guiyang Guizhou 550003, PR China; Guizhou Institute of Biology, Guiyang Guizhou, 550009, China.
| | - Jianrong Ma
- Key Laboratory of Reservoir Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China; State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550002, PR China; Chongqing school, University of Chinese Academy of Sciences, Chongqing 400714, PR China.
| | - Jiachun Zhang
- Guizhou Botanical Garden, Guizhou Academy of Sciences, Guiyang 550004, Guizhou, PR China
| | - Huijuan Liu
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550025, PR China
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Newsome L, Falagán C. The Microbiology of Metal Mine Waste: Bioremediation Applications and Implications for Planetary Health. GEOHEALTH 2021; 5:e2020GH000380. [PMID: 34632243 PMCID: PMC8490943 DOI: 10.1029/2020gh000380] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 05/13/2023]
Abstract
Mine wastes pollute the environment with metals and metalloids in toxic concentrations, causing problems for humans and wildlife. Microorganisms colonize and inhabit mine wastes, and can influence the environmental mobility of metals through metabolic activity, biogeochemical cycling and detoxification mechanisms. In this article we review the microbiology of the metals and metalloids most commonly associated with mine wastes: arsenic, cadmium, chromium, copper, lead, mercury, nickel and zinc. We discuss the molecular mechanisms by which bacteria, archaea, and fungi interact with contaminant metals and the consequences for metal fate in the environment, focusing on long-term field studies of metal-impacted mine wastes where possible. Metal contamination can decrease the efficiency of soil functioning and essential element cycling due to the need for microbes to expend energy to maintain and repair cells. However, microbial communities are able to tolerate and adapt to metal contamination, particularly when the contaminant metals are essential elements that are subject to homeostasis or have a close biochemical analog. Stimulating the development of microbially reducing conditions, for example in constructed wetlands, is beneficial for remediating many metals associated with mine wastes. It has been shown to be effective at low pH, circumneutral and high pH conditions in the laboratory and at pilot field-scale. Further demonstration of this technology at full field-scale is required, as is more research to optimize bioremediation and to investigate combined remediation strategies. Microbial activity has the potential to mitigate the impacts of metal mine wastes, and therefore lessen the impact of this pollution on planetary health.
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Affiliation(s)
- Laura Newsome
- Camborne School of Mines and Environment and Sustainability InstituteUniversity of ExeterPenrynUK
| | - Carmen Falagán
- Camborne School of Mines and Environment and Sustainability InstituteUniversity of ExeterPenrynUK
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Fortunato G, Vaz-Moreira I, Nunes OC, Manaia CM. Effect of copper and zinc as sulfate or nitrate salts on soil microbiome dynamics and bla VIM-positive Pseudomonas aeruginosa survival. JOURNAL OF HAZARDOUS MATERIALS 2021; 415:125631. [PMID: 33773246 DOI: 10.1016/j.jhazmat.2021.125631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 02/10/2021] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
The exposure of soil to metals and to antibiotic resistant bacteria may lead to the progressive deterioration of soil quality. The persistence of antibiotic resistant bacteria or antibiotic resistance genes in soil can be influenced by the microbial community or by soil amendments with metal salts. This work assessed the effect of soil amendment with copper and zinc, as sulfate or nitrate salts, on the fate of a carbapenem-resistant (blaVIM+) hospital effluent isolate of Pseudomonas aeruginosa (strain H1FC49) and on the variations of the microbial community composition. Microcosms with soil aged or not with copper and zinc salts (20 mM), and inoculated with P. aeruginosa H1FC49 were monitored at 0, 7, 14 and/or 30 days, for community composition (16S rRNA gene amplicon) and strain H1FC49 persistence. Data on culturable P. aeruginosa, quantitative PCR of the housekeeping gene ecf, and the presumably acquired genes blaVIM+ and integrase (intI1), and community composition were interpreted based on descriptive statistics and multivariate analysis. P. aeruginosa and the presumably acquired genes, were quantifiable in soil for up to one month, in both metal-amended and non-amended soil. Metal amendments were associated with a significant decrease of bacterial community diversity and richness. The persistence of P. aeruginosa and acquired genes in soils, combined with the adverse effect of metals on the bacterial community, highlight the vulnerability of soil to both types of exogenous contamination.
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Affiliation(s)
- Gianuario Fortunato
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| | - Ivone Vaz-Moreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| | - Olga C Nunes
- LEPABE, Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal.
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12
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Hu X, Liu X, Qiao L, Zhang S, Su K, Qiu Z, Li X, Zhao Q, Yu C. Study on the spatial distribution of ureolytic microorganisms in farmland soil around tailings with different heavy metal pollution. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 775:144946. [PMID: 33618300 DOI: 10.1016/j.scitotenv.2021.144946] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/02/2021] [Accepted: 01/03/2021] [Indexed: 06/12/2023]
Abstract
Ureolytic microorganisms, a kind of microorganism which can secrete urease and decompose urea, have great potential in remediation of soil heavy metals based on microbial induced carbonate precipitation. However, the horizontal and vertical distribution of ureolytic microbial community in heavy metals contaminated soils is poorly understood. In this study, urease genes in agricultural soils surrounding tailings were first investigated using metagenomic in two dimensions: heavy metal pollution (Low-L, Middle-M, High-H) and soil depth (0-20 cm, 20-40 cm, 40-60 cm, 60-80 cm, 80-100 cm). Results showed that the effect of heavy metal concentration on ureolytic microorganisms was indeed significant, while the changes of ureolytic microorganisms with increasing soil depth varied in the vertical direction at the same level of heavy metal contamination. H site had the highest diversity of ureolytic microorganisms except for the topsoil. And at the same heavy metal contamination level, the ureolytic microbial diversity was lower in deeper soils. Proteobacteria, Actinobacteria and Thaumarchaeota (Archaea) were the dominant phyla of ureolytic microorganisms in all three sites, accounting for more than 80% of the total. However, the respond to the heavy metal concentrations of three phyla were different, which were increasing, decreasing and essentially unchanged, respectively. Besides, other environmental factors such as SOM and pH had different effects on ureolytic microorganisms, with Proteobacteria being positively correlated and Actinobacteria being the opposite. Another phenomenon was that Actinobacteria and Verrucomicrobia were biomarkers of group L, which could significantly explain the difference with the other two sites. These results provided valuable information for further research on the response mechanism and remediation of heavy metal pollution by ureolytic microbial system.
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Affiliation(s)
- Xuesong Hu
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China
| | - Xiaoxia Liu
- Beijing Station of Agro-Environmental Monitoring, Test and Supervision Center of Agro-Environmental Quality, MOA, 100032 Beijing, China
| | - Longkai Qiao
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China
| | - Shuo Zhang
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China
| | - Kaiwen Su
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China
| | - Ziliang Qiu
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China
| | - Xianhong Li
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China
| | - Qiancheng Zhao
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China
| | - Caihong Yu
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China.
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13
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Microbial Community Composition Correlates with Metal Sorption in an Ombrotrophic Boreal Bog: Implications for Radionuclide Retention. SOIL SYSTEMS 2021. [DOI: 10.3390/soilsystems5010019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Microbial communities throughout the 6.5 m depth profile of a boreal ombrotrophic bog were characterized using amplicon sequencing of archaeal, fungal, and bacterial marker genes. Microbial populations and their relationship to oxic and anoxic batch sorption of radionuclides (using radioactive tracers of I, Se, Cs, Ni, and Ag) and the prevailing metal concentrations in the natural bog was investigated. The majority of the detected archaea belonged to the Crenarchaeota, Halobacterota, and Thermoplasmatota, whereas the fungal communities consisted of Ascomycota, Basidiomycota, and unclassified fungi. The bacterial communities consisted mostly of Acidobacteriota, Proteobacteria, and Chloroflexi. The occurrence of several microbial genera were found to statistically significantly correlate with metal concentrations as well as with Se, Cs, I, and Ag batch sorption data. We suggest that the metal concentrations of peat, gyttja, and clay layers affect the composition of the microbial populations in these nutrient-low conditions and that particularly parts of the bacterial and archaeal communities tolerate high concentrations of potentially toxic metals and may concurrently contribute to the total retention of metals and radionuclides in this ombrotrophic environment. In addition, the varying metal concentrations together with chemical, mineralogical, and physical factors may contribute to the shape of the total archaeal and bacterial populations and most probably shifts the populations for more metal resistant genera.
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14
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Ondreičková K, Piliarová M, Klčová L, Žofajová A, Gubiš J, Horník M, Gubišová M, Hudcovicová M, Kraic J. The impact of sewage sludge on the fungal communities in the rhizosphere and roots of barley and on barley yield. Open Life Sci 2021; 16:210-221. [PMID: 33817312 PMCID: PMC7968536 DOI: 10.1515/biol-2021-0024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/18/2020] [Accepted: 11/23/2020] [Indexed: 11/28/2022] Open
Abstract
Current problems with sewage sludge (SS) disposal could be solved by application to agricultural land considering its fertilizer properties and ability to improve soil condition. However, SS may contain heavy metals as well as pathogenic microorganisms. In this study, molecular analysis of partial 18S rRNA gene was used to study the impact of SS application into the soil on the genetic diversity of fungal communities, especially arbuscular mycorrhizal fungi in the rhizosphere and roots of barley. These samples were collected on three dates from the control soil without SS and from the soil with the addition of SS at the concentrations of 5 and 15 t ha-1. Fungal alpha diversity in the rhizosphere of barley was affected by SS differently than in barley roots. In addition, principal component analysis and cluster analysis revealed that fungal communities were strongly influenced by the SS addition into the soil, sample type, and the sampling date. This approach was complemented by an evaluation of the basic parameters of barley production and the response of these parameters to the presence of SS in the soil. The plant height increased with increasing SS concentration and the thousand seed weight significantly increased at the concentration of 5 t ha-1 SS but significantly decreased in 15 t ha-1.
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Affiliation(s)
- Katarína Ondreičková
- Department of Applied Biology and Genetics, National Agricultural and Food Centre – Research Institute of Plant Production, Bratislavská cesta 122, 921 68, Piešťany, Slovak Republic
| | - Michaela Piliarová
- Department of Biotechnologies, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Námestie J. Herdu 2, 917 01, Trnava, Slovak Republic
| | - Lenka Klčová
- Department of Applied Biology and Genetics, National Agricultural and Food Centre – Research Institute of Plant Production, Bratislavská cesta 122, 921 68, Piešťany, Slovak Republic
| | - Alžbeta Žofajová
- Department of Applied Biology and Genetics, National Agricultural and Food Centre – Research Institute of Plant Production, Bratislavská cesta 122, 921 68, Piešťany, Slovak Republic
| | - Jozef Gubiš
- Department of Applied Biology and Genetics, National Agricultural and Food Centre – Research Institute of Plant Production, Bratislavská cesta 122, 921 68, Piešťany, Slovak Republic
| | - Miroslav Horník
- Department of Ecochemistry and Radioecology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Námestie J. Herdu 2, 917 01, Trnava, Slovak Republic
| | - Marcela Gubišová
- Department of Applied Biology and Genetics, National Agricultural and Food Centre – Research Institute of Plant Production, Bratislavská cesta 122, 921 68, Piešťany, Slovak Republic
| | - Martina Hudcovicová
- Department of Applied Biology and Genetics, National Agricultural and Food Centre – Research Institute of Plant Production, Bratislavská cesta 122, 921 68, Piešťany, Slovak Republic
| | - Ján Kraic
- Department of Applied Biology and Genetics, National Agricultural and Food Centre – Research Institute of Plant Production, Bratislavská cesta 122, 921 68, Piešťany, Slovak Republic
- Department of Biotechnologies, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Námestie J. Herdu 2, 917 01, Trnava, Slovak Republic
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15
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Liu N, Liao P, Zhang J, Zhou Y, Luo L, Huang H, Zhang L. Characteristics of denitrification genes and relevant enzyme activities in heavy-metal polluted soils remediated by biochar and compost. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 739:139987. [PMID: 32535466 DOI: 10.1016/j.scitotenv.2020.139987] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/03/2020] [Accepted: 06/03/2020] [Indexed: 06/11/2023]
Abstract
Denitrification is an important process affecting nitrogen dynamics in soils. In this study, abundances of denitrification genes (narG, nirK, nirS, and nosZ) and activities of nitrite reductase (S-NiR), nitrate reductase (S-NR) were measured in heavy-metal polluted soils with different amendments of biochar and compost. The relationships between physical-chemical parameters, denitrification gene abundance, and enzyme activity were analyzed by Pearson correlation method. Results showed that compost addition significantly increased the abundances of functional genes (nirS, nosZ, narG), and the abundances of nirK and nirS might be sensitive to compost and biochar addition. Compost addition and its combination with biochar significantly decreased the S-NiR enzyme activity and stimulated the S-NR enzyme activity. Negative relationships were obtained between S-NiR activity and electric conductivity (EC), water soluble carbon (WSC), nitrate, ammonium, nirK, narG gene abundances. While S-NR activity significantly positively correlated with soil EC, WSC and nirK gene abundance. Biochar and compost amendments can alter soil nitrogen cycling by changing denitrifying functional gene and relevant enzyme activities in soils polluted by heavy metals.
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Affiliation(s)
- Nianhui Liu
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China; Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - Peng Liao
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - Jiachao Zhang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China.
| | - Yaoyu Zhou
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China.
| | - Lin Luo
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
| | - Hongli Huang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
| | - Lihua Zhang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
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16
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Liu YM, Cao WQ, Chen XX, Yu BG, Lang M, Chen XP, Zou CQ. The responses of soil enzyme activities, microbial biomass and microbial community structure to nine years of varied zinc application rates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 737:140245. [PMID: 32783848 DOI: 10.1016/j.scitotenv.2020.140245] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/30/2020] [Accepted: 06/13/2020] [Indexed: 05/27/2023]
Abstract
Zinc (Zn) fertilizer application can certainly improve the production and nutritional quality of cereal crops. However, Zn accumulation in the soil may lead to some deleterious environmental impacts in agroecosystems. The effects of long-term Zn application on soil microbial properties remain unclear, but it is imperative to understand such effects. In this study, we collected soil samples from a nine-year field experiment in a wheat-maize system that continuously received Zn applied at various rates (0, 2.3, 5.7, 11.4, 22.7 and 34.1 kg ha-1) to evaluate the soil enzymes, microbial biomass and microbial community structure. The results showed that Zn application at the rate of 5.7 kg ha-1 significantly increased the activities of urease, invertase, alkaline phosphatase and catalase in the soil, while the rate of 34.1 kg ha-1 significantly decreased the evaluated enzyme activities. The microbial biomass carbon (C) and nitrogen (N) were not affected by Zn application rates, although an increase in the microbial biomass C was observed in the 11.4 kg ha-1 treatment. Moreover, the alpha diversity of the bacterial and fungal communities did not vary among the nil Zn, optimal Zn (5.7 kg ha-1) and excess Zn (34.1 kg ha-1) treatments. However, the bacterial communities in the soil receiving the optimal and excess Zn application rates were slightly changed. Compared to the nil Zn treatment, the other Zn application rates increased the relative abundances of the Rhodospirillales, Gaiellales and Frankiales orders and decreased the abundance of the Latescibacteria phylum. The redundancy analysis further indicated that the soil bacterial community composition significantly correlated with the concentrations of soil DTPA-Zn and total Zn. These results highlight the importance of optimal Zn application in achieving high production and high grain quality while concurrently promoting soil microbial activity, improving the bacterial community and further maintaining the sustainability of the agroecological environment.
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Affiliation(s)
- Yu-Min Liu
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Wen-Qing Cao
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Xiu-Xiu Chen
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Bao-Gang Yu
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Ming Lang
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Xin-Ping Chen
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Chun-Qin Zou
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, China.
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17
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Kihara J, Bolo P, Kinyua M, Rurinda J, Piikki K. Micronutrient deficiencies in African soils and the human nutritional nexus: opportunities with staple crops. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2020; 42:3015-3033. [PMID: 31902042 PMCID: PMC7429550 DOI: 10.1007/s10653-019-00499-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/18/2019] [Indexed: 05/23/2023]
Abstract
A synthesis of available agronomic datasets and peer-reviewed scientific literature was conducted to: (1) assess the status of micronutrients in sub-Saharan Africa (SSA) arable soils, (2) improve the understanding of the relations between soil quality/management and crop nutritional quality and (3) evaluate the potential profitability of application of secondary and micronutrients to key food crops in SSA, namely maize (Zea mays L.), beans (Phaseolus spp. and Vicia faba L.), wheat (Triticum aestivum L.) and rice (Oryza sativa L.). We found that there is evidence of widespread but varying micronutrient deficiencies in SSA arable soils and that simultaneous deficiencies of multiple elements (co-occurrence) are prevalent. Zinc (Zn) predominates the list of micronutrients that are deficient in SSA arable soils. Boron (B), iron (Fe), molybdenum (Mo) and copper (Cu) deficiencies are also common. Micronutrient fertilization/agronomic biofortification increases micronutrient concentrations in edible plant organs, and it was profitable to apply fertilizers containing micronutrient elements in 60-80% of the cases. However, both the plant nutritional quality and profit had large variations. Possible causes of this variation may be differences in crop species and cultivars, fertilizer type and application methods, climate and initial soil conditions, and soil chemistry effects on nutrient availability for crop uptake. Therefore, micronutrient use efficiency can be improved by adapting the rates and types of fertilizers to site-specific soil and management conditions. To make region-wide nutritional changes using agronomic biofortification, major policy interventions are needed.
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Affiliation(s)
- J Kihara
- International Center for Tropical Agriculture (CIAT), Nairobi, Kenya.
| | - P Bolo
- International Center for Tropical Agriculture (CIAT), Nairobi, Kenya
| | - M Kinyua
- International Center for Tropical Agriculture (CIAT), Nairobi, Kenya
| | - J Rurinda
- International Plant Nutrition Institute (IPNI), Nairobi, Kenya
| | - K Piikki
- International Center for Tropical Agriculture (CIAT), Nairobi, Kenya
- Swedish University of Agricultural Sciences (SLU), Skara, Uppsala, Sweden
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18
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Fernández-González AJ, Wentzien NM, Villadas PJ, Valverde-Corredor A, Lasa AV, Gómez-Lama Cabanás C, Mercado-Blanco J, Fernández-López M. Comparative study of neighboring Holm oak and olive trees-belowground microbial communities subjected to different soil management. PLoS One 2020; 15:e0236796. [PMID: 32780734 PMCID: PMC7418964 DOI: 10.1371/journal.pone.0236796] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/13/2020] [Indexed: 11/22/2022] Open
Abstract
It is well-known that different plant species, and even plant varieties, promote different assemblages of the microbial communities associated with them. Here, we investigate how microbial communities (bacteria and fungi) undergo changes within the influence of woody plants (two olive cultivars, one tolerant and another susceptible to the soilborne fungal pathogen Verticillium dahliae, plus wild Holm oak) grown in the same soil but with different management (agricultural versus native). By the use of metabarcoding sequencing we determined that the native Holm oak trees rhizosphere bacterial communities were different from its bulk soil, with differences in some genera like Gp4, Gp6 and Solirubrobacter. Moreover, the agricultural management used in the olive orchard led to belowground microbiota differences with respect to the natural conditions both in bulk soils and rhizospheres. Indeed, Gemmatimonas and Fusarium were more abundant in olive orchard soils. However, agricultural management removed the differences in the microbial communities between the two olive cultivars, and these differences were minor respect to the olive bulk soil. According to our results, and at least under the agronomical conditions here examined, the composition and structure of the rhizospheric microbial communities do not seem to play a major role in olive tolerance to V. dahliae.
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Affiliation(s)
- Antonio J Fernández-González
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Nuria M Wentzien
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Pablo J Villadas
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | | | - Ana V Lasa
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | | | - Jesús Mercado-Blanco
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, CSIC, Córdoba, Spain
| | - Manuel Fernández-López
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
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19
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Nan L, Guo Q, Cao S. Archaeal community diversity in different types of saline-alkali soil in arid regions of Northwest China. J Biosci Bioeng 2020; 130:382-389. [PMID: 32682699 DOI: 10.1016/j.jbiosc.2020.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 05/08/2020] [Accepted: 06/01/2020] [Indexed: 10/23/2022]
Abstract
High-throughput sequencing was used to investigate the archaeal community structure and diversity, and associated influencing factors in the 5 subtypes and 13 genera of saline-alkali soil in Gansu Province, China. The results indicated the analysis of chemical parameters demonstrated statistically significant differences in these soils. Operational taxonomic units (OTUs), Chao 1, ACE, Simpson, and Shannon indexes of the archaeal community varied significantly in the 5 subtypes and 12 genera of soil except for chloride-type orthic solonchaks. The abundance was highest for sulfate-chloride-type meadow solonchaks and lowest for chloride-sulfate-type dry solonchaks. The diversity was highest for chloride-sulfate-type orthic solonchaks and lowest for sulfate-type orthic solonchaks. The archaeal community was dominated by the Euryarchaeota and Crenarchaeota. Except chloride-type orthic solonchaks; Halomicrobium in chloride-type meadow solonchaks (12.7%); Halobacterium in sulfate-chloride-type and chloride-sulfate-type dry solonchaks (11.1% and 9.2%, respectively); Candidatus Nitrososphaera in sulfate-chloride-type, chloride-sulfate-type, and sulphate-type meadow solonchaks; sulfate-type orthic solonchaks; and chloride bog solonchaks (9.0%, 21.6%, 27.0%, 45.3%, and 30.0%, respectively); Halorhabdus in sulfate-chloride-type orthic solonchaks, magnesium alkalized solonchaks, chloride-type dry solonchaks (15.7%, 11.5%, and 5.9%, respectively); and Haloarcula in chloride-sulfate-type orthic solonchaks (8.1%) were the most dominant archaea. Redundancy analysis showed that archaeal diversity was influenced by soil organic matter, total salt, sulfate anion, and zinc contents and pH. These results will lead to more comprehensive understanding of how 5 subtypes and 13 soil genera of saline-alkali soil affects microbial distribution.
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Affiliation(s)
- Lili Nan
- College of Grassland Science, Gansu Agricultural University, Lanzhou 730070, Gansu, People's Republic of China
| | - Quanen Guo
- College of Resource and Environment Sciences, Gansu Agricultural University, Lanzhou 730070, Gansu, People's Republic of China; Institute of Soil, Fertilizer and Water-saving, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China.
| | - Shiyu Cao
- Institute of Soil, Fertilizer and Water-saving, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
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20
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Thomas JC, Oladeinde A, Kieran TJ, Finger JW, Bayona‐Vásquez NJ, Cartee JC, Beasley JC, Seaman JC, McArthur JV, Rhodes OE, Glenn TC. Co-occurrence of antibiotic, biocide, and heavy metal resistance genes in bacteria from metal and radionuclide contaminated soils at the Savannah River Site. Microb Biotechnol 2020; 13:1179-1200. [PMID: 32363769 PMCID: PMC7264878 DOI: 10.1111/1751-7915.13578] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 01/20/2023] Open
Abstract
Contaminants such as heavy metals may contribute to the dissemination of antimicrobial resistance (AMR) by enriching resistance gene determinants via co-selection mechanisms. In the present study, a survey was performed on soils collected from four areas at the Savannah River Site (SRS), South Carolina, USA, with varying contaminant profiles: relatively pristine (Upper Three Runs), heavy metals (Ash Basins), radionuclides (Pond B) and heavy metal and radionuclides (Tim's Branch). Using 16S rRNA gene amplicon sequencing, we explored the structure and diversity of soil bacterial communities. Sites with legacies of metal and/or radionuclide contamination displayed significantly lower bacterial diversity compared to the reference site. Metagenomic analysis indicated that multidrug and vancomycin antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) including those associated with copper, arsenic, iron, nickel and zinc were prominent in all soils including the reference site. However, significant differences were found in the relative abundance and diversity of certain ARGs and MRGs in soils with metal/radionuclide contaminated soils compared to the reference site. Co-occurrence patterns revealed significant ARG/MRG subtypes in predominant soil taxa including Acidobacteriaceae, Bradyrhizobium, Mycobacterium, Streptomyces, Verrumicrobium, Actinomadura and Solirubacterales. Overall, the study emphasizes the potential risk of human activities on the dissemination of AMR in the environment.
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Affiliation(s)
- Jesse C. Thomas
- Department of Environmental Health ScienceUniversity of GeorgiaAthensGA30602USA
| | - Adelumola Oladeinde
- Bacterial Epidemiology and Antimicrobial Resistance Research UnitUnited States Department of AgricultureAthensGA30605USA
| | - Troy J. Kieran
- Department of Environmental Health ScienceUniversity of GeorgiaAthensGA30602USA
| | - John W. Finger
- Department of Biological SciencesAuburn UniversityAuburnAL36849USA
| | - Natalia J. Bayona‐Vásquez
- Department of Environmental Health ScienceUniversity of GeorgiaAthensGA30602USA
- Institute of BioinformaticsUniversity of GeorgiaAthensGA30602USA
| | - John C. Cartee
- Division of STD PreventionCenters for Disease Control and PreventionAtlantaGA30329USA
| | - James C. Beasley
- Savannah River Ecology LaboratoryUniversity of GeorgiaPO Drawer EAikenSC29802USA
- Warnell School of Forestry and Natural ResourcesUniversity of GeorgiaAthensGA30602USA
| | - John C. Seaman
- Savannah River Ecology LaboratoryUniversity of GeorgiaPO Drawer EAikenSC29802USA
| | - J Vuan McArthur
- Savannah River Ecology LaboratoryUniversity of GeorgiaPO Drawer EAikenSC29802USA
| | - Olin E. Rhodes
- Savannah River Ecology LaboratoryUniversity of GeorgiaPO Drawer EAikenSC29802USA
- Odum School of EcologyUniversity of GeorgiaAthensGA30602USA
| | - Travis C. Glenn
- Department of Environmental Health ScienceUniversity of GeorgiaAthensGA30602USA
- Institute of BioinformaticsUniversity of GeorgiaAthensGA30602USA
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Candan O, Candan ED. Bacterial diversity of the green turtle (Chelonia mydas) nest environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 720:137717. [PMID: 32325608 DOI: 10.1016/j.scitotenv.2020.137717] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/12/2020] [Accepted: 03/02/2020] [Indexed: 06/11/2023]
Abstract
The green turtle is an endangered species that is highly sensitive to environmental pollution that can adversely affect the healthy development of eggs. Moreover, the presence of some bacteria in nests can be regarded as an indicator of the pollution level in nesting areas. In our study, nest sand and egg contents were collected from Sugözü Beaches (Turkey), in the Mediterranean. Phenotypic and genotypic identification of bacteria were carried out by using conventional phenotypic methods, 16S rRNA gene sequencing respectively. The extended-spectrum beta-lactamase presence and carbapenem resistance of bacteria isolated from egg contents were determined. This is the first report of carbapenem resistance in the eggs. All strains were evaluated in three different categories including growth promoters in agriculture and aquaculture, pathogens that are found in human and animal, and biomonitoring aquatic pollution. According to our analysis, 67 bacterial species were identified from samples. This study is the first record of Alcaligenes, Zobellella, Lysinibacillus, Sphingobacterium, Achromobacter, Acinetobacter, Alcanivorax, Ochrobactrum, Microbacterium, Rhodococcus, and Stenotrophomonas isolated from sea turtles. Pathogens detected in the bacterial flora can threaten both sea turtles and field workers. These data can contribute to the development of new conservation strategies on the treatment of sea turtles, nest protection, and pollution detection on nesting beaches.
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Affiliation(s)
- Onur Candan
- Ordu University, Faculty of Arts and Sciences, Department of Molecular Biology and Genetics, 52200 Ordu, Turkey.
| | - Esra Deniz Candan
- Giresun University, Vocational School of Health Services, Department of Medical Services and Techniques, 28100 Giresun, Turkey
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Wang C, Wei M, Wang S, Wu B, Du D. Cadmium influences the litter decomposition of Solidago canadensis L. and soil N-fixing bacterial communities. CHEMOSPHERE 2020; 246:125717. [PMID: 31918081 DOI: 10.1016/j.chemosphere.2019.125717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 06/10/2023]
Abstract
It is important to illuminate the effects of litter decomposition of invasive alien species on soil N-fixing bacterial communities (SoNiBa), especially under heavy metal pollution to better outline the mechanisms for invasion success of invasive alien species. This study attempts to identify the effects of litter decomposition of Solidago canadensis L. on SoNiBa under cadmium (Cd) pollution with different concentrations (i.e., low concentration, 7.5 mg/kg soil; high concentration, 15 mg/kg soil) via a polyethylene litterbags-experiment. Electrical conductivity and total N of soil were the most important environmental factors for determining the variations of SoNiBa composition. S. canadensis did not significantly affect the alpha diversity of SoNiBa but significantly affect the beta diversity of SoNiBa and SoNiBa composition. Thus, SoNiBa composition, rather than alpha diversity of SoNiBa, was the most important determinant of the invasion success of S. canadensis. Cd with 15 mg/kg soil did not address distinct effects on alpha diversity of SoNiBa, but Cd with 7.5 mg/kg soil noticeably raised the number of species and species richness of SoNiBa mainly due to the hormonal effects. The combined S. canadensis and Cd with 15 mg/kg soil obviously decreased cumulative mass losses and the rate of litter decomposition (k) of S. canadensis, but the combined S. canadensis and Cd with 7.5 mg/kg soil evidently accelerated cumulative mass losses and k of S. canadensis. Thus, Cd with 7.5 mg/kg soil can accelerate litter decomposition of S. canadensis, but Cd with 15 mg/kg soil can decline litter decomposition of S. canadensis.
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Affiliation(s)
- Congyan Wang
- Institute of Environment and Ecology & School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China; State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, 200092, PR China.
| | - Mei Wei
- Institute of Environment and Ecology & School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Shu Wang
- Institute of Environment and Ecology & School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Bingde Wu
- Institute of Environment and Ecology & School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Daolin Du
- Institute of Environment and Ecology & School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
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Responses of Rhizosphere Fungal Communities to the Sewage Sludge Application into the Soil. Microorganisms 2019; 7:microorganisms7110505. [PMID: 31671795 PMCID: PMC6920848 DOI: 10.3390/microorganisms7110505] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/21/2019] [Accepted: 10/28/2019] [Indexed: 11/17/2022] Open
Abstract
Due to the increasing sewage sludge production in the world and problems with its disposal, an application of sludge to the soil appears to be a suitable solution considering its fertilizer properties and ability to improve the soil physical conditions. On the other hand, the sludge may also contain undesirable and toxic substances. Since soil microorganisms are sensitive to environmental changes, they can be used as indicators of soil quality. In this study, we used sewage sludge (SS) from two municipal wastewater treatment plants (SS-A and SS-B) in the dose of 5 t/ha and 15 t/ha in order to determine possible changes in the fungal community diversity, especially arbuscular mycorrhizal fungi (AMF), in the rhizosphere of Arundo donax L. Rhizosphere samples were collected in summer and autumn for two consecutive years and the fungal diversity was examined using terminal restriction fragment length polymorphism and 18S rDNA sequencing. Fungal alpha diversity was more affected by SS-A than SS-B probably due to the higher heavy metal content. However, based on principal component analysis and ANOSIM, significant changes in overall fungal diversity were not observed. Simultaneously, 18S rDNA sequencing showed that more various fungal taxa were detected in the sample with sewage sludge than in the control. Glomus sp. as a representative of AMF was the most represented. Moreover, Funneliformis in both samples and Rhizophagus in control with Septoglomus in the sludge sample were other representatives of AMF. Our results indicate that the short-term sewage sludge application into the soil does not cause a shift in the fungal community composition.
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New genus-specific primers for PCR identification of Rubrobacter strains. Antonie Van Leeuwenhoek 2019; 112:1863-1874. [PMID: 31407134 PMCID: PMC6834744 DOI: 10.1007/s10482-019-01314-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 08/01/2019] [Indexed: 12/02/2022]
Abstract
A set of oligonucleotide primers, Rubro223f and Rubro454r, were found to amplify a 267 nucleotide sequence of 16S rRNA genes of Rubrobacter type strains. The primers distinguished members of this genus from other deeply-rooted actinobacterial lineages corresponding to the genera Conexibacter, Gaiella, Parviterribacter, Patulibacter, Solirubrobacter and Thermoleophilum of the class Thermoleophilia. Amplification of DNA bands of about 267 nucleotides were generated from environmental DNA extracted from soil samples taken from two locations in the Atacama Desert. Sequencing of a DNA library prepared from the bands showed that all of the clones fell within the evolutionary radiation occupied by the genus Rubrobacter. Most of the clones were assigned to two lineages that were well separated from phyletic lines composed of Rubrobacter type strains. It can be concluded that primers Rubro223f and Rubro454r are specific for the genus Rubrobacter and can be used to detect the presence and abundance of members of this genus in the Atacama Desert and other biomes.
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Tang J, Zhang J, Ren L, Zhou Y, Gao J, Luo L, Yang Y, Peng Q, Huang H, Chen A. Diagnosis of soil contamination using microbiological indices: A review on heavy metal pollution. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 242:121-130. [PMID: 31028952 DOI: 10.1016/j.jenvman.2019.04.061] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 04/08/2019] [Accepted: 04/17/2019] [Indexed: 05/27/2023]
Abstract
Heavy metal contamination of soil has become a serious global issue because of their persistence in the environment and the non-biodegradable nature leading to their accumulation to toxic levels. In order to achieve early warning and prevent soil quality from deteriorating, it is necessary to select suitable indices to diagnose heavy metal pollution. Microbiological indices for monitoring soil pollution by heavy metals are gaining attention. However, the related researches are scattered, and critical review is imperative. This review is mainly to provide readers with an in-depth understanding of the merits and limitations of microbiological indices for heavy metals contaminated and remediated soils. Microbiological indicators include microbial abundance, community diversity and structure, functional activity. The changes of different microbiological indices and the mechanism of microbial response to heavy metal stress in soils are comprehensively summarized. Furthermore, research gaps and future directions of the microbial ecotoxicological diagnosis of soil contamination by heavy metals are also proposed and discussed.
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Affiliation(s)
- Jiayi Tang
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, China
| | - Jiachao Zhang
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, China.
| | - Liheng Ren
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, China
| | - Yaoyu Zhou
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, China.
| | - Jun Gao
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Lin Luo
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, China
| | - Yuan Yang
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, China
| | - Qinghui Peng
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, China
| | - Hongli Huang
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, China
| | - Anwei Chen
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, China
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26
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Colin Y, Goberna M, Verdú M, Navarro-Cano JA. Successional trajectories of soil bacterial communities in mine tailings: The role of plant functional traits. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 241:284-292. [PMID: 31009816 DOI: 10.1016/j.jenvman.2019.04.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 02/20/2019] [Accepted: 04/07/2019] [Indexed: 06/09/2023]
Abstract
Plant species identity is assumed to be a major driver of belowground microbial diversity and composition. However, diagnosing which plant functional traits are responsible for shaping microbial communities remains elusive. Primary succession on barren metalliferous mining substrates was selected as the framework to study above-belowground interactions, and plant functional traits that lead the successional trajectories of soil bacterial communities were identified. The impact of the plant functional group (i.e. trees, shrubs, dwarf shrubs, perennial grasses), a trait integrating the life span and morphological structure, on the bacterial primary succession was monitored. Bacterial diversity and composition was estimated along plant size gradients including over 90 scattered patches ranging from seedlings to mature multispecific patches. Soil bacterial diversity was affected by heavy metals levels and increased towards higher resource availability underneath mature patches, with stress-tolerant heterotrophs and phototrophs being replaced by competitive heterotrophs. The plant functional group modulated these general patterns and shrubs had the greatest impact belowground by inducing the largest increase in soil fertility. Functional traits related to leaf decomposability and root architecture further determined the composition and structure of bacterial communities. These results underline the importance of plant functional traits in the assembly of soil bacterial communities, and can help guiding restoration of degraded lands.
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Affiliation(s)
- Yannick Colin
- Centro de Investigaciones sobre Desertificación (CSIC-UVEG-GV), Carretera Moncada ‒ Náquera, km 4.5, Moncada, Valencia, 46113, Spain.
| | - Marta Goberna
- Centro de Investigaciones sobre Desertificación (CSIC-UVEG-GV), Carretera Moncada ‒ Náquera, km 4.5, Moncada, Valencia, 46113, Spain; Department of Environment and Agronomy, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Ctra. de la Coruña, km 7.5, E-28040, Madrid, Spain
| | - Miguel Verdú
- Centro de Investigaciones sobre Desertificación (CSIC-UVEG-GV), Carretera Moncada ‒ Náquera, km 4.5, Moncada, Valencia, 46113, Spain
| | - Jose A Navarro-Cano
- Centro de Investigaciones sobre Desertificación (CSIC-UVEG-GV), Carretera Moncada ‒ Náquera, km 4.5, Moncada, Valencia, 46113, Spain
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27
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Lemmel F, Maunoury-Danger F, Fanesi A, Leyval C, Cébron A. Soil Properties and Multi-Pollution Affect Taxonomic and Functional Bacterial Diversity in a Range of French Soils Displaying an Anthropisation Gradient. MICROBIAL ECOLOGY 2019; 77:993-1013. [PMID: 30467715 DOI: 10.1007/s00248-018-1297-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 11/16/2018] [Indexed: 05/20/2023]
Abstract
The intensive industrial activities of the twentieth century have left behind highly contaminated wasteland soils. It is well known that soil parameters and the presence of pollutants shape microbial communities. But in such industrial waste sites, the soil multi-contamination with organic (polycyclic aromatic hydrocarbons, PAH) and metallic (Zn, Pb, Cd) pollutants and long-term exposure may induce a selection pressure on microbial communities that may modify soil functioning. The aim of our study was to evaluate the impact of long-term multi-contamination and soil characteristics on bacterial taxonomic and functional diversity as related to the carbon cycle. We worked on 10 soils from northeast of France distributed into three groups (low anthropised controls, slag heaps, and settling ponds) based on their physico-chemical properties (texture, C, N) and pollution level. We assessed bacterial taxonomic diversity by 16S rDNA Illumina sequencing, and functional diversity using Biolog® and MicroResp™ microtiter plate tools. Although taxonomic diversity at the phylum level was not different among the soil groups, many operational taxonomic units were influenced by metal or PAH pollution, and by soil texture and total nitrogen content. Functional diversity was not influenced by PAH contamination while metal pollution selected microbial communities with reduced metabolic functional diversity but more tolerant to zinc. Limited microbial utilisation of carbon substrates in metal-polluted soils was mainly due to the nitrogen content. Based on these two observations, we hypothesised that reduced microbial activity and lower carbon cycle-related functional diversity may have contributed to the accumulation of organic matter in the soils that exhibited the highest levels of metal pollution.
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Affiliation(s)
- Florian Lemmel
- Université de Lorraine, CNRS, LIEC, 54000, Nancy, France
| | | | - Andrea Fanesi
- Université de Lorraine, CNRS, LIEC, 54000, Nancy, France
| | - Corinne Leyval
- Université de Lorraine, CNRS, LIEC, 54000, Nancy, France
| | - Aurélie Cébron
- Université de Lorraine, CNRS, LIEC, 54000, Nancy, France.
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28
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Zhao F, Ju F, Huang K, Mao Y, Zhang XX, Ren H, Zhang T. Comprehensive insights into the key components of bacterial assemblages in pharmaceutical wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 651:2148-2157. [PMID: 30326447 DOI: 10.1016/j.scitotenv.2018.10.101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/31/2018] [Accepted: 10/08/2018] [Indexed: 06/08/2023]
Abstract
Due to complexity and variety of pharmaceutical wastewater composition, little is known as for functionally important microflora of pharmaceutical wastewater treatment plants (pWWTPs). We compared bacterial composition and diversity of pWWTPs (27 sludge samples collected from 12 full-scale pWWTPs) with those of other industrial (iWWTPs) (27 samples) and municipal wastewater treatment plants (mWWTPs) (27 samples) through meta-analysis based on 16S rRNA gene amplicon sequencing, and identified putatively important organisms and their ecological correlations. Non-metric multidimensional scaling indicated that the pWWTPs, iWWTPs and mWWTPs showed distinctive differences in bacterial community composition (P < 1e-04), and the pWWTPs had significantly lower bacterial diversity than the mWWTPs (P < 1e-06). Thermotogae and Synergistetes phyla only strictly dominated in the pWWTPs, and 26, 30 and 6 specific genera were identified in the pWWTPs, mWWTPs and iWWTPs, respectively. Totally, 15 and 1300 OTUs were identified as core and occasional groups, representing 23.2% and 66.2% of the total read abundance of the pWWTPs, respectively. Permutational multivariate analysis of variance revealed that the bacterial components were clearly clustered corresponding to the types of pharmaceutical wastewater, and a total of 129 local specific OTUs were identified in the pWWTPs, among which anticancer antibiotics pWWTPs had the highest number of specific OTUs (40 ones). Co-occurrence network revealed that the species dominating in the same type of pWWTPs tended to co-occur much more frequently than theoretical random expectation. The results may extend our knowledge regarding the ecological status and correlation of the key microflora in pWWTPs.
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Affiliation(s)
- Fuzheng Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Feng Ju
- Environmental Biotechnology Lab, The University of Hong Kong, Hong Kong, China
| | - Kailong Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Yanping Mao
- Environmental Biotechnology Lab, The University of Hong Kong, Hong Kong, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Tong Zhang
- Environmental Biotechnology Lab, The University of Hong Kong, Hong Kong, China.
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Yang H, Wang J, Lv Z, Tian J, Peng Y, Peng X, Xu X, Song Q, Lv B, Chen Z, Sun Z, Wang Z. Metatranscriptome analysis of the intestinal microorganisms in Pardosa pseudoannulata in response to cadmium stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 159:1-9. [PMID: 29730401 DOI: 10.1016/j.ecoenv.2018.04.053] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/23/2018] [Accepted: 04/26/2018] [Indexed: 06/08/2023]
Abstract
Cadmium (Cd) generates a variety of physiological and ecological toxicity to spiders. However, little is known about the effects of Cd on symbiotic bacteria of spiders. Metatranscriptomics is increasing our knowledge of microorganisms in environment. To better understand the impact of Cd on the symbiotic bacteria of spiders, we generated and compared the metatranscriptomes of the intestinal microorganisms of Pardosa pseudoannulata with and without Cd stress. The community structure of intestinal microorganisms in P. pseudoannulata was composed of 4 kingdoms, namely bacteria, viruses, eukaryotes and archaea, including 46 phyla, 97 classes, 184 orders, 339 families, 470 genera, and 598 species. The abundance of eukaryotes, bacteria and viruses was decreased by 0.14%, 1.22% and 2.52% respectively while the archaea was increased by 99.16% when under Cd stress. We identified 1519 differentially expressed genes (DEGs), including 770 up-regulated and 749 down-regulated genes. The results of KEGG annotation revealed that the expression of genes that are involved in the carbon metabolism, protein and amino acid metabolism and synthesis, glucose metabolism, oxidative phosphorylation, and glutathione metabolism were influenced by Cd. Collectively, these findings showed that Cd significantly impacted the community structure and expression of related functional genes of intestinal microorganisms in P. pseudoannulata.
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Affiliation(s)
- Huilin Yang
- College of Orient Science & Technology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, Hunan, China; College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, Hunan, China.
| | - Juan Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, Hunan, China.
| | - Zhiyue Lv
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.
| | - Jianxiang Tian
- College of Continuing Education, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, Hunan, China.
| | - Yuande Peng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan 410205, China.
| | - Xianjin Peng
- College of Life Science, Hunan Normal University, Changsha 410006, Hunan, China.
| | - Xiang Xu
- College of Life Science, Hunan Normal University, Changsha 410006, Hunan, China.
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA.
| | - Bo Lv
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, Hunan, China.
| | - Zhaoyang Chen
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, Hunan, China.
| | - Zhiying Sun
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, Hunan, China.
| | - Zhi Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, Hunan, China; College of Life Science, Hunan Normal University, Changsha 410006, Hunan, China.
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Tipayno SC, Truu J, Samaddar S, Truu M, Preem J, Oopkaup K, Espenberg M, Chatterjee P, Kang Y, Kim K, Sa T. The bacterial community structure and functional profile in the heavy metal contaminated paddy soils, surrounding a nonferrous smelter in South Korea. Ecol Evol 2018; 8:6157-6168. [PMID: 29988438 PMCID: PMC6024150 DOI: 10.1002/ece3.4170] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 04/06/2018] [Accepted: 04/19/2018] [Indexed: 01/06/2023] Open
Abstract
The pollution of agricultural soils by the heavy metals affects the productivity of the land and has an impact on the quality of the surrounding ecosystems. This study investigated the bacterial community structure in the heavy metal contaminated sites along a smelter and a distantly located paddy field to elucidate the factors that are related to the alterations of the bacterial communities under the conditions of heavy metal pollution. Among the study sites, the bacterial communities in the soil did not show any significant differences in their richness and diversity. The soil bacterial communities at the three study sites were distinct from one another at each site, possessing a distinct set of bacterial phylotypes. Among the study sites, significant changes were observed in the abundances of the bacterial phyla and genera. The variations in the bacterial community structure were mostly related to the general soil properties at the phylum level, while at the finer taxonomic levels, the concentrations of arsenic (As) and lead (Pb) were the significant factors, affecting the community structure. The relative abundances of the genera Desulfatibacillum and Desulfovirga were negatively correlated to the concentrations of As, Pb, and cadmium (Cd) in the soil, while the genus Bacillus was positively correlated to the concentrations of As and Cd. According to the results of the prediction of bacterial community functions, the soil bacterial communities of the heavy metal polluted sites were characterized by the more abundant enzymes involved in DNA replication and repair, translation, transcription, and the nucleotide metabolism pathways, while the amino acid and lipid metabolism, as well as the biodegradation potential of xenobiotics, were reduced. Our results showed that the adaptation of the bacterial communities to the heavy metal contamination was predominantly attributed to the replacement process, while the changes in community richness were linked to the variations in the soil pH values.
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Affiliation(s)
- Sherlyn C. Tipayno
- Department of Environmental and Biological ChemistryChungbuk National UniversityCheongjuKorea
- Present address:
Department of BiologyBenguet State UniversityLa TrinidadPhilippines
| | - Jaak Truu
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Sandipan Samaddar
- Department of Environmental and Biological ChemistryChungbuk National UniversityCheongjuKorea
| | - Marika Truu
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Jens‐Konrad Preem
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Kristjan Oopkaup
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Mikk Espenberg
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Poulami Chatterjee
- Department of Environmental and Biological ChemistryChungbuk National UniversityCheongjuKorea
| | - Yeongyeong Kang
- Department of Environmental and Biological ChemistryChungbuk National UniversityCheongjuKorea
| | - Kiyoon Kim
- Department of Environmental and Biological ChemistryChungbuk National UniversityCheongjuKorea
| | - Tongmin Sa
- Department of Environmental and Biological ChemistryChungbuk National UniversityCheongjuKorea
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31
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De Oliveira VH, Tibbett M. Cd and Zn interactions and toxicity in ectomycorrhizal basidiomycetes in axenic culture. PeerJ 2018; 6:e4478. [PMID: 29568708 PMCID: PMC5845391 DOI: 10.7717/peerj.4478] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/19/2018] [Indexed: 11/20/2022] Open
Abstract
Background Metal contamination in soils affects both above- and belowground communities, including soil microorganisms. Ectomycorrhizal (ECM) fungi are an important component in belowground community and tolerant strains have great potential in enhancing plant-based remediation techniques. We assessed cadmium and zinc toxicity in five ECM species in liquid media (Hebeloma subsaponaceum; H. cylindrosporum; H. crustuliniforme; Scleroderma sp.; Austroboletus occidentalis) and investigated the potential of Zn to alleviate Cd toxicity. Due to highly divergent results reported in the literature, liquid and solid media were compared experimentally for the first time in terms of differential toxicity thresholds in Cd and Zn interactions. Methods A wide range of Cd and Zn concentrations were applied to ectomycorrhizal fungi in axenic cultures (in mg L−1): 0; 1; 3; 9; 27; 81; 243 for the Cd treatments, and 0; 1; 30; 90; 270; 810; 2,430 for Zn. Combined Zn and Cd treatments were also applied to H. subsaponaceum and Scleroderma sp. Dry weight was recorded after 30 days, and in case of solid medium treatments, radial growth was also measured. Results and Discussion All species were adversely affected by high levels of Cd and Zn, and A. occidentalis was the most sensitive, with considerable biomass decrease at 1 mg L−1 Cd, while Scleroderma sp. and H. subsaponaceum were the most tolerant, which are species commonly found in highly contaminated sites. Cd was generally 10 times more toxic than Zn, which may explain why Zn had little impact in alleviating Cd effects. In some cases, Cd and Zn interactions led to a synergistic toxicity, depending on the concentrations applied and type of media used. Increased tolerance patterns were detected in fungi grown in solid medium and may be the cause of divergent toxicity thresholds found in the literature. Furthermore, solid medium allows measuring radial growth/mycelial density as endpoints which are informative and in this case appeared be related to the high tolerance indices found in H. subsaponaceum.
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Affiliation(s)
- Vinicius H De Oliveira
- Centre for Agri-Environmental Research & Soil Research Centre, School of Agriculture, Policy and Development, University of Reading, Reading, Berkshire, United Kingdom
| | - Mark Tibbett
- Centre for Agri-Environmental Research & Soil Research Centre, School of Agriculture, Policy and Development, University of Reading, Reading, Berkshire, United Kingdom
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Hu Y, Dou X, Li J, Li F. Impervious Surfaces Alter Soil Bacterial Communities in Urban Areas: A Case Study in Beijing, China. Front Microbiol 2018; 9:226. [PMID: 29545776 PMCID: PMC5839015 DOI: 10.3389/fmicb.2018.00226] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 01/30/2018] [Indexed: 12/20/2022] Open
Abstract
The rapid expansion of urbanization has caused land cover change, especially the increasing area of impervious surfaces. Such alterations have significant effects on the soil ecosystem by impeding the exchange of gasses, water, and materials between soil and the atmosphere. It is unclear whether impervious surfaces have any effects on soil bacterial diversity and community composition. In the present study, we conducted an investigation of bacterial communities across five typical land cover types, including impervious surfaces (concrete), permeable pavement (bricks with round holes), shrub coverage (Buxus megistophylla Levl.), lawns (Festuca elata Keng ex E. Alexeev), and roadside trees (Sophora japonica Linn.) in Beijing, to explore the response of bacteria to impervious surfaces. The soil bacterial communities were addressed by high-throughput sequencing of the bacterial 16S rRNA gene. We found that Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, and Firmicutes were the predominant phyla in urban soils. Soil from impervious surfaces presented a lower bacterial diversity, and differed greatly from other types of land cover. Soil bacterial diversity was predominantly affected by Zn, dissolved organic carbon (DOC), and soil moisture content (SMC). The composition of the bacterial community was similar under shrub coverage, roadside trees, and lawns, but different from beneath impervious surfaces and permeable pavement. Variance partitioning analysis showed that edaphic properties contributed to 12% of the bacterial community variation, heavy metal pollution explained 3.6% of the variation, and interaction between the two explained 33% of the variance. Together, our data indicate that impervious surfaces induced changes in bacterial community composition and decrease of bacterial diversity. Interactions between edaphic properties and heavy metals were here found to change the composition of the bacterial community and diversity across areas with different types of land cover, and soil properties play a more important role than heavy metals.
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Affiliation(s)
- Yinhong Hu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaolin Dou
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Juanyong Li
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation and Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Feng Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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Yang L, Wu L, Liu W, Huang Y, Luo Y, Christie P. Dissipation of antibiotics in three different agricultural soils after repeated application of biosolids. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:104-114. [PMID: 27873114 DOI: 10.1007/s11356-016-8062-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 11/07/2016] [Indexed: 06/06/2023]
Abstract
Application of biosolids to agricultural soils is one of the pathways by which antibiotics can be introduced into agricultural ecosystems. A pot experiment was conducted with repeated soil amendment with biosolids to examine the concentrations of four classes of antibiotics (tetracyclines, sulfonamides, fluoroquinolones, and macrolides) and their dissipation in three different soil types in wheat-rice rotations. Antibiotics accumulate in the soils after repeated application of biosolids. Fluoroquinolones showed stronger accumulation and persistence in the test soils than the other three classes of antibiotics. The maximum residual antibiotic concentration was that of norfloxacin at 155 ± 16 μg kg-1 in the Typic Hapli-Stagnic Anthrosols (paddy soil). Predicted half-lives were up to 3.69 years, a much longer period than that between biosolid applications (twice each year on average). Antibiotic accumulation followed the rough order fluoroquinolones > tetracyclines > macrolides > sulfonamides, and the sulfonamides were seldom encountered. When biosolid application was suspended, the dissipation rate accelerated. Antibiotic dissipation was slightly slower when biosolids with high heavy metal concentrations were applied and microbial degradation may have been the main mechanism of dissipation. Norfloxacin persistence was positively correlated with its soil adsorption capacity. Cation exchange capacity and soil organic matter content may have vital roles in the soil adsorption of fluoroquinolones. Because of their persistence, the fluoroquinolones must be taken into account in the planning of biosolid applications in agricultural practice.
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Affiliation(s)
- Lu Yang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Longhua Wu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Wuxing Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yujuan Huang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yongming Luo
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
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Touceda-González M, Prieto-Fernández Á, Renella G, Giagnoni L, Sessitsch A, Brader G, Kumpiene J, Dimitriou I, Eriksson J, Friesl-Hanl W, Galazka R, Janssen J, Mench M, Müller I, Neu S, Puschenreiter M, Siebielec G, Vangronsveld J, Kidd PS. Microbial community structure and activity in trace element-contaminated soils phytomanaged by Gentle Remediation Options (GRO). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 231:237-251. [PMID: 28802993 DOI: 10.1016/j.envpol.2017.07.097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 07/28/2017] [Accepted: 07/28/2017] [Indexed: 06/07/2023]
Abstract
Gentle remediation options (GRO) are based on the combined use of plants, associated microorganisms and soil amendments, which can potentially restore soil functions and quality. We studied the effects of three GRO (aided-phytostabilisation, in situ stabilisation and phytoexclusion, and aided-phytoextraction) on the soil microbial biomass and respiration, the activities of hydrolase enzymes involved in the biogeochemical cycles of C, N, P, and S, and bacterial community structure of trace element contaminated soils (TECS) from six field trials across Europe. Community structure was studied using denaturing gradient gel electrophoresis (DGGE) fingerprinting of Bacteria, α- and β-Proteobacteria, Actinobacteria and Streptomycetaceae, and sequencing of DGGE bands characteristic of specific treatments. The number of copies of genes involved in ammonia oxidation and denitrification were determined by qPCR. Phytomanagement increased soil microbial biomass at three sites and respiration at the Biogeco site (France). Enzyme activities were consistently higher in treated soils compared to untreated soils at the Biogeco site. At this site, microbial biomass increased from 696 to 2352 mg ATP kg-1 soil, respiration increased from 7.4 to 40.1 mg C-CO2 kg-1 soil d-1, and enzyme activities were 2-11-fold higher in treated soils compared to untreated soil. Phytomanagement induced shifts in the bacterial community structure at both, the total community and functional group levels, and generally increased the number of copies of genes involved in the N cycle (nirK, nirS, nosZ, and amoA). The influence of the main soil physico-chemical properties and trace element availability were assessed and eventual site-specific effects elucidated. Overall, our results demonstrate that phytomanagement of TECS influences soil biological activity in the long term.
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Affiliation(s)
- M Touceda-González
- Instituto de Investigaciones Agrobiológicas de Galicia (IIAG), Consejo Superior de Investigaciones Científicas (CSIC), Aptdo. 122, Santiago de Compostela 15780, Spain.
| | - Á Prieto-Fernández
- Instituto de Investigaciones Agrobiológicas de Galicia (IIAG), Consejo Superior de Investigaciones Científicas (CSIC), Aptdo. 122, Santiago de Compostela 15780, Spain
| | - G Renella
- University of Florence, Department of Agrifood Production and Environmental Sciences, P.le delle Cascine 18, I-50144 Florence, Italy
| | - L Giagnoni
- University of Florence, Department of Agrifood Production and Environmental Sciences, P.le delle Cascine 18, I-50144 Florence, Italy
| | - A Sessitsch
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, 3430 Tulln, Austria
| | - G Brader
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, 3430 Tulln, Austria
| | - J Kumpiene
- Luleå University of Technology, Waste Science & Technology, SE-97187 Luleå, Sweden
| | - I Dimitriou
- Swedish University of Agriculture Sciences, Department of Crop Production Ecology, SE-750 07 Uppsala, Sweden
| | - J Eriksson
- Swedish University of Agriculture Sciences, Department of Soil and Environment, SE-750 07 Uppsala, 17, Sweden
| | - W Friesl-Hanl
- AIT Austrian Institute of Technology GmbH, Center for Energy, 3430 Tulln, Austria
| | - R Galazka
- Institute of Soil Science and Plant Cultivation, State Research Institute, Czartoryskich 8, 24-100 Pulawy, Poland
| | - J Janssen
- Hasselt University, Centre for Environmental Sciences, 23 Agoralaan building D, B-3590 Diepenbeek, Belgium
| | - M Mench
- BIOGECO, INRA, Univ. Bordeaux, 33615 Pessac, France
| | - I Müller
- Saxon State Office for Environment, Agriculture and Geology, Pillnitzer Platz 3, 01326 Dresden Pillnitz, Germany
| | - S Neu
- Saxon State Office for Environment, Agriculture and Geology, Pillnitzer Platz 3, 01326 Dresden Pillnitz, Germany
| | - M Puschenreiter
- University of Natural Resources and Life Sciences Vienna - BOKU, Department of Forest and Soil Sciences, 3430 Tulln, Austria
| | - G Siebielec
- Institute of Soil Science and Plant Cultivation, State Research Institute, Czartoryskich 8, 24-100 Pulawy, Poland
| | - J Vangronsveld
- Hasselt University, Centre for Environmental Sciences, 23 Agoralaan building D, B-3590 Diepenbeek, Belgium
| | - P S Kidd
- Instituto de Investigaciones Agrobiológicas de Galicia (IIAG), Consejo Superior de Investigaciones Científicas (CSIC), Aptdo. 122, Santiago de Compostela 15780, Spain
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Tian T, Chen Z, Tian Y, Gao L. Microbial diversity in solar greenhouse soils in Round-Bohai Bay-Region, China: The influence of cultivation year and environmental condition. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:23236-23249. [PMID: 28831706 DOI: 10.1007/s11356-017-9837-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 07/26/2017] [Indexed: 06/07/2023]
Abstract
Round-Bohai Bay (RBB)-Region is an important crop production area in China, where vegetables are mainly produced in solar greenhouses. However, excessive fertilization and monoculture have caused serious deterioration of soil quality in this region. Soil microbial communities play pivotal roles in many ecosystem processes and are recognized as integrative components of soil quality. Therefore, in this study, we investigated bacterial and fungal diversity in solar greenhouse soils covering a wide range of cultivation year (CY) and sampling site (SS), by using pyrosequencing technology. Surprisingly, CY and SS had little influence on bacterial and fungal relative abundance and diversity. However, environmental factors (EF) and soil available potassium (K) in particular made a significant contribution to the variation of soil bacterial and fungal communities. Specifically, K showed significant (P < 0.05) correlations with dominant bacterial phyla Bacteroidetes, Acidobacteria, Chloroflexi, and Planctomycetes and fungal phyla Ascomycota and Basidiomycota. These results suggested that soil EF appeared more important than CY and SS in shaping the compositions of bacterial and fungal communities. In addition, since fertilizer K has been in the long-term abused in RBB-Region, future vegetable production should pay more attention to K input to reduce the negative effect on soil microbial communities.
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Affiliation(s)
- Tian Tian
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, 2 Yuanmingyuan Xilu, Beijing, 100193, China
| | - Zhiqun Chen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, 2 Yuanmingyuan Xilu, Beijing, 100193, China
- College of Life Science, Linyi University, Shuangling Road, Linyi, 276005, China
| | - Yongqiang Tian
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, 2 Yuanmingyuan Xilu, Beijing, 100193, China
| | - Lihong Gao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, 2 Yuanmingyuan Xilu, Beijing, 100193, China.
- Round-Bohai Bay-Region Collaborative Innovation Center for Protected Vegetables, Shenyang Agricultural University, Dongling Road 120, Liaoning, 110866, China.
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Kasemodel MC, Lima JZ, Sakamoto IK, Varesche MBA, Trofino JC, Rodrigues VGS. Soil contamination assessment for Pb, Zn and Cd in a slag disposal area using the integration of geochemical and microbiological data. ENVIRONMENTAL MONITORING AND ASSESSMENT 2016; 188:698. [PMID: 27896584 DOI: 10.1007/s10661-016-5708-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 11/18/2016] [Indexed: 06/06/2023]
Abstract
Improper disposal of mining waste is still considered a global problem, and further details on the contamination by potentially toxic metals are required for a proper assessment. In this context, it is important to have a combined view of the chemical and biological changes in the mining dump area. Thus, the objective of this study was to evaluate the Pb, Zn and Cd contamination in a slag disposal area using the integration of geochemical and microbiological data. Analyses of soil organic matter (SOM), pH, Eh, pseudo-total concentration of metals, sequential extraction and microbial community by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) were conducted. Metal availability was evaluated based on the geoaccumulation index (I geo), ecological risk ([Formula: see text]), Risk Assessment Code (RAC) and experimental data, and different reference values were tested to assist in the interpretation of the indices. The soil pH was slightly acidic to neutral, the Eh values indicated oxidized conditions and the average SOM content varied from 12.10 to 53.60 g kg-1. The average pseudo-total concentrations of metals were in the order of Zn > Pb > Cd. Pb and Zn were mainly bound to the residual fraction and Fe-Mn oxides, and a significant proportion of Cd was bound to the exchangeable and carbonate fractions. The topsoil (0-20 cm) is highly contaminated (I geo) with Cd and has a very high potential ecological risk ([Formula: see text]). Higher bacterial diversity was mainly associated with higher metal concentrations. It is concluded that the integration of geochemical and microbiological data can provide an appropriate evaluation of mining waste-contaminated areas.
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Affiliation(s)
- Mariana Consiglio Kasemodel
- Department of Geotechnical Engineering, University of São Paulo, 400 Trabalhador São Carlense Ave., São Carlos, 13566-590, Brazil
| | - Jacqueline Zanin Lima
- Department of Geotechnical Engineering, University of São Paulo, 400 Trabalhador São Carlense Ave., São Carlos, 13566-590, Brazil
| | - Isabel Kimiko Sakamoto
- Department of Hydraulics and Sanitary Engineering, University of São Paulo, 400 Trabalhador São Carlense Ave., São Carlos, 13566-590, Brazil
| | - Maria Bernadete Amancio Varesche
- Department of Hydraulics and Sanitary Engineering, University of São Paulo, 400 Trabalhador São Carlense Ave., São Carlos, 13566-590, Brazil
| | - Julio Cesar Trofino
- Department of Hydraulics and Sanitary Engineering, University of São Paulo, 400 Trabalhador São Carlense Ave., São Carlos, 13566-590, Brazil
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Exploring the Influence of Environmental Factors on Bacterial Communities within the Rhizosphere of the Cu-tolerant plant, Elsholtzia splendens. Sci Rep 2016; 6:36302. [PMID: 27782202 PMCID: PMC5080579 DOI: 10.1038/srep36302] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 10/10/2016] [Indexed: 12/11/2022] Open
Abstract
Bacterial communities of rhizospheric soils play an important role in the tolerance and uptake of metal-tolerant/hyperaccumulating plants to metals, e.g. the Cu-tolerant Elsholtzia splendens native to China. In this work, pyrosequencing of the bacterial 16S rRNA gene was firstly applied to investigate the rhizospheric bacterial community of E. splendens grown at Cu contaminated sites. The 47 phyla including 11 dominant phyla (>1%) in E. splendens rhizosphere were presented. The effects of Cu and other environmental factors (total organic carbon, total nitrogen and pH) on the rhizospheric bacterial community were studied comprehensively. The phyla abundances were affected by the environmental factors to different extent, and we found pH, instead of Cu concentration, influenced UniFrac distance significantly and was identified as the most important environmental factor affecting bacterial community. In addition, the influence of environmental factors on gene profiles was explored according to the predicted metagenomes obtained by PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states). Our study illustrates a view about Cu-tolerant E. splendens rhizospheric bacterial communities (composition, diversity and gene profiles) and their influencing factors, giving a hand for the understanding on bacterial community is formed and affected in rhizosphere.
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Zhang MQ, Guo Y, Powell CA, Doud MS, Yang CY, Zhou H, Duan YP. Zinc treatment increases the titre of 'Candidatus Liberibacter asiaticus' in huanglongbing-affected citrus plants while affecting the bacterial microbiomes. J Appl Microbiol 2016; 120:1616-28. [PMID: 26909469 DOI: 10.1111/jam.13102] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 01/28/2016] [Accepted: 02/05/2016] [Indexed: 12/26/2022]
Abstract
AIMS Huanglongbing (HLB)-affected citrus often display zinc deficiency symptoms. In this study, supplemental zinc was applied to citrus to determine its effect on Candidatus Liberibacter asiaticus (Las) titre, HLB symptoms, and leaf microbiome. METHODS AND RESULTS HLB-affected citrus were treated with various amounts of zinc. The treatments promoted Las growth and affected microbiomes in citrus leaves. Phylochip(™) -based results indicated that 5475 of over 50 000 known Operational Taxonomic Units (OTUs) in 52 phyla were detected in the midribs of HLB-affected citrus, of which Proteobacteria was the most abundant, followed by Firmicutes and Actinobacteria. In comparison, the microbiomes of zinc-treated diseased plants had overall more OTUs with higher amounts of Proteobacteria, but decreased percentages of Firmicutes and Actinobacteria. In addition, more OTUs of siderophore-producing bacteria were present. Only zinc-sensitive Staphylococcaceae had higher OTU's in the diseased plants without zinc treatments. CONCLUSIONS Although HLB-affected citrus appear zinc deficient, zinc amendments increased the pathogen levels and shifted the microbiome. SIGNIFICANCE AND IMPACT OF THE STUDY HLB is currently the most devastating disease of citrus worldwide. Zinc is often applied to HLB-affected citrus due to zinc deficiency symptoms. This study provided new insights into the potential effects of zinc on HLB and the microbial ecology of citrus.
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Affiliation(s)
- M Q Zhang
- State Key Lab for Conservation and Utilization of Subtropical Agro-biological Resources, Guangxi University, Nanning, China.,IRREC-IFAS, University of Florida, Fort Pierce, FL, USA.,USHRL, USDA-ARS, Fort Pierce, FL, USA
| | - Y Guo
- IRREC-IFAS, University of Florida, Fort Pierce, FL, USA
| | - C A Powell
- IRREC-IFAS, University of Florida, Fort Pierce, FL, USA
| | - M S Doud
- USHRL, USDA-ARS, Fort Pierce, FL, USA
| | - C Y Yang
- IRREC-IFAS, University of Florida, Fort Pierce, FL, USA
| | - H Zhou
- State Key Lab for Conservation and Utilization of Subtropical Agro-biological Resources, Guangxi University, Nanning, China
| | - Y P Duan
- USHRL, USDA-ARS, Fort Pierce, FL, USA
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Tai Y, Li Z, Mcbride MB. Natural attenuation of toxic metal phytoavailability in 35-year-old sewage sludge-amended soil. ENVIRONMENTAL MONITORING AND ASSESSMENT 2016; 188:241. [PMID: 27007289 DOI: 10.1007/s10661-016-5254-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 03/16/2016] [Indexed: 06/05/2023]
Abstract
Toxic heavy metals persist in agricultural soils and ecosystem for many decades after their application as contaminants in sewage sludge and fertilizer products This study assessed the potential long-term risk of cadmium (Cd), lead (Pb), zinc (Zn), and copper (Cu) in land-applied sewage sludge to food crop contamination. A sewage sludge-amended soil (SAS) aged in the field more than 35 years was used in a greenhouse pot experiment with leafy vegetables (lettuce and amaranth) having strong Cd and Zn accumulation tendencies. Soil media with variable levels of available Cd, Zn, and Cu (measured using 0.01 M CaCl2 extraction) were prepared by diluting SAS with several levels of uncontaminated control soil. Despite long-term aging in the field, the sludge site soil still retains large reserves of heavy metals, residual organic matter, phosphorus, and other nutrients, but its characteristics appear to have stabilized over time. Nevertheless, lettuce and amaranth harvested from the sludge-treated soil had undesirable contents of Cd and Zn. The high plant uptake efficiency for Cd and Zn raises a concern regarding the quality and safety of leafy vegetables in particular, when these crops are grown on soils that have been amended heavily with sewage sludge products at any time in their past.
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Affiliation(s)
- Yiping Tai
- Research Center of Hydrobiology, Jinan University, Guangzhou, 510632, China
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Section of Soil and Crop Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Zhian Li
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Murray B Mcbride
- Section of Soil and Crop Sciences, Cornell University, Ithaca, NY, 14853, USA.
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Wyszkowska J, Boros-Lajszner E, Borowik A, Baćmaga M, Kucharski J, Tomkiel M. Implication of zinc excess on soil health. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2016; 51:261-70. [PMID: 26828860 DOI: 10.1080/10934529.2015.1128726] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
This study was undertaken to evaluate zinc's influence on the resistance of organotrophic bacteria, actinomyces, fungi, dehydrogenases, catalase and urease. The experiment was conducted in a greenhouse of the University of Warmia and Mazury (UWM) in Olsztyn, Poland. Plastic pots were filled with 3 kg of sandy loam with pHKCl - 7.0 each. The experimental variables were: zinc applied to soil at six doses: 100, 300, 600, 1,200, 2,400 and 4,800 mg of Zn(2+) kg(-1) in the form of ZnCl2 (zinc chloride), and species of plant: oat (Avena sativa L.) cv. Chwat and white mustard (Sinapis alba) cv. Rota. Soil without the addition of zinc served as the control. During the growing season, soil samples were subjected to microbiological analyses on experimental days 25 and 50 to determine the abundance of organotrophic bacteria, actinomyces and fungi, and the activity of dehydrogenases, catalase and urease, which provided a basis for determining the soil resistance index (RS). The physicochemical properties of soil were determined after harvest. The results of this study indicate that excessive concentrations of zinc have an adverse impact on microbial growth and the activity of soil enzymes. The resistance of organotrophic bacteria, actinomyces, fungi, dehydrogenases, catalase and urease decreased with an increase in the degree of soil contamination with zinc. Dehydrogenases were most sensitive and urease was least sensitive to soil contamination with zinc. Zinc also exerted an adverse influence on the physicochemical properties of soil and plant development. The growth of oat and white mustard plants was almost completely inhibited in response to the highest zinc doses of 2,400 and 4,800 mg Zn(2+) kg(-1).
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Affiliation(s)
- Jadwiga Wyszkowska
- a Department of Microbiology , University of Warmia and Mazury in Olsztyn , Olsztyn , Poland
| | - Edyta Boros-Lajszner
- a Department of Microbiology , University of Warmia and Mazury in Olsztyn , Olsztyn , Poland
| | - Agata Borowik
- a Department of Microbiology , University of Warmia and Mazury in Olsztyn , Olsztyn , Poland
| | - Małgorzata Baćmaga
- a Department of Microbiology , University of Warmia and Mazury in Olsztyn , Olsztyn , Poland
| | - Jan Kucharski
- a Department of Microbiology , University of Warmia and Mazury in Olsztyn , Olsztyn , Poland
| | - Monika Tomkiel
- a Department of Microbiology , University of Warmia and Mazury in Olsztyn , Olsztyn , Poland
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Gao M, Qi Y, Song W, Zhou Q. Biomarker analysis of combined oxytetracycline and zinc pollution in earthworms (Eisenia fetida). CHEMOSPHERE 2015; 139:229-234. [PMID: 26134676 DOI: 10.1016/j.chemosphere.2015.06.059] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 06/11/2015] [Accepted: 06/12/2015] [Indexed: 06/04/2023]
Abstract
To determine the interactive action of antibiotics and heavy metals, this study assessed pollutant-induced responses of cellular biomarkers in earthworms (Eisenia fetida) exposed to zinc (Zn(2+)) and oxytetracycline (OTC) in soil. Lysosomal membranes were damaged and coelomocyte apoptosis occurred with exposure to the individual and combined pollutants. Compared with Zn(2+) alone, lysosomal membrane stability and coelomocyte apoptosis decreased in the Zn(2+)-OTC combined treatment, possibly as a result of complexation of Zn(2+) and OTC at alkaline pH. Such complexation could reduce the toxicity of the pollutants. Lysosomal membrane stability and coelomocyte apoptosis are sensitive biomarkers and could be economical and rapid tools for the monitoring and assessment of a variety of pollutants.
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Affiliation(s)
- Minling Gao
- Department of Environmental and Chemical Engineering, Tianjin Polytechnic University, No. 399 Binshui Western Road, Xiqing District, Tianjin 300387, China.
| | - Yun Qi
- Department of Environmental and Chemical Engineering, Tianjin Polytechnic University, No. 399 Binshui Western Road, Xiqing District, Tianjin 300387, China.
| | - Wenhua Song
- Department of Environmental and Chemical Engineering, Tianjin Polytechnic University, No. 399 Binshui Western Road, Xiqing District, Tianjin 300387, China.
| | - Qian Zhou
- Department of Environmental and Chemical Engineering, Tianjin Polytechnic University, No. 399 Binshui Western Road, Xiqing District, Tianjin 300387, China.
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Bourioug M, Gimbert F, Alaoui-Sehmer L, Benbrahim M, Badot PM, Alaoui-Sossé B, Aleya L. Effects of sewage sludge amendment on snail growth and trace metal transfer in the soil-plant-snail food chain. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:17925-36. [PMID: 26165994 DOI: 10.1007/s11356-015-5006-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 07/01/2015] [Indexed: 06/04/2023]
Abstract
Cu, Zn, Pb, and Cd concentrations in a soil plant (Lactuca sativa) continuum were measured after sewage sludge amendment. The effects of sewage sludge on growth and trace metal bioaccumulation in snails (Cantareus aspersus) were investigated in a laboratory experiment specifically designed to identify contamination sources (e.g., soil and leaves). Application of sewage sludge increased trace metal concentrations in topsoil. However, except Zn, metal concentrations in lettuce leaves did not reflect those in soil. Lettuce leaves were the main source of Zn, Cu, and Cd in exposed snails. Bioaccumulation of Pb suggested its immediate transfer to snails via the soil. No apparent toxic effects of trace metal accumulation were observed in snails. Moreover, snail growth was significantly stimulated at high rates of sludge application. This hormesis effect may be due to the enhanced nutritional content of lettuce leaves exposed to sewage sludge.
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Affiliation(s)
- Mohamed Bourioug
- Jean-François Champollion University Center for Teaching and Research, Place Verdun, F-81000, Albi, France
| | - Frédéric Gimbert
- Chrono-Environnement UMR CNRS 6249, University of Bourgogne Franche-Comté, 16 Route de Gray, F-25000, Besançon, France
| | - Laurence Alaoui-Sehmer
- Chrono-Environnement UMR CNRS 6249, University of Bourgogne Franche-Comté, 16 Route de Gray, F-25000, Besançon, France
| | - Mohammed Benbrahim
- RITTMO Agroenvironnement, ZA Biopôle, 37 rue de Herrlisheim, CS 80023, F-68025, Colmar cedex, France
| | - Pierre-Marie Badot
- Chrono-Environnement UMR CNRS 6249, University of Bourgogne Franche-Comté, 16 Route de Gray, F-25000, Besançon, France
| | - Badr Alaoui-Sossé
- Chrono-Environnement UMR CNRS 6249, University of Bourgogne Franche-Comté, 16 Route de Gray, F-25000, Besançon, France
| | - Lotfi Aleya
- Chrono-Environnement UMR CNRS 6249, University of Bourgogne Franche-Comté, 16 Route de Gray, F-25000, Besançon, France.
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Bourioug M, Gimbert F, Alaoui-Sehmer L, Benbrahim M, Aleya L, Alaoui-Sossé B. Sewage sludge application in a plantation: effects on trace metal transfer in soil-plant-snail continuum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 502:309-314. [PMID: 25262293 DOI: 10.1016/j.scitotenv.2014.09.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/27/2014] [Accepted: 09/08/2014] [Indexed: 06/03/2023]
Abstract
We studied the potential bioaccumulation of Cu, Zn, Pb and Cd by the snail Cantareus aspersus and evaluated the risk of leaching after application of sewage sludge to forest plantation ecosystems. Sewage sludge was applied to the soil surface at two loading rates (0, and 6 tons ha(-1) in dry matter) without incorporation into the soil so as to identify the sources of trace metal contamination in soil and plants and to evaluate effects on snail growth. The results indicated a snail mortality rate of less than 1% during the experiment, while their dry weight decreased significantly (<0.001) in all treatment modalities. Thus, snails showed no acute toxicity symptoms after soil amendment with sewage sludge over the exposure period considered. Additions of sewage sludge led to higher levels of trace metals in forest litter compared to control subplots, but similar trace metal concentrations were observed in sampling plants. Bioaccumulation study demonstrated that Zn had not accumulated in snails compared to Cu which accumulated only after 28 days of exposure to amended subplots. However, Pb and Cd contents in snails increased significantly after 14 and 28 days of exposure in both the control and amended subplots. At the last sampling date, in comparison to controls the Cd increase was higher in snails exposed to amended subplots. Thus, sludge spread therefore appears to be responsible for the observed bioaccumulation for Cu and Cd after 28days of exposure. Concerning Pb accumulation, the results from litter-soil-plant compartments suggest that soil is this metal's best transfer source.
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Affiliation(s)
- Mohamed Bourioug
- Université de Franche-Comté, Laboratoire de Chrono-Environnement, UMR CNRS 6249, Besançon, France
| | - Frédéric Gimbert
- Université de Franche-Comté, Laboratoire de Chrono-Environnement, UMR CNRS 6249, Besançon, France
| | - Laurence Alaoui-Sehmer
- Université de Franche-Comté, Laboratoire de Chrono-Environnement, UMR CNRS 6249, Besançon, France
| | - Mohammed Benbrahim
- RITTMO Agroenvironnement, ZA Biopôle, 37 rue de Herrlisheim, CS 80023, F-68025 Colmar Cedex, France
| | - Lotfi Aleya
- Université de Franche-Comté, Laboratoire de Chrono-Environnement, UMR CNRS 6249, Besançon, France.
| | - Badr Alaoui-Sossé
- Université de Franche-Comté, Laboratoire de Chrono-Environnement, UMR CNRS 6249, Besançon, France
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Interaction between the microbial community and invading Escherichia coli O157:H7 in soils from vegetable fields. Appl Environ Microbiol 2013; 80:70-6. [PMID: 24123745 DOI: 10.1128/aem.03046-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The survival of Escherichia coli O157:H7 in soils can contaminate vegetables, fruits, drinking water, etc. However, data on the impact of E. coli O157:H7 on soil microbial communities are limited. In this study, we monitored the changes in the indigenous microbial community by using the phospholipid fatty acid (PLFA) method to investigate the interaction of the soil microbial community with E. coli O157:H7 in soils. Simple correlation analysis showed that the survival of E. coli O157:H7 in the test soils was negatively correlated with the ratio of Gram-negative (G(-)) to Gram-positive (G(+)) bacterial PLFAs (G(-)/G(+) ratio). In particular, levels of 14 PLFAs were negatively correlated with the survival time of E. coli O157:H7. The contents of actinomycetous and fungal PLFAs in the test soils declined significantly (P, <0.05) after 25 days of incubation with E. coli O157:H7. The G(-)/G(+) ratio declined slightly, while the ratio of bacterial to fungal PLFAs (B/F ratio) and the ratio of normal saturated PLFAs to monounsaturated PLFAs (S/M ratio) increased, after E. coli O157:H7 inoculation. Principal component analysis results further indicated that invasion by E. coli O157:H7 had some effects on the soil microbial community. Our data revealed that the toxicity of E. coli O157:H7 presents not only in its pathogenicity but also in its effect on soil microecology. Hence, close attention should be paid to the survival of E. coli O157:H7 and its potential for contaminating soils.
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Pauwels M, Frérot H, Souleman D, Vandenbulcke F. Using biomarkers in an evolutionary context: lessons from the analysis of biological responses of oligochaete annelids to metal exposure. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2013; 179:343-350. [PMID: 23707006 DOI: 10.1016/j.envpol.2013.05.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 04/27/2013] [Accepted: 05/01/2013] [Indexed: 06/02/2023]
Abstract
Anthropogenic activities may lead to the accumulation of inorganic and organic compounds in topsoils. Biota living in close contact with contaminated soils may experience stress at different levels of biological organization throughout the continuum from molecular to community level. Biological responses observed at the individual or infra-individual level of biological organization led to the development of biomarkers. The development of biomarkers consists often in evidencing biological modifications following a contaminant stress in laboratory conditions, using naïve organisms and it is sometime proposed to use the biological state of individuals from sentinel species collected in the field to evaluate the level of environmental exposure. However, considering the possibility of local adaptation following long-term exposure, organisms response sampled in the field may substantially differ from laboratory specimens. In this review, we discuss this point focusing on the definition and validity of molecular biomarkers of metal pollution using earthworms of the Lumbricidae family.
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Affiliation(s)
- Maxime Pauwels
- Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8198, Université Lille Nord de France, Bâtiment SN2, F-59655 Villeneuve d'Ascq Cedex, France
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Contin M, Goi D, De Nobili M. Land application of aerobic sewage sludge does not impair methane oxidation rates of soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2012; 441:10-8. [PMID: 23134765 DOI: 10.1016/j.scitotenv.2012.09.052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 09/05/2012] [Accepted: 09/22/2012] [Indexed: 05/26/2023]
Abstract
The aim of this study was to measure and compare methane oxidation rates of arable and grassland soils that received 7.5t ha⁻¹ y⁻¹ of noncontaminated aerobically treated sewage sludge for ten years. Arable soils showed generally lower methane oxidation rates (from 6 to 15∗10⁻³ h⁻¹) than grassland soils (from 26 to 33∗10³ h⁻¹). Oxidation rate constants (k) of soils amended with sewage sludge were remarkably close to their respective untreated controls, but a soil, that had received a tenfold sewage sludge application (i.e. 75 t ha⁻¹ y⁻¹), showed a statistically significantly higher k-value. Laboratory addition of up to 1000 mg Pb g⁻¹ soil to this soil did not cause any significant change in methane oxidation, but caused a decrease from 13.9 to 10.9×10⁻³ h⁻¹ in the control soil. Addition of Zn was much more toxic than Pb, with a significant decrease at 300 μg g⁻¹ soil rate and an almost complete inhibition at 1500 μg g⁻¹ soil rate. Higher resistance was evident of sewage sludge treated soil in comparison to control soil, for both biomass C and CH₄ oxidation activity.
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Affiliation(s)
- Marco Contin
- Department of Agriculture and Environmental Sciences, University of Udine, Via delle Scienze 208, 33100 Udine, Italy.
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Yang Y, Wang X, Shi J, Li J. The influence of the discharging sewage on microbial diversity in sludge from Dongting Lake. World J Microbiol Biotechnol 2012; 28:421-30. [PMID: 22806836 DOI: 10.1007/s11274-011-0831-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2011] [Accepted: 06/30/2011] [Indexed: 11/26/2022]
Abstract
Human activities have a tremendous impact not only on the macroscopic world, but also on the micro-organisms. Here, Amplified Ribosomal DNA Restriction Analysis (ARDRA) was used for assessing the effect of the industrial sewage on the microbial community in sludge of Dongting Lake, the second-largest freshwater lake in China. The sludge samples from the outfall of the representative nitrogenous fertilizer plant near the lake were collected in March, 2010, and the sludge samples from the surrounding waters were treated as the control. The multi-element analysis results showed that the content of nitrogen, phosphorus in Sample SY were 1.9 and 1.47 times of the control group respectively. Based on restriction patterns derived from ARDRA, 26 representative clones (15 clones in the SY group and 11 clones in the DZ group) were sequenced. The sequence data and phylogenetic analysis of 16S rRNA gene presented that microorganism diversity of two sludge samples were abundant. Bacterial diversity presented among the outfall samples was dominated by Aeromonas sp. (5.8%), Acidimicrobidae sp. (5.8%) and Gemmatimonas sp. (5.0%). In contrast, bacterial diversity presented among the control group was dominated by Xanthomonas sp. (8.0%), Lautropia sp. (5.8%) and Duganella sp. (5.1%). The results indicated that due to the excessive of nitrogen and phosphorus discharged by the nitrogen fertilizer plant, the eutrophication in Dongting Lake has great influence on the microbial community structure.
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Affiliation(s)
- Yu Yang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, People's Republic of China.
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Phytoremediation of Zinc-Contaminated Soil and Zinc-Biofortification for Human Nutrition. SPRINGERBRIEFS IN MOLECULAR SCIENCE 2012. [DOI: 10.1007/978-94-007-1439-7_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Perryman SE, Rees GN, Grace MR. Sediment bacterial community structure and function in response to C and Zn amendments: urban and nonurban streams. ACTA ACUST UNITED AC 2011. [DOI: 10.1899/11-009.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Shane E. Perryman
- Water Studies Centre and School of Chemistry, Monash University, Clayton Victoria 3800, Australia and CSIRO Land and Water and Murray-Darling Freshwater Research Centre, La Trobe University, Wodonga, Victoria 3689, Australia
| | - Gavin N. Rees
- CSIRO Land and Water and Murray-Darling Freshwater Research Centre, La Trobe University, Wodonga, Victoria 3689, Australia
| | - Michael R. Grace
- Water Studies Centre and School of Chemistry, Monash University, Clayton Victoria 3800, Australia
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