1
|
Banerjee S, Ghosh S, Chakraborty S, Sarkar D, Datta R, Bhattacharyya P. Synergistic impact of bioavailable PHEs and alkalinity on microbial diversity and traits in agricultural soil adjacent to chromium-asbestos mines. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 350:124021. [PMID: 38657890 DOI: 10.1016/j.envpol.2024.124021] [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: 12/02/2023] [Revised: 04/15/2024] [Accepted: 04/20/2024] [Indexed: 04/26/2024]
Abstract
Soil microbial communities undergo constant fluctuations, particularly in response to environmental factors. Although the deposition of toxic mine waste is recognized for introducing potentially hazardous elements (PHEs) into the soil, its specific impacts on microbial communities remain unclear. This study aims to explore the combined effects of soil alkalinity and bioavailable PHEs on microbial diversity and traits in agricultural soil adjacent to a chromium-asbestos mining area. By employing a comprehensive analysis, this study indicated that microbiological attributes were reduced in contaminated areas (zone 1), whereas both the levels of bioavailable PHEs (CrWs: 31.08 mg/kg, NiWs: 13.90 mg/kg) and alkalinity indices (CROSS, MCAR, MH) were significantly higher. The spatial distribution of soil alkalinity and bioavailable PHEs, primarily originating from chromium-asbestos mines, has been determined. This study also elucidates the negative relationship between soil stressors (Alkalinity and PHEs) and microbial activities (soil enzymatic activity, microbial respiration, and biomass carbon). The vector's length exhibited a notable difference between zone 1 (0.51) and zone 2 (0.32), indicating a substantial limitation on carbon (C). Also, the investigation of soil bacterial diversity unveiled notable disparities in the prevalence of microbial populations inside zone 1. Proteobacteria constituted 57.18% of the total population indicating a noteworthy prevalence in the contaminated soils. Finally, the random forest (RF) algorithm from machine learning was selected and proven to be a robust choice in Taylor diagrams for predicting the causative stressors responsible for the deterioration of soil microbial health. Therefore, this research offers insights into the health and resilience of soil microbial communities under synergistic stress conditions, which will aid environmentalists in planning future interventions and improving sustainable farming techniques.
Collapse
Affiliation(s)
- Sonali Banerjee
- Agricultural and Ecological Research Unit, Indian Statistical Institute, Giridih, Jharkhand, 815301, India
| | - Saibal Ghosh
- Agricultural and Ecological Research Unit, Indian Statistical Institute, Giridih, Jharkhand, 815301, India
| | - Shreya Chakraborty
- Agricultural and Ecological Research Unit, Indian Statistical Institute, Giridih, Jharkhand, 815301, India
| | - Dibyendu Sarkar
- Stevens Institute of Technology, Department of Civil, Environmental, and Ocean Engineering, Hoboken, NJ, 07030, USA
| | - Rupali Datta
- Department of Biological Science, Michigan Technological University, Michigan, USA
| | - Pradip Bhattacharyya
- Agricultural and Ecological Research Unit, Indian Statistical Institute, Giridih, Jharkhand, 815301, India.
| |
Collapse
|
2
|
Wang M, Song G, Zheng Z, Song Z, Mi X, Hua J, Wang Z. Effect of humic substances on the fraction of heavy metal and microbial response. Sci Rep 2024; 14:11206. [PMID: 38755178 PMCID: PMC11099172 DOI: 10.1038/s41598-024-61575-5] [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: 02/26/2024] [Accepted: 05/07/2024] [Indexed: 05/18/2024] Open
Abstract
Contamination of soils by Molybdenum (Mo) has raised increasing concern worldwide. Both fulvic acid (FA) and humic acid (HA) possess numerous positive properties, such as large specific surface areas and microporous structure that facilitates the immobilization of the heavy metal in soils. Despite these characteristics, there have been few studies on the microbiology effects of FA and HA. Therefore, this study aimed to assess the Mo immobilization effects of FA and HA, as well as the associated changes in microbial community in Mo-contaminated soils (with application rates of 0%, 0.5% and 1.0%). The result of the incubation demonstrated a decrease in soil pH (from 8.23 ~ 8.94 to 8.05 ~ 8.77). Importantly, both FA and HA reduced the exchangeable fraction and reducible fraction of Mo in the soil, thereby transforming Mo into a more stable form. Furthermore, the application of FA and HA led to an increase in the relative abundance of Actinobacteriota and Firmicutes, resulting in alterations to the microbial community structure. However, it is worth noting that due to the differing structures and properties of FA and HA, these outcomes were not entirely consistent. In summary, the aging of FA and HA in soil enhanced their capacity to immobilization Mo as a soil amendment. This suggests that they have the potential to serve as effective amendments for the remediation of Mo-contaminated soils.
Collapse
Affiliation(s)
- Mengmeng Wang
- North China University of Water Resources and Electric Power, Zhengzhou, 450046, People's Republic of China
| | - Gangfu Song
- North China University of Water Resources and Electric Power, Zhengzhou, 450046, People's Republic of China.
| | - Zhihong Zheng
- North China University of Water Resources and Electric Power, Zhengzhou, 450046, People's Republic of China
| | - Zhixin Song
- North China University of Water Resources and Electric Power, Zhengzhou, 450046, People's Republic of China
| | - Xiao Mi
- North China University of Water Resources and Electric Power, Zhengzhou, 450046, People's Republic of China.
| | - Jiajun Hua
- North China University of Water Resources and Electric Power, Zhengzhou, 450046, People's Republic of China
| | - Zihang Wang
- North China University of Water Resources and Electric Power, Zhengzhou, 450046, People's Republic of China
| |
Collapse
|
3
|
Godinho O, Klimek D, Jackiewicz A, Guedes B, Almeida E, Calisto R, Vitorino IR, Santos JDN, González I, Lobo-da-Cunha A, Calusinska M, Quinteira S, Lage OM. Stieleria tagensis sp. nov., a novel member of the phylum Planctomycetota isolated from Tagus River in Portugal. Antonie Van Leeuwenhoek 2023; 116:1209-1225. [PMID: 37737556 PMCID: PMC10541342 DOI: 10.1007/s10482-023-01877-2] [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: 02/28/2023] [Accepted: 08/30/2023] [Indexed: 09/23/2023]
Abstract
A bacterial strain was isolated from a brackish water sample of Tagus river, Alcochete, Portugal and was designated TO1_6T. It forms light pink colonies on M13 medium supplemented with N-acetylglucosamine. Cells are pear-shaped to spherical, form rosettes and divide by budding. Strain TO1_6T presents a mesophilic and neutrophilic profile, with optimum growth at 20 to 25 °C and pH 7.0 to 7.5, and vitamin supplementation is not required to promote its growth. The genome of the novel isolate is 7.77 Mbp in size and has a DNA G + C content of 56.3%. Based on its 16S rRNA gene sequence, this strain is affiliated with the phylum Planctomycetota. Further taxonomic characterization using additional phylogenetic markers, namely rpoB gene sequence (encoding the β-subunit of the DNA-dependent RNA polymerase), as well as Percentage of conserved proteins, average nucleotide identity and average amino acid identity, suggest the affiliation of strain TO1_6T to the genus Stieleria, a recently described taxon in the family Pirellulaceae, order Pirellulales and class Planctomycetia. Based on the genotypic, phylogenetic and physiological characterization, we here describe a new species represented by the type strain TO1_6T (= CECT 30432T, = LMG 32465T), for which the name Stieleria tagensis sp. nov. is proposed.
Collapse
Affiliation(s)
- Ofélia Godinho
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal.
| | - Dominika Klimek
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, Rue du Brill 41, 4422, Belvaux, Luxembourg
- The Faculty of Science, Technology and Medicine, FSTM, University of Luxembourg, 2 Avenue de l'Université, 4365, Esch-sur-Alzette, Luxembourg
| | - Adrianna Jackiewicz
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Bárbara Guedes
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Eduarda Almeida
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - Rita Calisto
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - Inês Rosado Vitorino
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - José Diogo Neves Santos
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - Ignacio González
- Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Fundación MEDINA, 18016, Granada, Spain
| | - Alexandre Lobo-da-Cunha
- Laboratório de Biologia Celular, Instituto de Ciências Biomédicas Abel Salazar, ICBAS, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Magdalena Calusinska
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, Rue du Brill 41, 4422, Belvaux, Luxembourg
| | - Sandra Quinteira
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
- BIOPOLIS/CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Rua Padre Armando Quintas, nº 7, 4485-661, Vairão, Portugal
- TOXRUN-Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL., Avenida Central de Gandra, 1317, 4585-116, Gandra, PRD, Portugal
| | - Olga Maria Lage
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| |
Collapse
|
4
|
Prosenkov A, Cagnon C, Gallego JLR, Pelaez AI. The microbiome of a brownfield highly polluted with mercury and arsenic. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 323:121305. [PMID: 36804142 DOI: 10.1016/j.envpol.2023.121305] [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: 11/18/2022] [Revised: 02/11/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Abandoned brownfields represent a challenge for their recovery. To apply sustainable remediation technologies, such as bioremediation or phytoremediation, indigenous microorganisms are essential agents since they are adapted to the ecology of the soil. Better understanding of microbial communities inhabiting those soils, identification of microorganisms that drive detoxification process and recognising their needs and interactions will significantly improve the outcome of the remediation. With this in mind we have carried out a detailed metagenomic analysis to explore the taxonomic and functional diversity of the prokaryotic and eukaryotic microbial communities in soils, several mineralogically distinct types of pyrometallurgic waste, and groundwater sediments of a former mercury mining and metallurgy site which harbour very high levels of arsenic and mercury pollution. Prokaryotic and eukaryotic communities were identified, which turned out to be more diverse in the surrounding contaminated soils compared to the pyrometallurgic waste. The highest diversity loss was observed in two environments most contaminated with mercury and arsenic (stupp, a solid mercury condenser residue and arsenic-rich soot from arsenic condensers). Interestingly, microbial communities in the stupp were dominated by an overwhelming majority of archaea of the phylum Crenarchaeota, while Ascomycota and Basidiomycota fungi comprised the fungal communities of both stump and soot, results that show the impressive ability of these previously unreported microorganisms to colonize these extreme brownfield environments. Functional predictions for mercury and arsenic resistance/detoxification genes show their increase in environments with higher levels of pollution. Our work establishes the bases to design sustainable remediation methods and, equally important, to study in depth the genetic and functional mechanisms that enable the subsistence of microbial populations in these extremely selective environments.
Collapse
Affiliation(s)
- Alexander Prosenkov
- Area of Microbiology, Department of Functional Biology, Environmental Biogeochemistry and Raw Materials Group and IUBA, University of Oviedo, 33006 Oviedo, Asturias, Spain
| | - Christine Cagnon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - José Luis R Gallego
- INDUROT and Environmental Biogeochemistry and Raw Materials Group, Campus of Mieres, University of Oviedo, 33600 Mieres, Asturias, Spain
| | - Ana Isabel Pelaez
- Area of Microbiology, Department of Functional Biology, Environmental Biogeochemistry and Raw Materials Group and IUBA, University of Oviedo, 33006 Oviedo, Asturias, Spain.
| |
Collapse
|
5
|
Yang R, Ma G, Liu C, Wang C, Kang X, Wu M, Zhang B. Effects of different heavy metal pollution levels on microbial community structure and risk assessment in Zn-Pb mining soils. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:52749-52761. [PMID: 36843164 DOI: 10.1007/s11356-023-26074-6] [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: 11/28/2022] [Accepted: 02/18/2023] [Indexed: 06/18/2023]
Abstract
Heavy metal contamination in soils seriously threatens human health and aggravates the global pollution burden. In this study, we investigated the risk of heavy metal contamination in soils at a Zn-Pb mineral processing plant in Longnan, China, and the effects of different heavy metal contamination levels on diverse microbial communities. Statistical analysis showed that, except for Ni, the average content of all detected metals (Zn, Pb, As, Cu, Cd, Hg) in the soil was higher than the background value of soil in the study area, which was most seriously contaminated with Pb and As. Comparison of functional divisions showed that heavy metal soil contamination was most serious in the raw material stacking area and the production area. Interpolation analysis showed that areas closer to the wastewater discharge area had higher contents of each heavy metal and were more seriously polluted. From the point of pollution index, the risk of heavy metal soil pollution in the study area was very high (RI = 2845.24, i.e., > 600), with Cd and Hg being the most serious pollutants compared with other heavy metals. Microbial community abundance, diversity, and structure differed at different levels of heavy metal contamination. The community diversity of bacteria decreased with increasing heavy metal concentrations, while no significant change in fungi was observed. Evidence from variation redundancy analysis (RDA) and the Spearman correlation analysis showed that the leading factors affecting microbial community composition were Cu, Cd, Hg, and pH. Actinobacteria and Gemmatimonadetes at the uncontaminated level (CL) were significantly and negatively correlated with the concentrations of Cu, Zn, Cd, and Pb. Proteobacteria and Chloroflexi at the severely contaminated level (SL) were significantly correlated with pH and Hg. However, heavy metal contamination had less effect on most of the dominant fungi. In conclusion, microbial communities such as Proteobacteria, Actinobacteria, Chloroflexi, and Ascomycota showed greater tolerance to heavy metals. These results could be used as important references for the remediation of heavy metal-contaminated soils.
Collapse
Affiliation(s)
- Ruiqi Yang
- College of Urban Environment, Lanzhou City University, Lanzhou, 730070, China.
| | - Gaogao Ma
- Lanzhou Mineral Exploration Institute, Gansu Nonferrous Metals Geological Prospecting Bureau, Lanzhou, 730000, China
| | - Chenglong Liu
- Lanzhou Mineral Exploration Institute, Gansu Nonferrous Metals Geological Prospecting Bureau, Lanzhou, 730000, China
| | - Chao Wang
- College of City Construction, Lanzhou City University, Lanzhou, 730070, China
| | - Xiaoyang Kang
- College of Urban Environment, Lanzhou City University, Lanzhou, 730070, China
| | - Minghui Wu
- Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650091, China
| | - Binglin Zhang
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| |
Collapse
|
6
|
Li J, Wu B, Luo Z, Lei N, Kuang H, Li Z. Immobilization of cadmium by mercapto-functionalized palygorskite under stimulated acid rain: Stability performance and micro-ecological response. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119400. [PMID: 35525516 DOI: 10.1016/j.envpol.2022.119400] [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: 01/19/2022] [Revised: 04/06/2022] [Accepted: 04/30/2022] [Indexed: 06/14/2023]
Abstract
The interaction of cadmium (Cd) pollution and acid rain stress has seriously threatened soil ecosystem and human health. However, there are still few effective amendments for the in-situ remediation in the Cd-contaminated acidified soil. In this study, the performance and mechanisms of palygorskite (PAL) and mercapto-functionalized PAL (MPAL) on Cd immobilization were investigated, and the stability as well as effects on soil micro-ecology under stimulated acid rain were also explored. Results showed that MPAL could react with Cd to form stable Cd-sulfhydryl and Cd-O complexes. The reduction of bioavailable Cd by MPAL was 121.19-164.86% higher than that by PAL. Notably, the Cd immobilization by MPAL remained stable within 90 days in which the concentrations of HOAc-extractable Cd were reduced by 18.28-25.12%, while the reducible and residual fractions were increased by 9.26-18.53% and 54.16%-479.01%, respectively. The sequential acid rain leaching demonstrated that soil after MPAL treatments had a strong H+ resistance, and the immobilized Cd showed prominent stability. In addition, activities of acid phosphatase, catalase and invertase in MPAL treated soil were significantly enhanced by 34.60%, 22.09% and 48.87%, respectively. After MPAL application, bacterial diversity was further improved with diversified sulfur metabolism biomarkers. The decreased abundance of Cd resistance genes including cadA, cadC, czcA, czcB, czcR and zipA also indicated that soil micro-ecology was improved by MPAL. These results showed that MPAL was an effective and eco-friendly amendment for the immobilization of Cd in contaminated soil.
Collapse
Affiliation(s)
- Jia Li
- State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil & Water Pollution, College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, PR China
| | - Bin Wu
- State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil & Water Pollution, College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, PR China.
| | - Zhi Luo
- State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil & Water Pollution, College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, PR China
| | - Ningfei Lei
- State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil & Water Pollution, College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, PR China
| | - Hongjie Kuang
- State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil & Water Pollution, College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, PR China
| | - Ziqing Li
- State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil & Water Pollution, College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, PR China
| |
Collapse
|
7
|
Wang W, Xiao S, Amanze C, Anaman R, Zeng W. Microbial community structures and their driving factors in a typical gathering area of antimony mining and smelting in South China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:50070-50084. [PMID: 35226270 DOI: 10.1007/s11356-022-19394-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/20/2022] [Indexed: 06/14/2023]
Abstract
This study investigated soil microbial community in a typical gathering area of antimony mining and smelting in South China. The physical and chemical properties of different soils (mining waste dumps, flotation tailings, and smelting slag) and depths (0-20 cm, 40-60 cm, and 80-100 cm) were compared. The results showed that antimony (Sb) and arsenic (As) were the main pollutants, and their concentrations were 5524.7 mg/kg and 3433.7 mg/kg, respectively. Xanthates were found in the flotation tailings and smelting slag, and the highest concentration was 585.1 mg/kg. The microbial communities were analyzed by high-throughput sequencing, and it was shown that Proteobacteria, Acidobacteria, Chlorobacterium, Bacteroides, and Actinomycetes were the dominant taxa at the phylum level. There were obvious differences in microbial community structure in different sites. The dominant microorganism in the mining site was Chujaibacter. Subgroup_2_unclassified and Gemmatimonadaceae_unclassified were the prevalent microorganisms in the flotation and smelting sites, respectively. As, Sb, and xanthates were the main factors affecting the diversity and composition of bacteria in the flotation tailings and smelting slag areas. Therefore, this study provides experimental guidance and a theoretical basis for soil antimony pollution quality assessment, biological treatment, and environmental remediation.
Collapse
Affiliation(s)
- Weinong Wang
- School of Minerals Processing and Bioengineering Central South University, Changsha, 410083, China
| | - Shanshan Xiao
- School of Minerals Processing and Bioengineering Central South University, Changsha, 410083, China
| | - Charles Amanze
- School of Minerals Processing and Bioengineering Central South University, Changsha, 410083, China
| | - Richmond Anaman
- School of Metallurgy and Environment, Central South University, Changsha, 410083, China
| | - Weimin Zeng
- School of Minerals Processing and Bioengineering Central South University, Changsha, 410083, China.
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China.
| |
Collapse
|
8
|
Effects of heavy metals on bacterial community structures in two lead-zinc tailings situated in northwestern China. Arch Microbiol 2021; 204:78. [PMID: 34954813 DOI: 10.1007/s00203-021-02699-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/25/2021] [Accepted: 11/06/2021] [Indexed: 10/19/2022]
Abstract
We evaluated the variations of bacterial communities in six heavy metal contaminated soils sampled from Yanzi Bian (YZB) and Shanping Cun (SPC) tailings located in northwestern China. Statistical analysis showed that both the heavy metals and soil chemical properties could affect the structure and diversity of the bacterial communities in the tailing soils. Cd, Cu, Zn, Cr, Pb, pH, SOM (soil organic matters), TP (total phosphorus) and TN (total nitrogen) were the main driving factors of the bacterial community variations. As a consequence, the relative abundances of certain bacterial phyla including Proteobacteria, Chloroflexi, Firmicutes, Nitrospirota and Bacteroidota were significantly increased in the tailing soils. Further, we found that the abundance increasement of these phyla were mainly contributed by certain species, such as s__unclassified_g__Thiobacillus (Proteobacteria), s__unclassified_g__Sulfobacillus (Firmicutes) and Leptospirillum ferriphilum (Nitrospirota). Thus, these species were considered to be strongly heavy metal tolerant. Together, our findings will provide a useful insight for further bioremediations of these contaminated areas.
Collapse
|
9
|
Wang F, Dong W, Zhao Z, Wang H, Li W, Chen G, Wang F, Zhao Y, Huang J, Zhou T. Heavy metal pollution in urban river sediment of different urban functional areas and its influence on microbial community structure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 778:146383. [PMID: 34030363 DOI: 10.1016/j.scitotenv.2021.146383] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 03/05/2021] [Accepted: 03/05/2021] [Indexed: 05/22/2023]
Abstract
In this study, the Songgang River (SR) was selected as a typical contaminated urban river in a highly urbanized city (Shenzhen) that is extensively polluted by heavy metals (HMs). Five representative sampling sites were selected from different urban functional areas along the SR, and the spatial and vertical distributions of HMs and the related environmental risk were investigated. In addition, the distribution variability, composition, and abundance of microbial communities, as well as the correlation between the abundance of the operational taxonomic units (OTUs) and the HM contents were analyzed. The spatial distribution of HMs in the sediment revealed wide variation among the different urban functional areas. Industrial and residential areas had higher HM contents, following the order of Cu > Zn > Ni > Cr > Pb. In addition, the vertical characterization (5-300 cm) of HM content showed a decreasing trend with depth, with a distinct layer around 120-180 cm that might have been caused by anthropogenic activity. An ecological risk assessment indicated that Cu, Ni, and Cr pose high potential risks in these industrial and residential areas (at the depth of 5-180 cm). Furthermore, microbial community analysis indicated that some HM-tolerant bacteria (e.g., Gallionella, Acidovorax, Arenimonas, Curvibacter, and Sideroxydans) were dominant in the 5-120 cm layer, corresponding to high HM contents. A canonical correspondence analysis and co-occurrence network further confirmed that there was a strong correlation among the urban functional areas, HM contents, and the abundance of microorganisms in the urban river sediment. The results of this study have the potential to provide a bio-augmentation strategy for the in-situ bioremediation of sediment contaminated by HMs.
Collapse
Affiliation(s)
- Feng Wang
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, PR China
| | - Wenyi Dong
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, PR China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Zilong Zhao
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, PR China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR China.
| | - Hongjie Wang
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, PR China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR China.
| | - Wenzheng Li
- School of Marine Science and Management, University of Sydney, Sydney, New South Wales 2220, Australia
| | - Guanhan Chen
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, PR China
| | - Feifei Wang
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, PR China
| | - Yue Zhao
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, PR China
| | - Jie Huang
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, PR China
| | - Ting Zhou
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, PR China
| |
Collapse
|
10
|
Tong H, Zheng C, Li B, Swanner ED, Liu C, Chen M, Xia Y, Liu Y, Ning Z, Li F, Feng X. Microaerophilic Oxidation of Fe(II) Coupled with Simultaneous Carbon Fixation and As(III) Oxidation and Sequestration in Karstic Paddy Soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:3634-3644. [PMID: 33411520 DOI: 10.1021/acs.est.0c05791] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Microaerophilic Fe(II)-oxidizing bacteria are often chemolithoautotrophs, and the Fe(III) (oxyhydr)oxides they form could immobilize arsenic (As). If such microbes are active in karstic paddy soils, their activity would help increase soil organic carbon and mitigate As contamination. We therefore used gel-stabilized gradient systems to cultivate microaerophilic Fe(II)-oxidizing bacteria from karstic paddy soil to investigate their capacity for Fe(II) oxidation, carbon fixation, and As sequestration. Stable isotope probing demonstrated the assimilation of inorganic carbon at a maximum rate of 8.02 mmol C m-2 d-1. Sequencing revealed that Bradyrhizobium, Cupriavidus, Hyphomicrobium, Kaistobacter, Mesorhizobium, Rhizobium, unclassified Phycisphaerales, and unclassified Opitutaceas were fixing carbon. Fe(II) oxidation produced Fe(III) (oxyhydr)oxides, which can absorb and/or coprecipitate As. Adding As(III) decreased the diversity of functional bacteria involved in carbon fixation, the relative abundance of predicted carbon fixation genes, and the amount of carbon fixed. Although the rate of Fe(II) oxidation was also lower in the presence of As(III), over 90% of the As(III) was sequestered after oxidation. The potential for microbially mediated As(III) oxidation was revealed by the presence of arsenite oxidase gene (aioA), denoting the potential of the Fe(II)-oxidizing and autotrophic microbial community to also oxidize As(III). Thisstudy demonstrates that carbon fixation coupled to Fe(II) oxidation can increase the carbon content in soils by microaerophilic Fe(II)-oxidizing bacteria, as well as accelerate As(III) oxidation and sequester it in association with Fe(III) (oxyhydr)oxides.
Collapse
Affiliation(s)
- Hui Tong
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou510650, China
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang550081, China
- Department of Geological and Atmospheric Sciences, Iowa State University, Ames50011, Iowa, United States
| | - Chunju Zheng
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang550081, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen518055, China
| | - Elizabeth D Swanner
- Department of Geological and Atmospheric Sciences, Iowa State University, Ames50011, Iowa, United States
| | - Chengshuai Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang550081, China
- CAS Center for Excellence in Quaternary Science and Global Change, Xi'an710061, China
| | - Manjia Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou510650, China
| | - Yafei Xia
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang550081, China
| | - Yuhui Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang550081, China
| | - Zengping Ning
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang550081, China
| | - Fangbai Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou510650, China
| | - Xinbin Feng
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang550081, China
- CAS Center for Excellence in Quaternary Science and Global Change, Xi'an710061, China
| |
Collapse
|
11
|
Xiao E, Cui J, Sun W, Jiang S, Huang M, Kong D, Wu Q, Xiao T, Sun X, Ning Z. Root microbiome assembly of As-hyperaccumulator Pteris vittata and its efficacy in arsenic requisition. Environ Microbiol 2021; 23:1959-1971. [PMID: 33145903 DOI: 10.1111/1462-2920.15299] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 10/25/2020] [Accepted: 10/29/2020] [Indexed: 11/29/2022]
Abstract
The assemblage of root-associated microorganisms plays important roles in improving their capability to adapt to environmental stress. Metal(loid) hyperaccumulators exhibit disparate adaptive capability compared to that of non-hyperaccumulators when faced with elevated contents of metal(loid)s. However, knowledge of the assemblage of root microbes of hyperaccumulators and their ecological roles in plant growth is still scarce. The present study used Pteris vittata as a model plant to study the microbial assemblage and its beneficial role in plant growth. We demonstrated that the assemblage of microbes from the associated bulk soil to the root compartment was based on their lifestyles. We used metagenomic analysis and identified that the assembled microbes were primarily involved in root-microbe interactions in P. vittata root. Notably, we identified that the assembled root microbiome played an important role in As requisition, which promoted the fitness and growth of P. vittata. This study provides new insights into the root microbiome and potential valuable knowledge to understand how the root microbiome contributes to the fitness of its host.
Collapse
Affiliation(s)
- Enzong Xiao
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Jinli Cui
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Weimin Sun
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental Science and Technology, Guangzhou, 510650, China
| | - Shiming Jiang
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Mengyan Huang
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Deguan Kong
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Qihang Wu
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Tangfu Xiao
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Xiaoxu Sun
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental Science and Technology, Guangzhou, 510650, China
| | - Zengping Ning
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China
| |
Collapse
|
12
|
Rajeev M, Sushmitha TJ, Aravindraja C, Toleti SR, Pandian SK. Exploring the impacts of heavy metals on spatial variations of sediment-associated bacterial communities. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 209:111808. [PMID: 33360289 DOI: 10.1016/j.ecoenv.2020.111808] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 05/12/2023]
Abstract
One of the fundamental objectives in modern ecology is to decipher how bacterial communities in natural environment respond to anthropogenic activities. In recent times consequences of marine pollution, especially with heavy metals (HMs) have received increasing attention. However, insights into the response of bacterial communities to HMs in coastal sediments of India remain scarce. Here, we analyzed HMs content in three areas, along the southern coastal region of India. Based on the calculated pollution indices viz., enrichment factor (EF), contamination factor (CF), geo-accumulation index (Igeo) and sediment quality guidelines (SQGs), the studied areas were classified as uncontaminated, moderately contaminated and significantly contaminated. To explore the response of bacterial community to HMs, sediment-associated microbiota was investigated using high-throughput 16S rRNA gene amplicon sequencing. The obtained metataxonomic results revealed that bacterial diversity and community composition varied considerably in significantly contaminated area than moderately contaminated and uncontaminated areas. Proportion of bacterial classes was higher for Gammaproteobacteria, Betaproteobacteria and Actinobacteria, but lower for Alphaproteobacteria and Flavobacteriia in significantly contaminated area. Also, samples of significantly contaminated area were dominated by well-documented metal-resistant bacterial genera such as Ralstonia and Arthrobacter. Canonical correspondence analysis (CCA) showed that spatial variability of bacterial community composition was strongly correlated with HMs content such as Chromium, Cadmium and Nickel. Further analysis using PICRUSt programme indicated that the predictive functional profile also varied considerably in significantly contaminated area. By linking HMs with bacterial compositional variations, the present study highlights the likely influence of HMs in shaping sedimentary microbiota of coastal regions.
Collapse
Affiliation(s)
- Meora Rajeev
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
| | - T J Sushmitha
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
| | | | - Subba Rao Toleti
- Water and Steam Chemistry Division, Bhabha Atomic Research Centre Facilities, Kalpakkam 603 102, Tamil Nadu, India
| | | |
Collapse
|
13
|
Martin-Pozas T, Sanchez-Moral S, Cuezva S, Jurado V, Saiz-Jimenez C, Perez-Lopez R, Carrey R, Otero N, Giesemann A, Well R, Calaforra JM, Fernandez-Cortes A. Biologically mediated release of endogenous N 2O and NO 2 gases in a hydrothermal, hypoxic subterranean environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 747:141218. [PMID: 32777502 DOI: 10.1016/j.scitotenv.2020.141218] [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: 06/02/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 06/11/2023]
Abstract
The migration of geogenic gases in continental areas with geothermal activity and active faults is an important process releasing greenhouse gases (GHG) to the lower troposphere. In this respect, caves in hypogenic environments are natural laboratories to study the compositional evolution of deep-endogenous fluids through the Critical Zone. Vapour Cave (Alhama, Murcia, Spain) is a hypogenic cave formed by the upwelling of hydrothermal CO2-rich fluids. Anomalous concentrations of N2O and NO2 were registered in the cave's subterranean atmosphere, averaging ten and five times the typical atmospheric backgrounds, respectively. We characterised the thermal conditions, gaseous compositions, sediments, and microbial communities at different depths in the cave. We did so to understand the relation between N-cycling microbial groups and the production and transformation of nitrogenous gases, as well as their coupled evolution with CO2 and CH4 during their migration through the Critical Zone to the lower troposphere. Our results showed an evident vertical stratification of selected microbial groups (Archaea and Bacteria) depending on the environmental parameters, including O2, temperature, and GHG concentration. Both the N2O isotope ratios and the predicted ecological functions of bacterial and archaeal communities suggest that N2O and NO2 emissions mainly depend on the nitrification by ammonia-oxidising microorganisms. Denitrification and abiotic reactions of the reactive intermediates NH2OH, NO, and NO2- are also plausible according to the results of the phylogenetic analyses of the microbial communities. Nitrite-dependent anaerobic methane oxidation by denitrifying methanotrophs of the NC10 phylum was also identified as a post-genetic process during migration of this gas to the surface. To the best of our knowledge, our report provides, for the first time, evidence of a niche densely populated by Micrarchaeia, which represents more than 50% of the total archaeal abundance. This raises many questions on the metabolic behaviour of this and other archaeal phyla.
Collapse
Affiliation(s)
- Tamara Martin-Pozas
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
| | - Sergio Sanchez-Moral
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
| | - Soledad Cuezva
- Plants and Ecosystems, Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium.
| | - Valme Jurado
- Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Institute of Natural Resources and Agricultural Biology (IRNAS-CSIC), 41012 Seville, Spain.
| | - Cesareo Saiz-Jimenez
- Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Institute of Natural Resources and Agricultural Biology (IRNAS-CSIC), 41012 Seville, Spain.
| | - Raul Perez-Lopez
- Geological Hazard Division, Geological Survey of Spain (IGME), 28003 Madrid, Spain.
| | - Raul Carrey
- Grup MAiMA, SGR Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), 08028 Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), UB, 08001 Barcelona, Spain.
| | - Neus Otero
- Grup MAiMA, SGR Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), 08028 Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), UB, 08001 Barcelona, Spain.
| | - Anette Giesemann
- Thünen Institute of Climate-Smart Agriculture, Federal Research Institute for Rural Areas, Forestry and Fisheries, 38116 Braunschweig, Germany.
| | - Reinhard Well
- Thünen Institute of Climate-Smart Agriculture, Federal Research Institute for Rural Areas, Forestry and Fisheries, 38116 Braunschweig, Germany.
| | - Jose M Calaforra
- Department of Biology and Geology, University of Almeria, 04120 Almeria, Spain.
| | | |
Collapse
|
14
|
Tartaglia M, Bastida F, Sciarrillo R, Guarino C. Soil Metaproteomics for the Study of the Relationships Between Microorganisms and Plants: A Review of Extraction Protocols and Ecological Insights. Int J Mol Sci 2020; 21:ijms21228455. [PMID: 33187080 PMCID: PMC7697097 DOI: 10.3390/ijms21228455] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/02/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022] Open
Abstract
Soil is a complex matrix where biotic and abiotic components establish a still unclear network involving bacteria, fungi, archaea, protists, protozoa, and roots that are in constant communication with each other. Understanding these interactions has recently focused on metagenomics, metatranscriptomics and less on metaproteomics studies. Metaproteomic allows total extraction of intracellular and extracellular proteins from soil samples, providing a complete picture of the physiological and functional state of the “soil community”. The advancement of high-performance mass spectrometry technologies was more rapid than the development of ad hoc extraction techniques for soil proteins. The protein extraction from environmental samples is biased due to interfering substances and the lower amount of proteins in comparison to cell cultures. Soil sample preparation and extraction methodology are crucial steps to obtain high-quality resolution and yields of proteins. This review focuses on the several soil protein extraction protocols to date to highlight the methodological challenges and critical issues for the application of proteomics to soil samples. This review concludes that improvements in soil protein extraction, together with the employment of ad hoc metagenome database, may enhance the identification of proteins with low abundance or from non-dominant populations and increase our capacity to predict functional changes in soil.
Collapse
Affiliation(s)
- Maria Tartaglia
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100 Benevento, Italy; (M.T.); (R.S.)
| | - Felipe Bastida
- CEBAS-CSIC, Department of Soil and Water Conservation, Campus Universitario de Espinardo, 30100 Murcia, Spain;
| | - Rosaria Sciarrillo
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100 Benevento, Italy; (M.T.); (R.S.)
| | - Carmine Guarino
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100 Benevento, Italy; (M.T.); (R.S.)
- Correspondence: ; Tel.: +39-824-305145
| |
Collapse
|
15
|
Zhao X, Sun Y, Huang J, Wang H, Tang D. Effects of soil heavy metal pollution on microbial activities and community diversity in different land use types in mining areas. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:20215-20226. [PMID: 32239406 DOI: 10.1007/s11356-020-08538-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 03/20/2020] [Indexed: 06/11/2023]
Abstract
Microbial activities and community structures play crucial roles in the soil environment and can be served as effective indicators to assess the ecological influence of heavy metal pollution in soil. This article selected soil samples from five land use types (mining area, mineral processing area, heap mining area, tailing area, and vegetable area) in the Shizishan mining area in Tongling, Anhui Province, China. The physicochemical properties, pollution characteristics, enzyme activities (catalase, urease, alkaline phosphatase, neutral phosphatase, cellulase, and sucrase), microbial biomass carbon (MBC), basal respiration (SBR), and metabolic entropy (qCO2) in soil were determined and compared, and the relationship between environmental factors and the microbial activities and community diversity was analyzed. The results showed that, according to the Nemerow's Pollution Index (PN), the values were the heap mining area (24.47) > mineral processing area (12.55) > mining area (9.81) > tailings area (6.02) > vegetable area (4.51). With the increase of heavy metal contamination in the sampling area, the six enzyme activities, MBC and SBR decreased, but the qCO2 increased. Principal coordinate analysis (PCoA) and canonical correlation analysis (CCA) showed that the land use types, soil moisture content (MC), heavy metal content, pH, MBC, SBR, and qCO2 were significantly affected by the microbial community. The most dominant phyla were Proteobacteria (34.73%), Bacteroidetes (9.25%), Acidobacteria (8.99%), and Chloroflexi (8.68%) at the phylum (0.01) level by a total of 18 phyla. It was also found that Firmicutes and Phormidium were more tolerant to heavy metals. These results contributed to an insight into key environmental variables shaping the microbial activities, community structure, and diversity under various land use types in mining area.
Collapse
Affiliation(s)
- Xingqing Zhao
- School of Environmental and Safety Engineering, Changzhou University, Gehu Middle Road 21, Changzhou, 213164, Jiangsu, People's Republic of China.
| | - Yu Sun
- School of Environmental and Safety Engineering, Changzhou University, Gehu Middle Road 21, Changzhou, 213164, Jiangsu, People's Republic of China
| | - Jian Huang
- School of Environmental and Safety Engineering, Changzhou University, Gehu Middle Road 21, Changzhou, 213164, Jiangsu, People's Republic of China
| | - Hui Wang
- School of Environmental and Safety Engineering, Changzhou University, Gehu Middle Road 21, Changzhou, 213164, Jiangsu, People's Republic of China
| | - Ding Tang
- School of Environmental and Safety Engineering, Changzhou University, Gehu Middle Road 21, Changzhou, 213164, Jiangsu, People's Republic of China
| |
Collapse
|
16
|
Lin Y, Ye Y, Hu Y, Shi H. The variation in microbial community structure under different heavy metal contamination levels in paddy soils. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 180:557-564. [PMID: 31128554 DOI: 10.1016/j.ecoenv.2019.05.057] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/15/2019] [Accepted: 05/17/2019] [Indexed: 05/25/2023]
Abstract
As a global pollution problem, heavy metal contamination poses a serious hazard to soil microorganisms which play an extremely important role in soil chemical cycling and ecological persistence. However, the effects that different levels of heavy metal contamination in soils have on microorganisms and the interactions between them are still unclear. The purpose of this research is to analyze the microbial structure under different levels of heavy metal contamination, find out heavy metal tolerant species under different environmental conditions, then provide useful reference for the bioremediation of contaminated farmland. In this study, 16s rRNA high-throughput sequencing technology was used to investigate the microbial communities in severe level (SL), moderate level (ML), light level (LL) and clean level (CL) of heavy metal contaminated soils, and the relationships between environment variables and microorganisms were analyzed. The results showed that the concentrations of heavy metals and soil physicochemical properties had various impacts on microbial community composition under different heavy metal contamination levels. Most dominant bacteria were in significant negative correlation with Cd in ML region, and significantly correlated with TN and OM in LL region. However, there was no significant correlation between dominant fungi and the physicochemical properties in LL region. And most of the dominant fungi were significantly correlated with the heavy metal concentrations in SL region. The bacterial phyla such as Proteobacteria, Acidobacteria and Bacteroidetes showed more tolerance with heavy metal contamination in SL, ML and LL regions, respectively. Meanwhile, the dominant fungi of Ascomycota, Basidiomycota, Chytridiomycota, Glomeromycota, Zygomycota and Rozellomycota showed stronger correlations with heavy metal contamination in SL and LL regions. These results indicated that some microorganisms had strong tolerance to heavy metal contamination and had certain heavy metals digestion ability, which can create an appropriate soil environment for the growth of food crops.
Collapse
Affiliation(s)
- Yaoben Lin
- Land Academy for National Development (LAND), Zhejiang University, Hangzhou, 310058, China; Land Ecological Restoration Engineering Technology Research Center of Shandong Province, Binzhou, 256600, China
| | - Yanmei Ye
- Land Academy for National Development (LAND), Zhejiang University, Hangzhou, 310058, China; Land Ecological Restoration Engineering Technology Research Center of Shandong Province, Binzhou, 256600, China.
| | - Yiming Hu
- Land Academy for National Development (LAND), Zhejiang University, Hangzhou, 310058, China; Land Ecological Restoration Engineering Technology Research Center of Shandong Province, Binzhou, 256600, China
| | - Haokun Shi
- Land Academy for National Development (LAND), Zhejiang University, Hangzhou, 310058, China; Land Ecological Restoration Engineering Technology Research Center of Shandong Province, Binzhou, 256600, China
| |
Collapse
|
17
|
Xiao S, Zhang Q, Chen X, Dong F, Chen H, Liu M, Ali I. Speciation Distribution of Heavy Metals in Uranium Mining Impacted Soils and Impact on Bacterial Community Revealed by High-Throughput Sequencing. Front Microbiol 2019; 10:1867. [PMID: 31456781 PMCID: PMC6700481 DOI: 10.3389/fmicb.2019.01867] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/29/2019] [Indexed: 11/30/2022] Open
Abstract
This study investigated the influence of heavy metals on bacterial community structure in a uranium mine. Soils from three differently polluted ditches (Yangchang ditch, Zhongchang ditch, and Sulimutang ditche) were collected from Zoige County, Sichuan province, China. Soil physicochemical properties and heavy metal concentrations were measured. Differences between bacterial communities were investigated using the high-throughput sequencing of the 16S rRNA genes. The obtained results demonstrated that bacterial richness index (Chao and Ace) were similar among three ditches, while the highest bacterial diversity index was detected in the severely contaminated soils. The compositions of bacterial communities varied among three examined sites, but Proteobacteria and Acidobacteria were abundant in all samples. Redundancy analysis revealed that soil organic matter, Cr and pH were the three major factors altering the bacterial community structure. Pearson correlation analysis indicated that the most significant correlations were observed between the contents of non-residual Cr and the abundances of bacterial genera, including Thiobacillus, Nitrospira, and other 10 genera. Among them, the abundances of Sphingomonas and Pseudomonas were significant and positively correlated with the concentrations of non-residual U and As. The results highlighted the factors influencing the bacterial community in uranium mines and contributed a better understanding of the effects of heavy metals on bacterial community structure by considering the fraction of heavy metals.
Collapse
Affiliation(s)
- Shiqi Xiao
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, China.,National Co-Innovation Center for Nuclear Waste Disposal and Environmental Safety, Southwest University of Science and Technology, Mianyang, China
| | - Qian Zhang
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, China.,National Co-Innovation Center for Nuclear Waste Disposal and Environmental Safety, Southwest University of Science and Technology, Mianyang, China
| | - Xiaoming Chen
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, China.,National Co-Innovation Center for Nuclear Waste Disposal and Environmental Safety, Southwest University of Science and Technology, Mianyang, China.,State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - Faqin Dong
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Hao Chen
- Sichuan Institute of Atomic Energy, Chengdu, China
| | - Mingxue Liu
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Imran Ali
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, China.,Institute of Biochemistry, University of Balochistan, Quetta, Pakistan
| |
Collapse
|
18
|
Antibiotic susceptibility of marine Planctomycetes. Antonie van Leeuwenhoek 2019; 112:1273-1280. [DOI: 10.1007/s10482-019-01259-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/19/2019] [Indexed: 10/27/2022]
|
19
|
Cui H, Liu LL, Dai JR, Yu XN, Guo X, Yi SJ, Zhou DY, Guo WH, Du N. Bacterial community shaped by heavy metals and contributing to health risks in cornfields. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 166:259-269. [PMID: 30273849 DOI: 10.1016/j.ecoenv.2018.09.096] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/18/2018] [Accepted: 09/21/2018] [Indexed: 05/21/2023]
Abstract
Scientists are increasingly aware that heavy metal contamination in soils, especially in farmland ecosystems, can negatively affect human health and alter the bacterial community that plays a critical role in plant growth and heavy metal accumulation. The goal of the present paper was to uncover how various heavy metals and non-metallic elements affect human health and bacterial diversity in cornfields and to explore the contribution of soil bacteria to heavy metal accumulation in crops. Soil samples were collected from five counties in Shandong Province, China, where abnormally high levels of heavy metals and metalloids were caused by mining and heavy industry. We calculated a hazard quotient (HQ) to evaluate the health risk these heavy metals cause and analyzed the soil bacterial community using 16S rRNA gene sequencing. The HQ results showed that As posed the greatest threat to human health followed by Pb although concentrations of all metals did not reach the health risk threshold. Meanwhile, principal component analysis (PCA) and redundancy analysis (RDA) revealed soil bacterial richness was significantly influenced by As, Ni, and Cr as well as pH and phosphorus, but not by the species diversity of aboveground weeds. The most abundant bacteria in our study region were heavy metal tolerant groups, specifically Actinobacteria and Proteobacteria. Moreover, correlation analysis suggested that Actinobacteria might reduce the phytoaccumulation of Cr, Cu, Zn, and Hg in corn, while Proteobacteria might weaken phytoaccumulation of Pb, Ni, As, and Cd. Our results verified that heavy metals play an important role in shaping the soil bacterial community. Using native bacteria in farmland provides a potential biological strategy for reducing the health risk posed by heavy metals related to food consumption.
Collapse
Affiliation(s)
- Han Cui
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Le-Le Liu
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Jie-Rui Dai
- Shandong Institute of Geological Survey, Jinan 250000, China
| | - Xiao-Na Yu
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Xiao Guo
- School of landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China
| | - Shi-Jie Yi
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Da-You Zhou
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Wei-Hua Guo
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Ning Du
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, Qingdao 266237, China.
| |
Collapse
|
20
|
Wu B, Hou S, Peng D, Wang Y, Wang C, Xu F, Xu H. Response of soil micro-ecology to different levels of cadmium in alkaline soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 166:116-122. [PMID: 30253286 DOI: 10.1016/j.ecoenv.2018.09.076] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 09/16/2018] [Accepted: 09/18/2018] [Indexed: 05/12/2023]
Abstract
Although the effect of heavy metal on soil microbial diversity was widely studied, the interaction among micro-ecological environment in heavy metal contaminated soil was less known. In this study, we systematically investigated the influence of cadmium (Cd) on soil micro-ecological environment (pH, nutrient content, soil enzyme activities, microbial biomass, bacterial and fungal diversities). Results showed that pH values slightly decreased with the Cd level increase, whereas the nutrient content including of Olsen-P (OSP), Alkeline-N (ALN), Olsen-K (OSK) and organic matter (OM) did not show significant difference in different treatments. In contrast to physicochemical properties, the biochemical qualities were easily influenced by Cd pollutant, resulting in soil microbial numbers and enzyme activities significantly decreased. High-throughput sequencing showed that microbial community composition was significantly affected by heavy metal. For bacteria, Actinobacteria abundance significantly decreased in Cd treated soil, corresponding to Proteobacteria and Firmicutes increased. For fungi, the most dominant phyla member (Ascomycota) was significantly decreased whereas Zygomycota significantly increased with Cd addition. These results further revealed the integral interrelation of micro-ecology environmental players under the stress of different Cd levels.
Collapse
Affiliation(s)
- Bin Wu
- Key Laboratory of Bio-Resource and Eco-Evironment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Siyu Hou
- Key Laboratory of Bio-Resource and Eco-Evironment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Dinghua Peng
- Key Laboratory of Bio-Resource and Eco-Evironment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Ying Wang
- Key Laboratory of Bio-Resource and Eco-Evironment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Can Wang
- Key Laboratory of Bio-Resource and Eco-Evironment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Fei Xu
- Key Laboratory of Bio-Resource and Eco-Evironment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Heng Xu
- Key Laboratory of Bio-Resource and Eco-Evironment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China.
| |
Collapse
|
21
|
Hemmat-Jou MH, Safari-Sinegani AA, Mirzaie-Asl A, Tahmourespour A. Analysis of microbial communities in heavy metals-contaminated soils using the metagenomic approach. ECOTOXICOLOGY (LONDON, ENGLAND) 2018; 27:1281-1291. [PMID: 30242595 DOI: 10.1007/s10646-018-1981-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/01/2018] [Indexed: 06/08/2023]
Abstract
Soil pollution occurring at mining sites has adverse impacts on soil microbial diversity. New approaches, such as metagenomics approach, have become a powerful tool to investigate biodiversity of soil microbial communities. In the current study, metagenomics approach was used to investigate the microbial diversity of soils contaminated with different concentrations of lead (Pb) and zinc (Zn). The contaminated soils were collected from a Pb and Zn mine. The soil total DNA was extracted and 16S rDNA genes were amplified using universal primers. The PCR amplicons were sequenced and bioinformatic analysis of metagenomes was conducted to identify prokaryotic diversity in the Pb- and Zn-contaminated soils. The results indicated that the ten most abundant bacteria in all samples were Solirubrobacter (Actinobacteria), Geobacter (Proteobacteria), Edaphobacter (Acidobacteria), Pseudomonas (Proteobacteria), Gemmatiomonas (Gemmatimonadetes), Nitrosomonas, Xanthobacter, and Sphingomonas (Proteobacteria), Pedobacter (Bacterioidetes), and Ktedonobacter (Chloroflexi), descendingly. Archaea were also numerous, and Nitrososphaerales which are important in the nitrogen cycle had the highest abundance in the samples. Although, alpha and beta diversity showed negative effects of Pb and Zn contamination on soil microbial communities, microbial diversity of the contaminated soils was not subjected to a significant change. This study provided valuable insights into microbial composition in heavy metals-contaminated soils.
Collapse
Affiliation(s)
- M H Hemmat-Jou
- Department of Soil Science, College of Agriculture, Bu-Ali Sina University, Hamedan, 6517838695, Iran.
| | - A A Safari-Sinegani
- Department of Soil Science, College of Agriculture, Bu-Ali Sina University, Hamedan, 6517838695, Iran
| | - A Mirzaie-Asl
- Department of Biotechnology, College of Agriculture, Bu-Ali Sina University, Hamedan, 6517838695, Iran
| | - A Tahmourespour
- Department of Basic Medical Sciences, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan, Iran
| |
Collapse
|
22
|
Kisková J, Perháčová Z, Vlčko L, Sedláková J, Kvasnová S, Pristaš P. The Bacterial Population of Neutral Mine Drainage Water of Elizabeth's Shaft (Slovinky, Slovakia). Curr Microbiol 2018; 75:988-996. [PMID: 29532150 PMCID: PMC7160218 DOI: 10.1007/s00284-018-1472-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 03/05/2018] [Indexed: 11/25/2022]
Abstract
Although neutral mine drainage is the less frequent subject of the interest than acid mine drainage, it can have adverse environmental effects caused mainly by precipitation of dissolved Fe. The aim of the study was to characterize the composition of bacterial population in environment with high concentration of iron and sulfur compounds represented by neutral mine drainage water of Elizabeth's shaft, Slovinky (Slovakia). Direct microscopic observations, cultivation methods, and 454 pyrosequencing of the 16S rRNA gene amplicons were used to examine the bacterial population. Microscopic observations identified iron-oxidizing Proteobacteria of the genera Gallionella and Leptothrix which occurrence was not changed during the years 2008-2014. Using 454 pyrosequencing, there were identified members of 204 bacterial genera that belonged to 25 phyla. Proteobacteria (69.55%), followed by Chloroflexi (10.31%) and Actinobacteria (4.24%) dominated the bacterial community. Genera Azotobacter (24.52%) and Pseudomonas (14.15%), followed by iron-oxidizing Proteobacteria Dechloromonas (11%) and Methyloversatilis (8.53%) were most abundant within bacterial community. Typical sulfur bacteria were detected with lower frequency, e.g., Desulfobacteraceae (0.25%), Desulfovibrionaceae (0.16%), or Desulfobulbaceae (0.11%). Our data indicate that the composition of bacterial community of the Elizabeth's shaft drainage water reflects observed neutral pH, high level of iron and sulfur ions in this aquatic habitat.
Collapse
Affiliation(s)
- Jana Kisková
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, 041 54, Košice, Slovakia.
| | - Zuzana Perháčová
- Department of Biology and General Ecology, Faculty of Ecology and Environmental Sciences, Technical University in Zvolen, 960 53, Zvolen, Slovakia
| | - Ladislav Vlčko
- Department of Biology and General Ecology, Faculty of Ecology and Environmental Sciences, Technical University in Zvolen, 960 53, Zvolen, Slovakia
| | - Jana Sedláková
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, 041 54, Košice, Slovakia
| | - Simona Kvasnová
- Department of Biology and Ecology, Faculty of Natural Science, Matej Bel University, 974 01, Banská Bystrica, Slovakia
| | - Peter Pristaš
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, 041 54, Košice, Slovakia
- Institute of Animal Physiology, Centre of Biosciences of Slovak Academy of Sciences, 041 01, Košice, Slovakia
| |
Collapse
|
23
|
Wiegand S, Jogler M, Jogler C. On the maverick Planctomycetes. FEMS Microbiol Rev 2018; 42:739-760. [DOI: 10.1093/femsre/fuy029] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/22/2018] [Indexed: 01/01/2023] Open
Affiliation(s)
- Sandra Wiegand
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
| | - Mareike Jogler
- Leibniz Institute DSMZ, Inhoffenstraße 7b, 38124 Braunschweig, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
| |
Collapse
|
24
|
Fernandes CC, Kishi LT, Lopes EM, Omori WP, Souza JAMD, Alves LMC, Lemos EGDM. Bacterial communities in mining soils and surrounding areas under regeneration process in a former ore mine. Braz J Microbiol 2018; 49:489-502. [PMID: 29452849 PMCID: PMC6066727 DOI: 10.1016/j.bjm.2017.12.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 11/06/2017] [Accepted: 12/04/2017] [Indexed: 01/19/2023] Open
Abstract
Human activities on the Earth's surface change the landscape of natural ecosystems. Mining practices are one of the most severe human activities, drastically altering the chemical, physical and biological properties of the soil environment. Bacterial communities in soil play an important role in the maintenance of ecological relationships. This work shows bacterial diversity, metabolic repertoire and physiological behavior in five ecosystems samples with different levels of impact. These ecosystems belong to a historical area in Iron Quadrangle, Minas Gerais, Brazil, which suffered mining activities until its total depletion without recovery since today. The results revealed Proteobacteria as the most predominant phylum followed by Acidobacteria, Verrucomicrobia, Planctomycetes, and Bacteroidetes. Soils that have not undergone anthropological actions exhibit an increase ability to degrade carbon sources. The richest soil with the high diversity was found in ecosystems that have suffered anthropogenic action. Our study shows profile of diversity inferring metabolic profile, which may elucidate the mechanisms underlying changes in community structure in situ mining sites in Brazil. Our data comes from contributing to know the bacterial diversity, relationship between these bacteria and can explore strategies for natural bioremediation in mining areas or adjacent areas under regeneration process in iron mining areas.
Collapse
Affiliation(s)
- Camila Cesário Fernandes
- UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - Luciano Takeshi Kishi
- UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - Erica Mendes Lopes
- UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - Wellington Pine Omori
- UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Biologia Aplicada à Agropecuária, Laboratório de Genética Aplicada, Jaboticabal, SP, Brazil
| | - Jackson Antonio Marcondes de Souza
- UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Biologia Aplicada à Agropecuária, Laboratório de Genética Aplicada, Jaboticabal, SP, Brazil
| | - Lucia Maria Carareto Alves
- UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - Eliana Gertrudes de Macedo Lemos
- UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Jaboticabal, SP, Brazil.
| |
Collapse
|
25
|
Li X, Meng D, Li J, Yin H, Liu H, Liu X, Cheng C, Xiao Y, Liu Z, Yan M. Response of soil microbial communities and microbial interactions to long-term heavy metal contamination. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 231:908-917. [PMID: 28886536 DOI: 10.1016/j.envpol.2017.08.057] [Citation(s) in RCA: 221] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 08/14/2017] [Accepted: 08/14/2017] [Indexed: 05/07/2023]
Abstract
Due to the persistence of metals in the ecosystem and their threat to all living organisms, effects of heavy metal on soil microbial communities were widely studied. However, little was known about the interactions among microorganisms in heavy metal-contaminated soils. In the present study, microbial communities in Non (CON), moderately (CL) and severely (CH) contaminated soils were investigated through high-throughput Illumina sequencing of 16s rRNA gene amplicons, and networks were constructed to show the interactions among microbes. Results showed that the microbial community composition was significantly, while the microbial diversity was not significantly affected by heavy metal contamination. Bacteria showed various response to heavy metals. Bacteria that positively correlated with Cd, e.g. Acidobacteria_Gp and Proteobacteria_thiobacillus, had more links between nodes and more positive interactions among microbes in CL- and CH-networks, while bacteria that negatively correlated with Cd, e.g. Longilinea, Gp2 and Gp4 had fewer network links and more negative interactions in CL and CH-networks. Unlike bacteria, members of the archaeal domain, i.e. phyla Crenarchaeota and Euryarchaeota, class Thermoprotei and order Thermoplasmatales showed only positive correlation with Cd and had more network interactions in CH-networks. The present study indicated that (i) the microbial community composition, as well as network interactions was shift to strengthen adaptability of microorganisms to heavy metal contamination, (ii) archaea were resistant to heavy metal contamination and may contribute to the adaption to heavy metals. It was proposed that the contribution might be achieved either by improving environment conditions or by cooperative interactions.
Collapse
Affiliation(s)
- Xiaoqi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China; School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Juan Li
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Hongwei Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Cheng Cheng
- School of Life Science, Hunan University of Science and Technology, Yuhu District, Xiangtan, Hunan Province 411201, China
| | - Yunhua Xiao
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Mingli Yan
- School of Life Science, Hunan University of Science and Technology, Yuhu District, Xiangtan, Hunan Province 411201, China.
| |
Collapse
|
26
|
Zhu YG, Xue XM, Kappler A, Rosen BP, Meharg AA. Linking Genes to Microbial Biogeochemical Cycling: Lessons from Arsenic. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:7326-7339. [PMID: 28602082 PMCID: PMC5871744 DOI: 10.1021/acs.est.7b00689] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The biotransformation of arsenic is highly relevant to the arsenic biogeochemical cycle. Identification of the molecular details of microbial pathways of arsenic biotransformation coupled with analyses of microbial communities by meta-omics can provide insights into detailed aspects of the complexities of this biocycle. Arsenic transformations couple to other biogeochemical cycles, and to the fate of both nutrients and other toxic environmental contaminants. Microbial redox metabolism of iron, carbon, sulfur, and nitrogen affects the redox and bioavailability of arsenic species. In this critical review we illustrate the biogeochemical processes and genes involved in arsenic biotransformations. We discuss how current and future metagenomic-, metatranscriptomic-, metaproteomic-, and metabolomic-based methods will help to decipher individual microbial arsenic transformation processes, and their connections to other biogeochemical cycle. These insights will allow future use of microbial metabolic capabilities for new biotechnological solutions to environmental problems. To understand the complex nature of inorganic and organic arsenic species and the fate of environmental arsenic will require integrating systematic approaches with biogeochemical modeling. Finally, from the lessons learned from these studies of arsenic biogeochemistry, we will be able to predict how the environment changes arsenic, and, in response, how arsenic biotransformations change the environment.
Collapse
Affiliation(s)
- Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xi-Mei Xue
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen 72076, Germany
| | - Barry P Rosen
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199, United States
| | - Andrew A Meharg
- Institute for Global Food Security, Queen’s University Belfast, Belfast BT9 5HN, United Kingdom
| |
Collapse
|
27
|
Yang Y, Mu Y, Zeng XC, Wu W, Yuan J, Liu Y, Guoji E, Luo F, Chen X, Li H, Wang J. Functional genes and thermophilic microorganisms responsible for arsenite oxidation from the shallow sediment of an untraversed hot spring outlet. ECOTOXICOLOGY (LONDON, ENGLAND) 2017; 26:490-501. [PMID: 28251437 DOI: 10.1007/s10646-017-1779-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/08/2017] [Indexed: 06/06/2023]
Abstract
Hot Springs have unique geochemical features. Microorganisms-mediated arsenite oxidation is one of the major biogeochemical processes occurred in some hot springs. This study aimed to understand the diversities of genes and microorganisms involved in arsenite oxidation from the outlet of an untraversed hot spring located at an altitude of 4226 m. Microcosm assay indicated that the microbial community from the hot spring was able to efficiently oxidize As(III) using glucose, lactic acid, yeast extract or sodium bicarbonate as the sole carbon source. The microbial community contained 7 phyla of microorganisms, of which Proteobacteria and Firmicutes are largely dominant; this composition is unique and differs significantly from those of other described hot springs. Twenty one novel arsenite oxidase genes were identified from the samples, which are affiliated with the arsenite oxidase families of α-Proteobacteria, β-Proteobacteria or Archaea; this highlights the high diversity of the arsenite-oxidizing microorganisms from the hot spring. A cultivable arsenite-oxidizer Chelatococcu sp. GHS311 was also isolated from the sample using enrichment technique. It can completely convert 75.0 mg/L As(III) into As(V) in 18 days at 45 °C. The arsenite oxidase of GHS311 shares the maximal sequence identity (84.7%) to that of Hydrogenophaga sp. CL3, a non-thermotolerant bacterium. At the temperature lower than 30 °C or higher than 65 °C, the growth of this strain was completely inhibited. These data help us to better understand the diversity and functional features of the thermophilic arsenite-oxidizing microorganisms from hot springs.
Collapse
Affiliation(s)
- Ye Yang
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| | - Yao Mu
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| | - Xian-Chun Zeng
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China.
| | - Weiwei Wu
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| | - Jie Yuan
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| | - Yichen Liu
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| | - E Guoji
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| | - Feng Luo
- School of Medicine, Jianghan University, Wuhan, 430056, People's Republic of China.
| | - Xiaoming Chen
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| | - Hao Li
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| | - Jianing Wang
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| |
Collapse
|
28
|
Ntougias S, Polkowska Ż, Nikolaki S, Dionyssopoulou E, Stathopoulou P, Doudoumis V, Ruman M, Kozak K, Namieśnik J, Tsiamis G. Bacterial Community Structures in Freshwater Polar Environments of Svalbard. Microbes Environ 2016; 31:401-409. [PMID: 27725345 PMCID: PMC5158112 DOI: 10.1264/jsme2.me16074] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Two thirds of Svalbard archipelago islands in the High Arctic are permanently covered with glacial ice and snow. Polar bacterial communities in the southern part of Svalbard were characterized using an amplicon sequencing approach. A total of 52,928 pyrosequencing reads were analyzed in order to reveal bacterial community structures in stream and lake surface water samples from the Fuglebekken and Revvatnet basins of southern Svalbard. Depending on the samples examined, bacterial communities at a higher taxonomic level mainly consisted either of Bacteroidetes, Betaproteobacteria, and Microgenomates (OP11) or Planctomycetes, Betaproteobacteria, and Bacteroidetes members, whereas a population of Microgenomates was prominent in 2 samples. At the lower taxonomic level, bacterial communities mostly comprised Microgenomates, Comamonadaceae, Flavobacteriaceae, Legionellales, SM2F11, Parcubacteria (OD1), and TM7 members at different proportions in each sample. The abundance of OTUs shared in common among samples was greater than 70%, with the exception of samples in which the proliferation of Planctomycetaceae, Phycisphaeraceae, and Candidatus Methylacidiphilum spp. lowered their relative abundance. A multi-variable analysis indicated that As, Pb, and Sb were the main environmental factors influencing bacterial profiles. We concluded that the bacterial communities in the polar aquatic ecosystems examined mainly consisted of freshwater and marine microorganisms involved in detritus mineralization, with a high proportion of zooplankton-associated taxa also being identified.
Collapse
Affiliation(s)
- Spyridon Ntougias
- Department of Environmental Engineering, Democritus University of Thrace
| | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Abstract
ABSTRACT
Soil microbial forensics can be defined as the study of how microorganisms can be applied to forensic investigations. The field of soil microbial forensics is of increasing interest and applies techniques commonly used in diverse disciplines in order to identify microbes and determine their abundances, complexities, and interactions with soil and surrounding objects. Emerging new techniques are also providing insights into the complexity of microbes in soil. Soil may harbor unique microbes that may reflect specific physical and chemical characteristics indicating site specificity. While applications of some of these techniques in the field of soil microbial forensics are still in early stages, we are still gaining insight into how microorganisms may be more robustly used in forensic investigations.
Collapse
|
30
|
Cordi A, Pagnout C, Devin S, Poirel J, Billard P, Dollard MA, Bauda P. Determination of physiological, taxonomic, and molecular characteristics of a cultivable arsenic-resistant bacterial community. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:13753-13763. [PMID: 25721523 DOI: 10.1007/s11356-014-3840-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 11/10/2014] [Indexed: 06/04/2023]
Abstract
A collection of 219 bacterial arsenic-resistant isolates was constituted from neutral arsenic mine drainage sediments. Isolates were grown aerobically or anaerobically during 21 days on solid DR2A medium using agar or gelan gum as gelling agent, with 7 mM As(III) or 20 mM As(V) as selective pressure. Interestingly, the sum of the different incubation conditions used (arsenic form, gelling agent, oxygen pressure) results in an overall increase of the isolate diversity. Isolated strains mainly belonged to Proteobacteria (63%), Actinobacteria (25%), and Bacteroidetes (10%). The most representative genera were Pseudomonas (20%), Acinetobacter (8%), and Serratia (15%) among the Proteobacteria; Rhodococcus (13%) and Microbacterium (5%) among Actinobacteria; and Flavobacterium (13%) among the Bacteroidetes. Isolates were screened for the presence of arsenic-related genes (arsB, ACR3(1), ACR3(2), aioA, arsM, and arrA). In this way, 106 ACR3(1)-, 74 arsB-, 22 aioA-, 14 ACR3(2)-, and one arsM-positive PCR products were obtained and sequenced. Analysis of isolate sensitivity toward metalloids (arsenite, arsenate, and antimonite) revealed correlations between taxonomy, sensitivity, and genotype. Antimonite sensitivity correlated with the presence of ACR3(1) mainly present in Bacteroidetes and Actinobacteria, and arsenite or antimonite resistance correlated with arsB gene presence. The presence of either aioA gene or several different arsenite carrier genes did not ensure a high level of arsenic resistance in the tested conditions.
Collapse
Affiliation(s)
- A Cordi
- Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), UMR 7360, CNRS, Université de Lorraine, Campus Bridoux, rue du Général Delestraint, 57070, Metz, France
| | | | | | | | | | | | | |
Collapse
|
31
|
Faure D, Bonin P, Duran R. Environmental microbiology as a mosaic of explored ecosystems and issues. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:13577-13598. [PMID: 26310700 DOI: 10.1007/s11356-015-5164-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 08/04/2015] [Indexed: 06/04/2023]
Abstract
Microbes are phylogenetically (Archaea, Bacteria, Eukarya, and viruses) and functionally diverse. They colonize highly varied environments and rapidly respond to and evolve as a response to local and global environmental changes, including those induced by pollutants resulting from human activities. This review exemplifies the Microbial Ecology EC2CO consortium's efforts to explore the biology, ecology, diversity, and roles of microbes in aquatic and continental ecosystems.
Collapse
Affiliation(s)
- Denis Faure
- Institut de Biologie Intégrative de la Cellule, CNRS-CEA-Université Paris-Sud, Saclay Plant Sciences, 91198, Gif-sur-Yvette cedex, France,
| | | | | |
Collapse
|
32
|
Metagenome of a microbial community inhabiting a metal-rich tropical stream sediment. PLoS One 2015; 10:e0119465. [PMID: 25742617 PMCID: PMC4351183 DOI: 10.1371/journal.pone.0119465] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 01/29/2015] [Indexed: 12/21/2022] Open
Abstract
Here, we describe the metagenome and functional composition of a microbial community in a historically metal-contaminated tropical freshwater stream sediment. The sediment was collected from the Mina Stream located in the Iron Quadrangle (Brazil), one of the world's largest mining regions. Environmental DNA was extracted and was sequenced using SOLiD technology, and a total of 7.9 Gbp was produced. A taxonomic profile that was obtained by comparison to the Greengenes database revealed a complex microbial community with a dominance of Proteobacteria and Parvarcheota. Contigs were recruited by bacterial and archaeal genomes, especially Candidatus Nitrospira defluvii and Nitrosopumilus maritimus, and their presence implicated them in the process of N cycling in the Mina Stream sediment (MSS). Functional reconstruction revealed a large, diverse set of genes for ammonium assimilation and ammonification. These processes have been implicated in the maintenance of the N cycle and the health of the sediment. SEED subsystems functional annotation unveiled a high degree of diversity of metal resistance genes, suggesting that the prokaryotic community is adapted to metal contamination. Furthermore, a high metabolic diversity was detected in the MSS, suggesting that the historical arsenic contamination is no longer affecting the prokaryotic community. These results expand the current knowledge of the microbial taxonomic and functional composition of tropical metal-contaminated freshwater sediments.
Collapse
|
33
|
Gillan DC, Roosa S, Kunath B, Billon G, Wattiez R. The long-term adaptation of bacterial communities in metal-contaminated sediments: a metaproteogenomic study. Environ Microbiol 2014; 17:1991-2005. [DOI: 10.1111/1462-2920.12627] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 09/05/2014] [Indexed: 11/29/2022]
Affiliation(s)
- David C. Gillan
- Proteomics and Microbiology Lab; Research Institute for Biosciences; Université de Mons; 20 place du Parc Mons B-7000 Belgium
| | - Stéphanie Roosa
- Proteomics and Microbiology Lab; Research Institute for Biosciences; Université de Mons; 20 place du Parc Mons B-7000 Belgium
| | - Benoit Kunath
- Proteomics and Microbiology Lab; Research Institute for Biosciences; Université de Mons; 20 place du Parc Mons B-7000 Belgium
| | - Gabriel Billon
- Géosystèmes Lab; UFR de Chimie; Lille-1 University, Sciences and Technologies; Villeneuve d'Ascq 59655 France
| | - Ruddy Wattiez
- Proteomics and Microbiology Lab; Research Institute for Biosciences; Université de Mons; 20 place du Parc Mons B-7000 Belgium
| |
Collapse
|
34
|
Proteomics of arsenic stress in the gram-positive organism Exiguobacterium sp. PS NCIM 5463. Appl Microbiol Biotechnol 2014; 98:6761-73. [PMID: 24931308 DOI: 10.1007/s00253-014-5873-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 05/22/2014] [Accepted: 05/25/2014] [Indexed: 10/25/2022]
Abstract
The general responses of microorganisms to environmental onslaughts are modulated by altering the gene expression pattern to reduce damage in the cell and produce compensating stress responses. The present study attempts to unravel the response of the Gram-positive Exiguobacterium sp. PS NCIM 5463 in the presence of [As(III)] and arsenate [As(V)] using comparative proteomics via two-dimension gel electrophoresis (2-DE) coupled with identification of proteins using matrix-assisted laser desorption/ionisation (MALDI-TOF/MALDI-TOF/TOF). Out of 926 Coomassie-stained proteins, 45 were differentially expressed (p < 0.05). Considering the resolution and abundance level, 24 spots (peptides) were subjected to MALDI analysis, identified and categorised into several functional categories, viz., nitrogen metabolism, energy and stress regulators, carbohydrate metabolism, protein synthesis components and others. A functional role of each protein is discussed in Exiguobacterium sp. PS 5463 under arsenic stress and validated at their transcript level using a quantitative real-time polymerase chain reaction. Unlike previous reports that unravel the responses toward arsenic stress in Gram-negative organisms, the present study identified new proteins under arsenic stress in a Gram-positive organism, Exiguobacterium sp. PS NCIM 5463, which could elucidate the physiology of organisms under arsenic stress.
Collapse
|
35
|
Lage OM, Bondoso J. Planctomycetes and macroalgae, a striking association. Front Microbiol 2014; 5:267. [PMID: 24917860 PMCID: PMC4042473 DOI: 10.3389/fmicb.2014.00267] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/15/2014] [Indexed: 12/31/2022] Open
Abstract
Planctomycetes are part of the complex microbial biofilm community of a wide range of macroalgae. Recently, some studies began to unveil the great diversity of Planctomycetes present in this microenvironment and the interactions between the two organisms. Culture dependent and independent methods revealed the existence of a great number of species but, so far, only less than 10 species have been isolated. Planctomycetes comprise the genera Rhodopirellula, Blastopirellula, and Planctomyces, Phycisphaera and the uncultured class OM190 and some other taxa have only been found in this association. Several factors favor the colonization of macroalgal surfaces by planctomycetes. Many species possess holdfasts for attachment. The macroalgae secrete various sulfated polysaccharides that are the substrate for the abundant sulfatases produced by planctomycetes. Specificity between planctomycetes and macroalgae seem to exist which may be related to the chemical nature of the polysaccharides produced by each macroalga. Furthermore, the peptidoglycan-free cell wall of planctomycetes allows them to resist the action of several antimicrobial compounds produced by the macroalgae or other bacteria in the biofilm community that are effective against biofouling by other microorganisms. Despite the increase in our knowledge on the successful planctomycetes-macroalgae association, a great effort to fully understand this interaction is needed.
Collapse
Affiliation(s)
- Olga M Lage
- Department of Biology, Faculty of Sciences, University of Porto Porto, Portugal ; CIMAR/CIIMAR - Interdisciplinary Centre for Marine and Environmental Research, University of Porto Porto, Portugal
| | - Joana Bondoso
- Department of Biology, Faculty of Sciences, University of Porto Porto, Portugal ; CIMAR/CIIMAR - Interdisciplinary Centre for Marine and Environmental Research, University of Porto Porto, Portugal
| |
Collapse
|
36
|
Pereira LB, Vicentini R, Ottoboni LMM. Changes in the bacterial community of soil from a neutral mine drainage channel. PLoS One 2014; 9:e96605. [PMID: 24796430 PMCID: PMC4010462 DOI: 10.1371/journal.pone.0096605] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 04/09/2014] [Indexed: 02/02/2023] Open
Abstract
Mine drainage is an important environmental disturbance that affects the chemical and biological components in natural resources. However, little is known about the effects of neutral mine drainage on the soil bacteria community. Here, a high-throughput 16S rDNA pyrosequencing approach was used to evaluate differences in composition, structure, and diversity of bacteria communities in samples from a neutral drainage channel, and soil next to the channel, at the Sossego copper mine in Brazil. Advanced statistical analyses were used to explore the relationships between the biological and chemical data. The results showed that the neutral mine drainage caused changes in the composition and structure of the microbial community, but not in its diversity. The Deinococcus/Thermus phylum, especially the Meiothermus genus, was in large part responsible for the differences between the communities, and was positively associated with the presence of copper and other heavy metals in the environmental samples. Other important parameters that influenced the bacterial diversity and composition were the elements potassium, sodium, nickel, and zinc, as well as pH. The findings contribute to the understanding of bacterial diversity in soils impacted by neutral mine drainage, and demonstrate that heavy metals play an important role in shaping the microbial population in mine environments.
Collapse
Affiliation(s)
- Letícia Bianca Pereira
- Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas – UNICAMP, Campinas, SP, Brazil
| | - Renato Vicentini
- Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas – UNICAMP, Campinas, SP, Brazil
| | - Laura M. M. Ottoboni
- Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas – UNICAMP, Campinas, SP, Brazil
- * E-mail:
| |
Collapse
|
37
|
Cébron A, Arsène-Ploetze F, Bauda P, Bertin PN, Billard P, Carapito C, Devin S, Goulhen-Chollet F, Poirel J, Leyval C. Rapid impact of phenanthrene and arsenic on bacterial community structure and activities in sand batches. MICROBIAL ECOLOGY 2014; 67:129-44. [PMID: 24189653 DOI: 10.1007/s00248-013-0313-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 10/10/2013] [Indexed: 05/08/2023]
Abstract
The impact of both organic and inorganic pollution on the structure of soil microbial communities is poorly documented. A short-time batch experiment (6 days) was conducted to study the impact of both types of pollutants on the taxonomic, metabolic and functional diversity of soil bacteria. For this purpose sand spiked with phenanthrene (500 mg kg(-1) sand) or arsenic (arsenite 0.66 mM and arsenate 12.5 mM) was supplemented with artificial root exudates and was inoculated with bacteria originated from an aged PAH and heavy-metal-polluted soil. The bacterial community was characterised using bacterial strain isolation, TTGE fingerprinting and proteomics. Without pollutant, or with phenanthrene or arsenic, there were no significant differences in the abundance of bacteria and the communities were dominated by Pseudomonas and Paenibacillus genera. However, at the concentrations used, both phenanthrene or arsenic were toxic as shown by the decrease in mineralisation activities. Using community-level physiological profiles (Biolog Ecoplates™) or differential proteomics, we observed that the pollutants had an impact on the community physiology, in particular phenanthrene induced a general cellular stress response with changes in the central metabolism and membrane protein synthesis. Real-time PCR quantification of functional genes and transcripts revealed that arsenic induced the transcription of functional arsenic resistance and speciation genes (arsB, ACR3 and aioA), while no transcription of PAH-degradation genes (PAH-dioxygenase and catechol-dioxygenase) was detected with phenanthrene. Altogether, in our tested conditions, pollutants do not have a major effect on community abundance or taxonomic composition but rather have an impact on metabolic and functional bacterial properties.
Collapse
Affiliation(s)
- A Cébron
- LIEC UMR7360, CNRS-Université de Lorraine, Faculté des Sciences et Technologies, BP 70239, 54506, Vandoeuvre-lès-Nancy Cedex, France,
| | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Cavalca L, Corsini A, Zaccheo P, Andreoni V, Muyzer G. Microbial transformations of arsenic: perspectives for biological removal of arsenic from water. Future Microbiol 2013; 8:753-68. [DOI: 10.2217/fmb.13.38] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Arsenic is present in many environments and is released by various natural processes and anthropogenic actions. Although arsenic is recognized to cause a wide range of adverse health effects in humans, diverse bacteria can metabolize it by detoxification and energy conservation reactions. This review highlights the current understanding of the ecology, biochemistry and genomics of these bacteria, and their potential application in the treatment of arsenic-polluted water.
Collapse
Affiliation(s)
- Lucia Cavalca
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milano, Italy.
| | - Anna Corsini
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milano, Italy
| | - Patrizia Zaccheo
- Dipartimento di Scienze Agrarie e Ambientali – Produzione, Territorio, Agroenergia (DiSAA), Università degli Studi di Milano, Milano, Italy
| | - Vincenza Andreoni
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milano, Italy
| | - Gerard Muyzer
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milano, Italy
- Institute for Biodiversity & Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| |
Collapse
|
39
|
Hettich RL, Pan C, Chourey K, Giannone RJ. Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities. Anal Chem 2013; 85:4203-14. [PMID: 23469896 PMCID: PMC3696428 DOI: 10.1021/ac303053e] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The availability of extensive genome information for many different microbes, including unculturable species in mixed communities from environmental samples, has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, and proteomic information. To this end, metaproteomics exploits the power of high-performance mass spectrometry for extensive characterization of the complete suite of proteins expressed by a microbial community in an environmental sample.
Collapse
|
40
|
The prokaryotic community of a historically mining-impacted tropical stream sediment is as diverse as that from a pristine stream sediment. Extremophiles 2013; 17:301-9. [PMID: 23389654 DOI: 10.1007/s00792-013-0517-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 01/10/2013] [Indexed: 10/27/2022]
Abstract
Mining negatively affects the environment by producing large quantities of metallic tailings, such as those contaminated with arsenic, with harmful consequences for human and aquatic life. A culture-independent molecular analysis was performed to assess the prokaryotic diversity and community structural changes of the tropical historically metal-contaminated Mina stream (MS) and the relatively pristine Mutuca stream (MTS) sediments. A total of 234 bacterial operational taxonomic units (OTUs) were affiliated with 14 (MS) and 17 (MTS) phyla and 53 OTUs were associated with two archaeal phyla. Although the bacterial community compositions of these sediments were markedly distinct, no significant difference in the diversity indices between the bacterial communities was observed. Additionally, the rarefaction and diversity indices indicated a higher bacterial diversity than archaeal diversity. Most of the OTUs were affiliated with the Proteobacteria and Bacteroidetes phyla. Alphaproteobacteria, Gemmatimonadetes and Actinobacteria were only found in the MS clone library. Crenarchaeal 16S rDNA sequences constituted 75 % of the MS archaeal clones, whereas Euryarchaeota were dominant in the MTS clones. Despite the markedly different characteristics of these streams, their bacterial communities harbor high diversity, suggesting that historically mining-impacted sediments promote diversity. The findings also provide basis for further investigation of members of Alphaproteobacteria as potential biological indicators of arsenic-rich sediments.
Collapse
|
41
|
Lami R, Jones LC, Cottrell MT, Lafferty BJ, Ginder-Vogel M, Sparks DL, Kirchman DL. Arsenite modifies structure of soil microbial communities and arsenite oxidization potential. FEMS Microbiol Ecol 2013; 84:270-9. [DOI: 10.1111/1574-6941.12061] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2011] [Revised: 12/02/2012] [Accepted: 12/08/2012] [Indexed: 02/06/2023] Open
Affiliation(s)
| | - L. Camille Jones
- Department of Plant and Soil Sciences; University of Delaware; Newark; DE; USA
| | | | - Brandon J. Lafferty
- Department of Plant and Soil Sciences; University of Delaware; Newark; DE; USA
| | - M. Ginder-Vogel
- Department of Plant and Soil Sciences; University of Delaware; Newark; DE; USA
| | - Donald L. Sparks
- Department of Plant and Soil Sciences; University of Delaware; Newark; DE; USA
| | - David L. Kirchman
- School of Marine Science and Policy; University of Delaware; Lewes; DE; USA
| |
Collapse
|
42
|
Sacheti P, Bhonsle H, Patil R, Kulkarni MJ, Srikanth R, Gade W. Arsenomics of Exiguobacterium sp. PS (NCIM 5463). RSC Adv 2013. [DOI: 10.1039/c3ra40897c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
|
43
|
Hettich RL, Sharma R, Chourey K, Giannone RJ. Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities. Curr Opin Microbiol 2012; 15:373-80. [PMID: 22632760 DOI: 10.1016/j.mib.2012.04.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 04/27/2012] [Indexed: 10/28/2022]
Abstract
The availability of genome information for microbial consortia, including unculturable species, from environmental samples has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, and proteomic information. This provides a unique opportunity to characterize the molecular activities and interactions of these microbial systems at a comprehensive level never before possible. Such information not only provides details about the organizational, functional, and metabolic activities of such systems, but also the untapped reserve of molecular activities that might be invoked and exploited under certain environmental conditions. Since bacteria naturally exist in complex ecosystems, it is imperative to develop and utilize analytical approaches that can provide molecular level details on systems consisting of mixed microbial membership. This is the realm of metaproteomics-the characterization of the complement of proteins expressed by a microbial community in an environmental sample.
Collapse
|
44
|
Bonin P, Faure D. Environmental microbiology at the heart of ecosystem dynamics. Res Microbiol 2011; 162:817-9. [PMID: 22000989 DOI: 10.1016/j.resmic.2011.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
|
45
|
Unsuspected diversity of arsenite-oxidizing bacteria as revealed by widespread distribution of the aoxB gene in prokaryotes. Appl Environ Microbiol 2011; 77:4685-92. [PMID: 21571879 DOI: 10.1128/aem.02884-10] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, new strains were isolated from an environment with elevated arsenic levels, Sainte-Marie-aux-Mines (France), and the diversity of aoxB genes encoding the arsenite oxidase large subunit was investigated. The distribution of bacterial aoxB genes is wider than what was previously thought. AoxB subfamilies characterized by specific signatures were identified. An exhaustive analysis of AoxB sequences from this study and from public databases shows that horizontal gene transfer has likely played a role in the spreading of aoxB in prokaryotic communities.
Collapse
|