1
|
Rob MM, Akhter D, Islam T, Bhattacharjya DK, Shoaib Khan MS, Islam F, Chen J. Copper stress in rice: Perception, signaling, bioremediation and future prospects. JOURNAL OF PLANT PHYSIOLOGY 2024; 302:154314. [PMID: 39033671 DOI: 10.1016/j.jplph.2024.154314] [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: 03/04/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024]
Abstract
Copper (Cu) is an indispensable micronutrient for plants, animals, and microorganisms and plays a vital role in different physiological processes. However, excessive Cu accumulation in agricultural soil, often through anthropogenic action, poses a potential risk to plant health and crop productivity. This review article provided a comprehensive overview of the available information regarding Cu dynamics in agricultural soils, major sources of Cu contamination, factors influencing its mobility and bioavailability, and mechanisms of Cu uptake and translocation in rice plants. This review examined the impact of Cu toxicity on the germination, growth, and photosynthesis of rice plants. It also highlighted molecular mechanisms underlying Cu stress signaling and the plant defense strategy, involving chelation, compartmentalization, and antioxidant responses. This review also identified significant areas that need further research, such as Cu uptake mechanism in rice, Cu signaling process, and the assessment of Cu-polluted paddy soil and rice toxicity under diverse environmental conditions. The development of rice varieties with reduced Cu accumulation through comprehensive breeding programs is also necessary. Regulatory measures, fungicide management, plant selection, soil and environmental investigation are recommended to prevent Cu buildup in agricultural lands to achieve sustainable agricultural goals.
Collapse
Affiliation(s)
- Md Mahfuzur Rob
- Department of Horticulture, Faculty of Agriculture, Sylhet Agricultural University, Sylhe, 3100, Bangladesh
| | - Delara Akhter
- Department of Genetics and Plant Breeding, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Tariqul Islam
- Department of Agricultural Construction and Environmental Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Debu Kumar Bhattacharjya
- Department of Biochemistry, Sher-e-Bangla Agricultural University, Sherebangla Nagar, Dhaka, 1207, Bangladesh
| | | | - Faisal Islam
- International Genome Center, Jiangsu University, Zhenjiang, 212013, China.
| | - Jian Chen
- International Genome Center, Jiangsu University, Zhenjiang, 212013, China.
| |
Collapse
|
2
|
Longan ER, Fay JC. The distribution of beneficial mutational effects between two sister yeast species poorly explains natural outcomes of vineyard adaptation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597243. [PMID: 38895255 PMCID: PMC11185594 DOI: 10.1101/2024.06.03.597243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Domesticated strains of Saccharomyces cerevisiae have adapted to resist copper and sulfite, two chemical stressors commonly used in winemaking. S. paradoxus, has not adapted to these chemicals despite being consistently present in sympatry with S. cerevisiae in vineyards. This contrast represents a case of apparent evolutionary constraints favoring greater adaptive capacity in S. cerevisiae. In this study, we used a comparative mutagenesis approach to test whether S. paradoxus is mutationally constrained with respect to acquiring greater copper and sulfite resistance. For both species, we assayed the rate, effect size, and pleiotropic costs of resistance mutations and sequenced a subset of 150 mutants isolated from our screen. We found that the distributions of mutational effects displayed by the two species were very similar and poorly explained the natural pattern. We also found that chromosome VIII aneuploidy and loss of function mutations in PMA1 confer copper resistance in both species, whereas loss of function mutations in REG1 were only a viable route to copper resistance in S. cerevisiae. We also observed a single de novo duplication of the CUP1 gene in S. paradoxus but none in S. cerevisiae. For sulfite, loss of function mutations in RTS1 and KSP1 confer resistance in both species, but mutations in RTS1 have larger average effects in S. paradoxus. Our results show that even when the distributions of mutational effects are largely similar, species can differ in the adaptive paths available to them. They also demonstrate that assays of the distribution of mutational effects may lack predictive insight concerning adaptive outcomes.
Collapse
Affiliation(s)
- Emery R. Longan
- University of Rochester, Department of Biology, Rochester, NY, 14620 USA
| | - Justin C. Fay
- University of Rochester, Department of Biology, Rochester, NY, 14620 USA
| |
Collapse
|
3
|
Mallano AI, Yu J, Dina T, Li F, Ling T, Ahmad N, Bennetzen J, Tong W. Soil and fine root-associated microbial communities are niche dependent and influenced by copper fungicide treatment during tea plant cultivation. HORTICULTURE RESEARCH 2023; 10:uhac285. [PMID: 36938566 PMCID: PMC10015337 DOI: 10.1093/hr/uhac285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 12/08/2022] [Indexed: 06/18/2023]
Affiliation(s)
| | | | - Tabys Dina
- School of Medicine, Nazarbayev University, Nur-Sultan 020000, Kazakhstan
| | - Fangdong Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
- School of Science, Anhui Agricultural University, Hefei 230036, China
| | - Tiejun Ling
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Naveed Ahmad
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | | | - Wei Tong
- Corresponding authors. E-mail: ;
| |
Collapse
|
4
|
Steiner M, Pingel M, Falquet L, Giffard B, Griesser M, Leyer I, Preda C, Uzman D, Bacher S, Reineke A. Local conditions matter: Minimal and variable effects of soil disturbance on microbial communities and functions in European vineyards. PLoS One 2023; 18:e0280516. [PMID: 36706082 PMCID: PMC9882891 DOI: 10.1371/journal.pone.0280516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 12/29/2022] [Indexed: 01/28/2023] Open
Abstract
Soil tillage or herbicide applications are commonly used in agriculture for weed control. These measures may also represent a disturbance for soil microbial communities and their functions. However, the generality of response patterns of microbial communities and functions to disturbance have rarely been studied at large geographical scales. We investigated how a soil disturbance gradient (low, intermediate, high), realized by either tillage or herbicide application, affects diversity and composition of soil bacterial and fungal communities as well as soil functions in vineyards across five European countries. Microbial alpha-diversity metrics responded to soil disturbance sporadically, but inconsistently across countries. Increasing soil disturbance changed soil microbial community composition at the European level. However, the effects of soil disturbance on the variation of microbial communities were smaller compared to the effects of location and soil covariates. Microbial respiration was consistently impaired by soil disturbance, while effects on decomposition of organic substrates were inconsistent and showed positive and negative responses depending on the respective country. Therefore, we conclude that it is difficult to extrapolate results from one locality to others because microbial communities and environmental conditions vary strongly over larger geographical scales.
Collapse
Affiliation(s)
- Magdalena Steiner
- Ecology and Evolution, Department of Biology, University of Fribourg, Fribourg, Switzerland
- * E-mail: (MS); (MP)
| | - Martin Pingel
- Department of Applied Ecology, Geisenheim University, Geisenheim, Germany
- * E-mail: (MS); (MP)
| | - Laurent Falquet
- Ecology and Evolution, Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Brice Giffard
- Bordeaux Sciences Agro, UMR 1065 SAVE Santé et Agroécologie du Vignoble, INRA, ISVV, Gradignan, France
| | - Michaela Griesser
- Department of Crop Sciences, Institute of Viticulture and Pomology, University of Natural Resources and Life Sciences Vienna (BOKU), Tulln, Austria
| | - Ilona Leyer
- Department of Applied Ecology, Geisenheim University, Geisenheim, Germany
| | - Cristina Preda
- Department of Natural Sciences, Aleea Universitatii, Ovidius University of Constanta, Constanta, Romania
| | - Deniz Uzman
- Department of Crop Protection, Geisenheim University, Geisenheim, Germany
| | - Sven Bacher
- Ecology and Evolution, Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Annette Reineke
- Department of Crop Protection, Geisenheim University, Geisenheim, Germany
| |
Collapse
|
5
|
Marques ACR, Hindersmann J, Trentin E, De Conti L, Drescher GL, Somavilla A, Tabaldi LA, Schawalbert R, Birck TP, Nicoloso FT, Brunetto G. Physiological and biochemical characterization of copper-toxicity tolerance mechanism in grass species native to Pampa Biome and Atlantic Forest for use in phytoremediation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:5076-5088. [PMID: 35978233 DOI: 10.1007/s11356-022-22570-3] [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: 08/13/2021] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Orchards and vineyards account for significant copper (Cu) accumulation in the soil due to frequent Cu fungicide applications to control leaf diseases. Although grass species are distributed in these areas likely because of their physiological mechanisms to combat Cu toxicity-related stress, the aim of the present study is to identify grass species presenting biochemical-physiological responses that feature adaptive Cu toxicity tolerance mechanisms. Three grass species native to the Pampa and Atlantic Forest biomes (Paspalum notatum, P. plicatulum, and P. urvillei) and an exotic species (Cynodon dactylon) were tested. Plants were cultivated in pots filled with 4 kg of typic Hapludalf soil, under two Cu availability, control, and toxicity conditions (80 mg Cu kg soil-1). Photosynthetic parameters, relative growth rate, root dry matter, shoot dry matter, the activity of stress-fighting enzymes (superoxide dismutase and guaiacol peroxidase), root biometry, soluble organic carbon, soil pH, and electrical conductivity were evaluated. P. notatum and P. urvillei have physiological characteristics that allow high translocation factor and Cu accumulation in the root and shoot, and it allows their use in phytoremediation processes due to (1) greater activity of stress-fighting enzymes such as POD in the shoot; (2) to larger diameter roots, which allow greater Cu complexation in them - they are lesser sensitive to stress caused by Cu than the other species; and (3) greater soluble organic carbon exudation in the rhizosphere than species P. plicatulum and C. dactylon, which can complex Cu2+ and reduce the presence of forms toxic to plants.
Collapse
Affiliation(s)
- Anderson Cesar Ramos Marques
- Department of Agricultural Sciences, Regional Integrated University of Alto Uruguai and Missões (URI), Street Assis Brazil, 709, Frederico Westphalen, RS, 98400-000, Brazil.
| | - Jacson Hindersmann
- Department of Soil Science, Federal University of Santa Maria, Rural Science Centre, Roraima Avenue, 1000, Santa Maria, RS, 97105-900, Brazil
| | - Edicarla Trentin
- Department of Soil Science, Federal University of Santa Maria, Rural Science Centre, Roraima Avenue, 1000, Santa Maria, RS, 97105-900, Brazil
| | - Lessandro De Conti
- Farroupilha Federal Institute of Science and Technology (IFFa), Street Fábio João Andolhe, 1100, Santo Augusto, RS, 98590-000, Brazil
| | - Gerson Laerson Drescher
- University of Arkansas System Division of Agriculture, 1366 West Altheimer Drive, Fayetteville, AR, 72704, USA
| | - André Somavilla
- Department of Soil Science, Federal University of Santa Maria, Rural Science Centre, Roraima Avenue, 1000, Santa Maria, RS, 97105-900, Brazil
| | - Luciane Almeri Tabaldi
- Department of Biology, Federal University of Santa Maria, Natural Science Centre, Roraima Avenue, 1000, Santa Maria, RS, 97105-900, Brazil
| | - Raíssa Schawalbert
- Department of Biology, Federal University of Santa Maria, Natural Science Centre, Roraima Avenue, 1000, Santa Maria, RS, 97105-900, Brazil
| | - Thalia Preussler Birck
- Department of Biology, Federal University of Santa Maria, Natural Science Centre, Roraima Avenue, 1000, Santa Maria, RS, 97105-900, Brazil
| | - Fernando Teixeira Nicoloso
- Department of Biology, Federal University of Santa Maria, Natural Science Centre, Roraima Avenue, 1000, Santa Maria, RS, 97105-900, Brazil
| | - Gustavo Brunetto
- Department of Soil Science, Federal University of Santa Maria, Rural Science Centre, Roraima Avenue, 1000, Santa Maria, RS, 97105-900, Brazil
| |
Collapse
|
6
|
De Bernardi A, Marini E, Casucci C, Tiano L, Marcheggiani F, Vischetti C. Copper Monitoring in Vineyard Soils of Central Italy Subjected to Three Antifungal Treatments, and Effects of Sub-Lethal Copper Doses on the Earthworm Eisenia fetida. TOXICS 2022; 10:toxics10060310. [PMID: 35736918 PMCID: PMC9228243 DOI: 10.3390/toxics10060310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/25/2022] [Accepted: 06/06/2022] [Indexed: 01/27/2023]
Abstract
The extensive employment of copper-based fungicides has increased copper concentration in vineyard soils. The present study's objectives were to monitor copper concentration in two vineyard soils during two cropping seasons and study the ecotoxicological effects on the earthworm Eisenia fetida. Total, soluble, and bioavailable copper fractions were measured at the end of two cropping seasons and different depths in two vineyards of central Italy, characterised by three anticryptogamic control methods: copper compounds, chitosan, and combined treatments of them. A laboratory experiment to assess the effects on Eisenia fetida was conducted with soil samples collected in the vineyards with a mean copper concentration of 60 mg/kg and two higher concentrations of 90 and 150 mg/kg. Results showed low levels of total copper concentration in the first 20 cm of soils, regardless of antifungal treatment, highlighting prudent management of the vineyards under study, but the soluble fractions showed a significant increase in all samples during the two cropping seasons. At the dose of 150 mg/kg, earthworms suffer during the first two days, showing weight loss and DNA damage, but they are able to recover until day 28, showing no permanent harm at this copper concentration in soil.
Collapse
Affiliation(s)
- Arianna De Bernardi
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy; (A.D.B.); (E.M.); (C.C.)
| | - Enrica Marini
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy; (A.D.B.); (E.M.); (C.C.)
| | - Cristiano Casucci
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy; (A.D.B.); (E.M.); (C.C.)
| | - Luca Tiano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy; (L.T.); (F.M.)
| | - Fabio Marcheggiani
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy; (L.T.); (F.M.)
| | - Costantino Vischetti
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy; (A.D.B.); (E.M.); (C.C.)
- Correspondence: ; Tel.: +39-071-2204264
| |
Collapse
|
7
|
Yang M, Liu Y, Liao Y, Tang C, Wen Z, Fazal A, Yang R, Qi J, Hong Z, Li Y, Yang Y. Excess copper promotes catabolic activity of gram-positive bacteria and resistance of gram-negative bacteria but inhibits fungal community in soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:22602-22612. [PMID: 34792767 DOI: 10.1007/s11356-021-17510-6] [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: 07/28/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
The extensive use of copper fungicides has resulted in significant non-target effects on soil microbial communities. However, the documented effects are often variable and contradictory, depending on the methods used to assess them. In this study, we examined the effects of copper accumulation in surface soils on microbial catabolic activity, active biomass and composition, and sensitive bacterial species. The community-level catabolic profiles (CLCPs) showed that both normal (50 mg CuSO4 kg-1 soil) and high dosages (tenfold rate) of CuSO4 significantly increased the catabolic diversity of gram-positive bacteria, while the high dosage increased the overall catabolic activity of gram-negative bacteria. The phospholipid fatty acid (PLFA) analysis showed that the high dosage reduced the biomass of gram-positive bacteria by 27% but did not affect that of gram-negative bacteria. In comparison, the normal and high dosages decreased the fungal biomass by 34% and 58%, respectively. Furthermore, 16S rRNA-denaturing gradient gel electrophoresis (DGGE) fingerprint revealed that more than two-thirds of identified bands belonged to gram-negative bacteria. Some Cu-resistant gram-negative bacterial genera, such as Actinobacterium, Pseudomonas, and Proteobacterium, were detected in the soil to which the high dosage of CuSO4 had been applied. In conclusion, an excess application of CuSO4 increased the catabolic diversity of gram-positive bacteria and induced resistance in gram-negative bacteria, whereas the active fungal community displayed a dosage-dependent response to CuSO4 and can thus be used as a sensitive indicator of copper contamination.
Collapse
Affiliation(s)
- Minkai Yang
- Institute of Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yehao Liu
- Institute of Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yonghui Liao
- Institute of Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Caixian Tang
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Zhongling Wen
- Institute of Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Aliya Fazal
- Institute of Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Rongwu Yang
- Institute of Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jinliang Qi
- Institute of Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Zhi Hong
- Institute of Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
| | - Yongchun Li
- Institute of Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
- State Key Laboratory of Subtropical Silviculture, College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou, 311300, China.
| | - Yonghua Yang
- Institute of Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
| |
Collapse
|
8
|
Sunilkumar CR, Stephen-Victor E, Naripogu KB, Samanth Kumar J, Nuthan BR, Marulasiddaswamy KM, Kini KR, Geetha N. Differential Multi-cellularity Is Required for the Adaptation for Bacillus licheniformis to Withstand Heavy Metals Toxicity. Indian J Microbiol 2021; 61:524-529. [PMID: 34744208 DOI: 10.1007/s12088-021-00958-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/14/2021] [Indexed: 12/28/2022] Open
Abstract
Bacillus licheniformis is a multi-metal tolerant bacteria, isolated from the paddy rhizospheric soil sample. Upon the multiple metal toxicity, B. licheniformis altered their phenotypic/morphogenesis. Here we examined the effects of cadmium (Cd2+), chromium (Cr2+), and mercury (Hg2+) on the morphogenesis of B. licheniformis in comparison to control. We found that the ability of bacteria to grow effectively in presence of cadmium and chromium comes at a cost of acquiring cell density-driven mobility and reformation of filamentous to donut shape respectively. In particular, when bacteria grown on mercury it showed the bacteriostatic strategy to resist mercury. Furthermore, the findings suggest a large variation in the production of exo-polysaccharides (EPS) and suggest the possible role of EPS in gaining resistance to cadmium and chromium. Together this study identifies previously unknown characteristics of B. licheniformis to participate in bioremediation and provides the first evidence on positive effects of bacterial morphogenesis and the involvement of EPS in bacteria to resisting metal toxicity.
Collapse
Affiliation(s)
- Channarayapatna-Ramesh Sunilkumar
- Global Association of Scientific Young Minds (GASYM), Mysuru, India.,Research Institute for Interdisciplinary Sciences, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530 Japan.,Laboratory of Microbial Metabolism and Stress Response, Department of Biotechnology, SDM and MMK College for Women, Mysuru, India
| | - Emmanuel Stephen-Victor
- Global Association of Scientific Young Minds (GASYM), Mysuru, India.,Department of Pediatrics, Harvard Medical School, Boston, USA
| | - Kishore Babu Naripogu
- Global Association of Scientific Young Minds (GASYM), Mysuru, India.,Research Institute for Interdisciplinary Sciences, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530 Japan
| | - J Samanth Kumar
- Department of Studies in Biotechnology, Manasagangotri, University of Mysore, Mysuru, India
| | - Bettadapura Rameshgowda Nuthan
- Global Association of Scientific Young Minds (GASYM), Mysuru, India.,Department of Studies in Microbiology, Manasagangotri, University of Mysore, Mysuru, India
| | - K M Marulasiddaswamy
- Global Association of Scientific Young Minds (GASYM), Mysuru, India.,Department of Studies in Biotechnology, Manasagangotri, University of Mysore, Mysuru, India
| | | | - Nagaraja Geetha
- Global Association of Scientific Young Minds (GASYM), Mysuru, India.,Department of Studies in Biotechnology, Manasagangotri, University of Mysore, Mysuru, India
| |
Collapse
|
9
|
A Smart and Sustainable Future for Viticulture Is Rooted in Soil: How to Face Cu Toxicity. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11030907] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In recent decades, agriculture has faced the fundamental challenge of needing to increase food production and quality in order to meet the requirements of a growing global population. Similarly, viticulture has also been undergoing change. Several countries are reducing their vineyard areas, and several others are increasing them. In addition, viticulture is moving towards higher altitudes and latitudes due to climate change. Furthermore, global warming is also exacerbating the incidence of fungal diseases in vineyards, forcing farmers to apply agrochemicals to preserve production yields and quality. The repeated application of copper (Cu)-based fungicides in conventional and organic farming has caused a stepwise accumulation of Cu in vineyard soils, posing environmental and toxicological threats. High Cu concentrations in soils can have multiple impacts on agricultural systems. In fact, it can (i) alter the chemical-physical properties of soils, thus compromising their fertility; (ii) induce toxicity phenomena in plants, producing detrimental effects on growth and productivity; and (iii) affect the microbial biodiversity of soils, thereby influencing some microbial-driven soil processes. However, several indirect (e.g., management of rhizosphere processes through intercropping and/or fertilization strategies) and direct (e.g., exploitation of vine resistant genotypes) strategies have been proposed to restrain Cu accumulation in soils. Furthermore, the application of precision and smart viticulture paradigms and their related technologies could allow a timely, localized and balanced distribution of agrochemicals to achieve the required goals. The present review highlights the necessity of applying multidisciplinary approaches to meet the requisites of sustainability demanded of modern viticulture.
Collapse
|
10
|
Molecular characterization, antibiogram and distribution of zntA gene in zinc-resistant Escherichia coli population recovered from anthropogenically-influenced surface water sources in Nigeria. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100789] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
11
|
Genomic analysis of Bacillus cereus NWUAB01 and its heavy metal removal from polluted soil. Sci Rep 2020; 10:19660. [PMID: 33184305 PMCID: PMC7665202 DOI: 10.1038/s41598-020-75170-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 09/28/2020] [Indexed: 11/08/2022] Open
Abstract
Microorganisms that display unique biotechnological characteristics are usually selected for industrial applications. Bacillus cereus NWUAB01 was isolated from a mining soil and its heavy metal resistance was determined on Luria-Bertani agar. The biosurfactant production was determined by screening methods such as drop collapse, emulsification and surface tension measurement. The biosurfactant produced was evaluated for metal removal (100 mg/L of each metal) from contaminated soil. The genome of the organism was sequenced using Illumina Miseq platform. Strain NWUAB01 tolerated 200 mg/L of Cd and Cr, and was also tolerant to 1000 mg/L of Pb. The biosurfactant was characterised as a lipopeptide with a metal-complexing property. The biosurfactant had a surface tension of 39.5 mN/m with metal removal efficiency of 69%, 54% and 43% for Pb, Cd and Cr respectively. The genome revealed genes responsible for metal transport/resistance and biosynthetic gene clusters involved in the synthesis of various secondary metabolites. Putative genes for transport/resistance to cadmium, chromium, copper, arsenic, lead and zinc were present in the genome. Genes responsible for biopolymer synthesis were also present in the genome. This study highlights biosurfactant production and heavy metal removal of strain NWUAB01 that can be harnessed for biotechnological applications.
Collapse
|
12
|
Hendgen M, Döring J, Stöhrer V, Schulze F, Lehnart R, Kauer R. Spatial Differentiation of Physical and Chemical Soil Parameters under Integrated, Organic, and Biodynamic Viticulture. PLANTS 2020; 9:plants9101361. [PMID: 33066535 PMCID: PMC7602175 DOI: 10.3390/plants9101361] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/08/2020] [Accepted: 10/10/2020] [Indexed: 11/16/2022]
Abstract
Vineyard soils show an increased risk of degradation due to being intensively cultivated. The preservation of soil integrity and fertility is a key concept of organic and biodynamic farming. However, both systems are also subject to criticism due to their higher amount of plant protection products used and their increased traffic intensity compared to integrated viticulture, both detrimental to soil quality. The aim of this study was therefore to assess long-term effects of these three management systems on chemical and physical soil quality parameters. For this purpose, topsoil samples were taken in a long-term field trial vineyard at different positions and examined for bulk density, available water capacity (AWC), soil organic carbon (SOC), N, pH, and for total and bioavailable copper (Cu) concentrations. Biodynamic plots had a lower bulk density and higher SOC concentration than the integrated ones, which is probably due to the species-rich cover crop mixture used in the inter-row. However, organic and biodynamic farming showed an accumulation of copper in the under-vine area and in the tractor track, which is problematic for soil fertility in the long-term. Therefore, alternatives for copper in plant protection are necessary to ensure sustainable soil quality through organic and biodynamic viticulture.
Collapse
Affiliation(s)
- Maximilian Hendgen
- Department of Soil Science and Plant Nutrition, Hochschule Geisenheim University, Geisenheim, D–65366 Hessen, Germany;
- Correspondence: ; Tel.: +49-(0)6722-502-445
| | - Johanna Döring
- Department of General and Organic Viticulture, Hochschule Geisenheim University, Geisenheim, D–65366 Hessen, Germany; (J.D.); (V.S.); (F.S.); (R.K.)
| | - Verena Stöhrer
- Department of General and Organic Viticulture, Hochschule Geisenheim University, Geisenheim, D–65366 Hessen, Germany; (J.D.); (V.S.); (F.S.); (R.K.)
| | - Fabian Schulze
- Department of General and Organic Viticulture, Hochschule Geisenheim University, Geisenheim, D–65366 Hessen, Germany; (J.D.); (V.S.); (F.S.); (R.K.)
| | - Ruth Lehnart
- Department of Soil Science and Plant Nutrition, Hochschule Geisenheim University, Geisenheim, D–65366 Hessen, Germany;
| | - Randolf Kauer
- Department of General and Organic Viticulture, Hochschule Geisenheim University, Geisenheim, D–65366 Hessen, Germany; (J.D.); (V.S.); (F.S.); (R.K.)
| |
Collapse
|
13
|
Shaw JLA, Ernakovich JG, Judy JD, Farrell M, Whatmuff M, Kirby J. Long-term effects of copper exposure to agricultural soil function and microbial community structure at a controlled and experimental field site. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 263:114411. [PMID: 32247199 DOI: 10.1016/j.envpol.2020.114411] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 02/25/2020] [Accepted: 03/17/2020] [Indexed: 05/27/2023]
Abstract
The long-term effect of heavy metals on soil microbial communities and their function is relatively unknown and little work has been done in field settings. To address this gap, we revisited a field-based experiment, 12 years after the application of copper (Cu) to agricultural soils, with treatment concentrations ranging from 0 to 3310 mg Cu kg-1 soil. We measured the long-term effects of Cu exposure to soils using multiple functionality assessments and environmental DNA-based community analyses. The assessment results revealed that soils that received moderate to high Cu doses had still not recovered functionality 12-years post exposure. However, plots that received doses of 200 mg kg-1 Cu or less appeared to have a functionality index not dissimilar to control plots. Environmental DNA analyses of the microbial communities revealed a high level of beta diversity in low Cu treatment plots, whereas communities within high Cu treatment plots had similar community structures to one another (low beta diversity), indicating that specific Cu-tolerant or dormant taxa are selected for in high-Cu environments. Interestingly, high Cu plots had higher within-sample taxa counts (alpha diversity) compared with controls and low Cu plots. We hypothesise that taxa in high Cu plots activated dormancy mechanisms, such that their genetic signal remained present, whilst the functionality of the soil was reduced. Many species identified in high Cu plots are known to have associated dormancy mechanisms and survive in high stress environments. Understanding how these mechanisms collectively contribute to contaminant outcomes is of great importance for the goals of predicting and managing microbial communities and their function. As we found that Cu concentrations above 200 mg kg-1 can cause significant functionality loss and a selective pressure on microbial communities, it is recommended that Cu concentrations above 200 mg kg-1are avoided in agricultural soils.
Collapse
Affiliation(s)
- J L A Shaw
- Commonwealth Scientific and Industrial Research Organisation, Land and Water, Waite Road, Urrbrae, 5064, Australia.
| | - J G Ernakovich
- Commonwealth Scientific and Industrial Research Organisation, Agriculture & Food, Waite Road, Urrbrae, 5064, Australia; Department of Natural Resources and the Environment, University of New Hampshire, College Road, Durham, NH, 03824, USA
| | - J D Judy
- Commonwealth Scientific and Industrial Research Organisation, Land and Water, Waite Road, Urrbrae, 5064, Australia; University of Florida, Soil and Water Sciences Department, 1692 McCarty Dr, Gainesville, FL, 32603, USA
| | - M Farrell
- Commonwealth Scientific and Industrial Research Organisation, Agriculture & Food, Waite Road, Urrbrae, 5064, Australia
| | - M Whatmuff
- Agriculture NSW, NSW Department of Primary Industries, Private Mail Bag, 4008 Narellan, NSW, 2567, Australia
| | - J Kirby
- Commonwealth Scientific and Industrial Research Organisation, Land and Water, Waite Road, Urrbrae, 5064, Australia
| |
Collapse
|
14
|
Anusha P, Natarajan D. Bioremediation potency of multi metal tolerant native bacteria Bacillus cereus isolated from bauxite mines, kolli hills, Tamilnadu- A lab to land approach. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101581] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
15
|
Domingues VS, de Souza Monteiro A, Júlio ADL, Queiroz ALL, Dos Santos VL. Diversity of Metal-Resistant and Tensoactive-Producing Culturable Heterotrophic Bacteria Isolated from a Copper Mine in Brazilian Amazonia. Sci Rep 2020; 10:6171. [PMID: 32277075 PMCID: PMC7148335 DOI: 10.1038/s41598-020-62780-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/11/2020] [Indexed: 12/20/2022] Open
Abstract
Bacterial extracellular polymeric substances (EPSs) present diverse properties of biotechnological interest, such as surface modification, metal adsorption and hydrophobic substances solubilization through surface tension reduction. Thus, there is a growing demand for new producing strains and structurally variable biomolecules with different properties. One approach for scanning this biodiversity consists of exploring environments under selective pressures. The aim of this study was to evaluate the composition of culturable heterotrophic bacterial communities from five different sites from a copper mine in the Amazon biome by an enrichment technique to obtain metal resistant bacteria (lead, arsenic, cadmium, copper and zinc) capable of producing EPSs. The bacterial densities at the sites varied from 2.42 × 103 to 1.34 × 108 NMP mL-1 and the 77 bacterial isolates obtained were classified in four divisions, β-Proteobacteria (16.88%), γ-Proteobacteria (7.29%), Firmicutes (61%) and Actinobacteria (12.98%). Bacillus, Alcaligenes, and Lysinibacillus were the most dominant among the 16 observed genera, but the relative frequency of each varied according to the sample and the metal used in the enrichment culture. 58% of the bacterial strains (45) could produce EPSs. From these, 33 strains showed emulsifying activity (E24), and 9 of them reached values higher than 49%. Only Actinomyces viscosus E3.Pb5 and Bacillus subtilis group E3.As2 reduced the medium surface tension to values lower than 35 mN m-1. It was possible to confirm the high presence of bacteria capable of producing EPSs with tensoactive properties in Amazon copper mines and the evolutionary pressure exerted by the heavy metals during enrichment. These molecules can be tested as an alternative for use in processes that involve the removal of metals, such as the bioremediation of contaminated environments.
Collapse
Affiliation(s)
- Vitor Sousa Domingues
- Laboratory of Applied Microbiology, Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais. Address: Avenida Presidente Antônio Carlos, 6627 - Pampulha/ICB, Bloco F4, sala 159, C.P. 486, Belo Horizonte, MG, 31270-901, Brazil
| | - Andrea de Souza Monteiro
- Laboratory of Applied Microbiology, Universidade CEUMA, UNICEUMA, Address: Rua Josué Moentello, Jardim Renascença, São Luís, MA, CEP 65075120, Brazil
| | - Aline Daniela Lopes Júlio
- Laboratory of Applied Microbiology, Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais. Address: Avenida Presidente Antônio Carlos, 6627 - Pampulha/ICB, Bloco F4, sala 159, C.P. 486, Belo Horizonte, MG, 31270-901, Brazil
| | - Ana Luiza Lemos Queiroz
- Laboratory of Applied Microbiology, Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais. Address: Avenida Presidente Antônio Carlos, 6627 - Pampulha/ICB, Bloco F4, sala 159, C.P. 486, Belo Horizonte, MG, 31270-901, Brazil
| | - Vera Lúcia Dos Santos
- Laboratory of Applied Microbiology, Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais. Address: Avenida Presidente Antônio Carlos, 6627 - Pampulha/ICB, Bloco F4, sala 159, C.P. 486, Belo Horizonte, MG, 31270-901, Brazil.
| |
Collapse
|
16
|
Kang W, Zheng J, Bao J, Wang Z, Zheng Y, He JZ, Hu HW. Characterization of the copper resistance mechanism and bioremediation potential of an Acinetobacter calcoaceticus strain isolated from copper mine sludge. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:7922-7933. [PMID: 31893366 DOI: 10.1007/s11356-019-07303-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
Bioremediation is one of the most effective ways for removal of heavy metals and restoration of contaminated sites. This study investigated the copper (Cu) resistance mechanism and bioremediation potential of an Acinetobacter calcoaceticus strain KW3 isolated from sludge of Cu mine. The effect of Cu concentrations on the bacterial growth, biomass, and adsorption capacity, as well as the effect of contact time on the adsorption process was evaluated in a batch biosorption test. The strain exhibited strong tolerance of Cu, and the minimal inhibitory concentration was around 400 mg Cu2+ L-1, at which the maximum adsorption capacity was 14.1 mg g-1 dry cell mass. Cell walls and intracellular soluble components adsorbed 51.2% and 46.6% of Cu2+, respectively, suggesting that the strain not only adsorbed Cu2+ on the surface but also metastasized ions into cells. The adsorption and kinetic data were well fitted with Freundlich isotherm and Pseudo-second-order models, suggesting that cell surface had a high affinity for Cu2+ and the chemisorption could be the main adsorption mechanism. Scanning electron microscope and Fourier transform infrared spectroscopy analysis revealed that hydroxyl, carboxylic, amide, sulfate, and phosphate on cell walls might be involved in the biosorption process. Two-dimensional gel electrophoresis and MALDI-TOF/TOF mass spectrometry revealed that some oxidoreductases, in particular Cu resistance protein A (CopA) expression levels, were upregulated. Antioxidant defense and P1B-type ATPases CopA efflux might play a crucial role in maintaining cellular homeostasis and intracellular detoxification. To our knowledge, this is the first time that Cu resistance mechanisms, especially intracellular enzymatic mechanisms, were identified in an A. calcoaceticus KW3 strain.
Collapse
Affiliation(s)
- Wei Kang
- School of Environmental Science and Engineering, Hubei Key Laboratory of Mine Environmental Pollution Control and Remediation, Hubei Polytechnic University, Huangshi, 435003, China
- Hubei Provincial Key Laboratory of Mining Area Environmental Pollution Control and Remediation, Hubei Polytechnic University, Huangshi, 435003, China
| | - Jin Zheng
- Hubei Provincial Key Laboratory of Mining Area Environmental Pollution Control and Remediation, Hubei Polytechnic University, Huangshi, 435003, China
| | - Jianguo Bao
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430070, China
| | - Zhen Wang
- Hubei Provincial Key Laboratory of Mining Area Environmental Pollution Control and Remediation, Hubei Polytechnic University, Huangshi, 435003, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430070, China
| | - Yong Zheng
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China
| | - Ji-Zheng He
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Hang-Wei Hu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China.
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.
| |
Collapse
|
17
|
Vázquez-Blanco R, Arias-Estévez M, Bååth E, Fernández-Calviño D. Comparison of Cu salts and commercial Cu based fungicides on toxicity towards microorganisms in soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 257:113585. [PMID: 31753627 DOI: 10.1016/j.envpol.2019.113585] [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: 08/29/2019] [Revised: 10/23/2019] [Accepted: 11/05/2019] [Indexed: 05/15/2023]
Abstract
Microbial responses to Cu pollution as a function of Cu sources (Cu salts and commercial Cu fungicides) were assessed in a soil using basal soil respiration, and bacterial and fungal community growth, as endpoints. The soil was amended with different concentrations (0-32 mmol Cu kg-1) of Cu nitrate, Cu sulfate, Bordeaux mixture and 3 types of Cu oxychloride. Cu salts decreased soil pH, while this was not found with the other Cu sources. This difference in soil pH effects caused differences in the respiration, bacterial growth and fungal growth response. Basal soil respiration was negatively affected by Cu addition when the soil was spiked with Cu salts, but almost unaffected by commercial Cu fungicides. Bacterial growth was significantly and negatively affected by Cu addition for all the Cu sources, but Cu toxicity was higher for Cu salts than for commercial Cu fungicides. Fungal growth response was also different for Cu salts and commercial Cu fungicides, but only in the long-term. High Cu amendments using Cu salts stimulated fungal growth, whereas for commercial Cu fungicides, these concentrations inhibited fungal growth. Thus, the use of products similar to those used in commercial fungicides is a recommended practice for Cu risk assessments in soil.
Collapse
Affiliation(s)
- Raquel Vázquez-Blanco
- Departamento de Bioloxía Vexetal e Ciencia do Solo, Facultade de Ciencias, Universidade de Vigo, As Lagoas s/n, 32004, Ourense, Spain
| | - Manuel Arias-Estévez
- Departamento de Bioloxía Vexetal e Ciencia do Solo, Facultade de Ciencias, Universidade de Vigo, As Lagoas s/n, 32004, Ourense, Spain
| | - Erland Bååth
- Section of Microbial Ecology, Department of Biology, Ecology Building, Lund University, SE-22362, Lund, Sweden
| | - David Fernández-Calviño
- Departamento de Bioloxía Vexetal e Ciencia do Solo, Facultade de Ciencias, Universidade de Vigo, As Lagoas s/n, 32004, Ourense, Spain.
| |
Collapse
|
18
|
Mukherjee A, Reddy MS. Metatranscriptomics: an approach for retrieving novel eukaryotic genes from polluted and related environments. 3 Biotech 2020; 10:71. [PMID: 32030340 DOI: 10.1007/s13205-020-2057-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 01/06/2020] [Indexed: 02/02/2023] Open
Abstract
Metatranscriptomics, a subset of metagenomics, provides valuable information about the whole gene expression profiling of complex microbial communities of an ecosystem. Metagenomic studies mainly focus on the genomic content and identification of microbes present within a community, while metatranscriptomics provides the diversity of the active genes within such community, their expression profile and how these levels change due to change in environmental conditions. Metatranscriptomics has been applied to different types of environments, from the study of human microbiomes, to those found in plants, animals, within soils and in aquatic systems. Metatranscriptomics, based on the utilization of mRNA isolated from environmental samples, is a suitable approach to mine the eukaryotic gene pool for genes of biotechnological relevance. Also, it is imperative to develop different bioinformatic pipelines to analyse the data obtained from metatranscriptomic analysis. In the present review, we summarise the metatranscriptomics applied to soil environments to study the functional diversity, and discuss approaches for isolating the genes involved in organic matter degradation and providing tolerance to toxic metals, role of metatranscriptomics in microbiome research, various bioinformatics pipelines used in data analysis and technical challenges for gaining biologically meaningful insight of this approach.
Collapse
Affiliation(s)
- Arkadeep Mukherjee
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab 147004 India
| | - M Sudhakara Reddy
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab 147004 India
| |
Collapse
|
19
|
Ayangbenro AS, Babalola OO, Aremu OS. Bioflocculant production and heavy metal sorption by metal resistant bacterial isolates from gold mining soil. CHEMOSPHERE 2019; 231:113-120. [PMID: 31128345 DOI: 10.1016/j.chemosphere.2019.05.092] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 05/06/2019] [Accepted: 05/12/2019] [Indexed: 06/09/2023]
Abstract
Two bioflocculant producing bacterial isolates from mining soil samples were investigated for their application in heavy metal removal. The bacterial isolates were identified as Pseudomonas koreensis and Pantoea sp. using 16S rRNA gene. Cadmium resistant genes cadA and CzcD were detected in Pantoea sp. while P. koreensis harbor CzcD and chrA responsible for Cd and Cr resistance respectively. The isolates showed maximum flocculating activity of 71.3% and 51.7% with glucose and yield of 2.98 g L-1 and 3.26 g L-1 for Pantoea sp. and P. koreensis respectively. The optimum flocculating activity was achieved at pH 7.5 and temperature of 30 °C. Fourier transform infrared analysis of the bioflocculants produced by the two isolates showed the presence of carboxyl, hydroxyl and amino groups characteristic of polysaccharide and protein. Heavy metal sorption by bioflocculant of Pantoea sp. removed 51.2% Cd, 52.5% Cr and 80.5% Pb while that of P. koreensis removed 48.5% Cd, 42.5% Cr and 73.7% Pb. The bioflocculants produced have potential in metal removal from industrial wastes.
Collapse
Affiliation(s)
- Ayansina Segun Ayangbenro
- Food Security and Safety Niche,Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche,Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa.
| | - Oluwole Samuel Aremu
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| |
Collapse
|
20
|
Gupta VVSR, Bramley RGV, Greenfield P, Yu J, Herderich MJ. Vineyard Soil Microbiome Composition Related to Rotundone Concentration in Australian Cool Climate 'Peppery' Shiraz Grapes. Front Microbiol 2019; 10:1607. [PMID: 31379773 PMCID: PMC6646731 DOI: 10.3389/fmicb.2019.01607] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/26/2019] [Indexed: 11/26/2022] Open
Abstract
Soil microbial communities have an integral association with plants and play an important role in shaping plant nutrition, health, crop productivity and product quality. The influence of bacteria and fungi on wine fermentation is well known. However, little is known about the role of soil microbes, other than microbial pathogens, on grape composition or their role in vintage or site (terroir) impacts on grape composition. In this study, we used an amplicon sequencing approach to investigate the potential relationships between soil microbes and inherent spatial variation in grape metabolite composition – specifically, the concentration of the ‘impact aroma compound’ rotundone in Shiraz grapes (Vitis vinifera L.) grown in a 6.1 ha vineyard in the Grampians region of Victoria, Australia. Previous work had demonstrated temporal stability in patterns of within-vineyard spatial variation in rotundone concentration, enabling identification of defined ‘zones’ of inherently ‘low’ or ‘high’ concentration of this grape metabolite. 16S rRNA and ITS region-amplicon sequencing analysis of microbial communities in the surface soils collected from these zones indicated marked differences between zones in the genetic diversity and composition of the soil bacterial and fungal microbiome. Soils in the High rotundone zone exhibited higher diversity of bacteria, but lower diversity of fungi, compared to the soils in the Low rotundone zone. In addition, the network analysis of the microbial community in the High rotundone zone soils appeared well structured, especially with respect to the bacterial community, compared to that in the Low rotundone zone soils. The key differences in the microbial community structure between the rotundone zones are obvious for taxa/groups of both bacteria and fungi, particularly for bacteria belonging to Acidobacteria-GP4 and GP7, Rhizobiales, Gaiellaceae, Alphaproteobacteria and the Nectriaceae and Tremellaceae families of fungi. Although mulching in some parts of the vineyard caused changes in bacterial and fungal composition and overall microbial catabolic diversity and activity, its effects did not mask the rotundone zone-based variation. This finding of a systematic rotundone zone-based variation in soil microbiomes suggests an opportunity to bring together understanding of microbial ecology, plant biochemistry, and viticultural management for improved management of grape metabolism, composition and wine flavor.
Collapse
Affiliation(s)
| | | | | | - Julian Yu
- School of Life Sciences, Arizona State University, Mesa, AZ, United States
| | | |
Collapse
|
21
|
Jordaan K, Comeau AM, Khasa DP, Bezuidenhout CC. An integrated insight into the response of bacterial communities to anthropogenic contaminants in a river: A case study of the Wonderfonteinspruit catchment area, South Africa. PLoS One 2019; 14:e0216758. [PMID: 31112559 PMCID: PMC6528982 DOI: 10.1371/journal.pone.0216758] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 04/26/2019] [Indexed: 01/03/2023] Open
Abstract
Bacterial communities in human-impacted rivers and streams are exposed to multiple anthropogenic contaminants, which can eventually lead to biodiversity loss and function. The Wonderfonteinspruit catchment area is impacted by operational and abandoned gold mines, farms, and formal and informal settlements. In this study, we used 16S rRNA gene high-throughput sequencing to characterize bacterial communities in the lower Wonderfonteinspruit and their response to various contaminant sources. The results showed that composition and structure of bacterial communities differed significantly (P<0.05) between less (downstream) and more (upstream) polluted sites. The taxonomic and functional gene dissimilarities significantly correlated with each other, while downstream sites had more distinct functional genes. The relative abundance of Proteobacteria, Bacteroidetes and Actinobacteria was higher at upstream sites, while Acidobacteria, Cyanobacteria, Firmicutes and Verrucomicrobia were prominent at downstream sites. In addition, upstream sites were rich in genera pathogenic and/or potentially pathogenic to humans. Multivariate and correlation analyses suggest that bacterial diversity was significantly (P<0.05) impacted by pH and heavy metals (cobalt, arsenic, chromium, nickel and uranium). A significant fraction (~14%) of the compositional variation was explained by a combination of anthropogenic inputs, of which mining (~6%) was the main contributor to bacterial community variation. Network analysis indicated that bacterial communities had non-random inter- and intra-phyla associations and that the main taxa showed both positive and negative linkages to environmental parameters. Our results suggest that species sorting, due to environmental parameters, was the main process that structured bacterial communities. Furthermore, upstream sites had higher relative abundances of genes involved in xenobiotic degradation, suggesting stronger removal of polycyclic aromatic hydrocarbons and other organic compounds. This study provides insights into the influences of anthropogenic land use on bacterial community structure and functions in the lower Wonderfonteinspruit.
Collapse
Affiliation(s)
- K. Jordaan
- Unit for Environmental Sciences and Management, Microbiology, North-West University, South Africa, Potchefstroom, South Africa
- * E-mail:
| | - A. M. Comeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - D. P. Khasa
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - C. C. Bezuidenhout
- Unit for Environmental Sciences and Management, Microbiology, North-West University, South Africa, Potchefstroom, South Africa
| |
Collapse
|
22
|
Mahamoud Ahmed A, Lyautey E, Bonnineau C, Dabrin A, Pesce S. Environmental Concentrations of Copper, Alone or in Mixture With Arsenic, Can Impact River Sediment Microbial Community Structure and Functions. Front Microbiol 2018; 9:1852. [PMID: 30158909 PMCID: PMC6104476 DOI: 10.3389/fmicb.2018.01852] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/24/2018] [Indexed: 12/03/2022] Open
Abstract
In many aquatic ecosystems, sediments are an essential compartment, which supports high levels of specific and functional biodiversity thus contributing to ecological functioning. Sediments are exposed to inputs from ground or surface waters and from surrounding watershed that can lead to the accumulation of toxic and persistent contaminants potentially harmful for benthic sediment-living communities, including microbial assemblages. As benthic microbial communities play crucial roles in ecological processes such as organic matter recycling and biomass production, we performed a 21-day laboratory channel experiment to assess the structural and functional impact of metals on natural microbial communities chronically exposed to sediments spiked with copper (Cu) and/or arsenic (As) alone or mixed at environmentally relevant concentrations (40 mg kg-1 for each metal). Heterotrophic microbial community responses to metals were evaluated both in terms of genetic structure (using ARISA analysis) and functional potential (using exoenzymatic, metabolic and functional genes analyses). Exposure to Cu had rapid marked effects on the structure and most of the functions of the exposed communities. Exposure to As had almost undetectable effects, possibly due to both lack of As bioavailability or toxicity toward the exposed communities. However, when the two metals were combined, certain functional responses suggested a possible interaction between Cu and As toxicity on heterotrophic communities. We also observed temporal dynamics in the functional response of sediment communities to chronic Cu exposure, alone or in mixture, with some functions being resilient and others being impacted throughout the experiment or only after several weeks of exposure. Taken together, these findings reveal that metal contamination of sediment could impact both the genetic structure and the functional potential of chronically exposed microbial communities. Given their functional role in aquatic ecosystems, it poses an ecological risk as it may impact ecosystem functioning.
Collapse
Affiliation(s)
- Ayanleh Mahamoud Ahmed
- Irstea, UR RiverLy, Centre de Lyon-Villeurbanne, Villeurbanne, France
- CARRTEL, Univ. Savoie Mont Blanc, INRA, Chambéry, France
- Centre de Recherche, Université de Djibouti, Djibouti, Djibouti
| | - Emilie Lyautey
- CARRTEL, Univ. Savoie Mont Blanc, INRA, Chambéry, France
| | - Chloé Bonnineau
- Irstea, UR RiverLy, Centre de Lyon-Villeurbanne, Villeurbanne, France
| | - Aymeric Dabrin
- Irstea, UR RiverLy, Centre de Lyon-Villeurbanne, Villeurbanne, France
| | - Stéphane Pesce
- Irstea, UR RiverLy, Centre de Lyon-Villeurbanne, Villeurbanne, France
| |
Collapse
|
23
|
El dein Abdel-lateif KS, Mansour SR, El-Badawy MF, Shohayeb MM. Isolation and molecular characterization ofFrankiastrains resistant to some heavy metals. J Basic Microbiol 2018; 58:720-729. [DOI: 10.1002/jobm.201800122] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 06/11/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Khalid Salah El dein Abdel-lateif
- Department of Pharmaceutical Microbiology, College of Pharmacy; Taif University; Taif Saudi Arabia
- Department of Genetics, Faculty of Agriculture; Menoufia University; Egypt
| | - Samira R. Mansour
- Botany Department, Faculty of Science; Suez Canal University; Ismailia Egypt
| | - Mohamed F. El-Badawy
- Department of Pharmaceutical Microbiology, College of Pharmacy; Taif University; Taif Saudi Arabia
- Department of Microbiology and Immunology, Faculty of Pharmacy; Misr University for Science and Technology; Egypt
| | - Mohamed M. Shohayeb
- Department of Pharmaceutical Microbiology, College of Pharmacy; Taif University; Taif Saudi Arabia
- Department of Microbiology, Faculty of Pharmacy; Tanta University; Egypt
| |
Collapse
|
24
|
Effects of different management regimes on microbial biodiversity in vineyard soils. Sci Rep 2018; 8:9393. [PMID: 29925862 PMCID: PMC6010416 DOI: 10.1038/s41598-018-27743-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 06/05/2018] [Indexed: 01/22/2023] Open
Abstract
An active and diverse soil biota is important for maintaining crop productivity and quality, and preservation of these traits is a major goal of sustainable farming. This study aimed at unravelling the impact of different management practices on soil fungal and bacterial biodiversity in vineyards as a model for permanent crops. Species diversity was assessed using an amplicon sequencing approach in a long-term field experiment in the Rheingau wine region of Germany where integrated, organic and biodynamic management practices had been in place for 10 years. Fungal community composition under integrated management differed significantly from organic and biodynamic management, whereas fungal species richness remained unaffected. Soil under integrated management had a significantly reduced bacterial species richness compared to organic, but community composition was similar to organically and biodynamically managed soils. Highest fungal richness was obtained under cover crop between rows in topsoil, arising from cover cropping and organic carbon supply.
Collapse
|
25
|
Phenotypic, Genotypic and Symbiotic Characterization of Rhizobial Isolates Nodulating Acacia sp. in Morocco. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2018. [DOI: 10.22207/jpam.12.1.30] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
26
|
High-throughput sequencing of microbial community diversity in soil, grapes, leaves, grape juice and wine of grapevine from China. PLoS One 2018; 13:e0193097. [PMID: 29565999 PMCID: PMC5863948 DOI: 10.1371/journal.pone.0193097] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 02/04/2018] [Indexed: 11/20/2022] Open
Abstract
In this study Illumina MiSeq was performed to investigate microbial diversity in soil, leaves, grape, grape juice and wine. A total of 1,043,102 fungal Internal Transcribed Spacer (ITS) reads and 2,422,188 high quality bacterial 16S rDNA sequences were used for taxonomic classification, revealed five fungal and eight bacterial phyla. At the genus level, the dominant fungi were Ascomycota, Sordariales, Tetracladium and Geomyces in soil, Aureobasidium and Pleosporaceae in grapes leaves, Aureobasidium in grape and grape juice. The dominant bacteria were Kaistobacter, Arthrobacter, Skermanella and Sphingomonas in soil, Pseudomonas, Acinetobacter and Kaistobacter in grape and grapes leaves, and Oenococcus in grape juice and wine. Principal coordinate analysis showed structural separation between the composition of fungi and bacteria in all samples. This is the first study to understand microbiome population in soil, grape, grapes leaves, grape juice and wine in Xinjiang through High-throughput Sequencing and identify microorganisms like Saccharomyces cerevisiae and Oenococcus spp. that may contribute to the quality and flavor of wine.
Collapse
|
27
|
Seasonal and Interannual Fluctuation of the Microbial Soil Community in a Maize Field under Long-Term Conservation Agriculture Management. SUSTAINABILITY 2017. [DOI: 10.3390/su9050778] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
28
|
Sharaff M, Kamat S, Archana G. Analysis of copper tolerant rhizobacteria from the industrial belt of Gujarat, western India for plant growth promotion in metal polluted agriculture soils. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 138:113-121. [PMID: 28038338 DOI: 10.1016/j.ecoenv.2016.12.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 12/12/2016] [Accepted: 12/16/2016] [Indexed: 06/06/2023]
Abstract
Agricultural sites irrigated for long term with water polluted by industrial effluents containing heavy metals might adversely affect the soil microbial communities and crop yield. Hence it is important to study rhizobacterial communities and their metal tolerance in such affected agricultural fields to restore soil fertility and ecosystem. Present work deals with the study of rhizobacterial communities from plants grown in copper (Cu) contaminated agricultural fields along the industrial zone of Gujarat, India and are compared with communities from a Cu mine site. Microbial communities from rhizosphere soil samples varied in the magnitude of their Cu tolerance index indicating differences in long term pollution effects. Culture dependent denaturing gradient gel electrophoresis (CD-DGGE) of bacterial communities revealed the diverse composition at the sampling sites and a reduced total diversity due to Cu toxicity. Analysis of 16S rRNA gene diversity of Cu tolerant rhizobacteria revealed the predominance of Enterobacter spp. and Pseudomonas spp. under Cu stress conditions. Cu tolerant bacterial isolates that were able to promote growth of mung bean plants in vitro under Cu stress were obtained from these samples. Cu tolerant rhizobacterium P36 identified as Enterobacter sp. exhibited multiple plant growth promoting traits and significantly alleviated Cu toxicity to mung bean plants by reducing the accumulation of Cu in plant roots and promoted the plant growth in CuSO4 amended soils.
Collapse
Affiliation(s)
- Murali Sharaff
- Department of Microbiology & Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India
| | - Shalmali Kamat
- Department of Microbiology & Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India
| | - G Archana
- Department of Microbiology & Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India.
| |
Collapse
|
29
|
Khalid SAL. Isolation and characterization of heavy metals resistant Rhizobium isolates from different governorates in Egypt. ACTA ACUST UNITED AC 2017. [DOI: 10.5897/ajb2017.15930] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
|
30
|
Kasemodel MC, Lima JZ, Sakamoto IK, Varesche MBA, Trofino JC, Rodrigues VGS. Soil contamination assessment for Pb, Zn and Cd in a slag disposal area using the integration of geochemical and microbiological data. ENVIRONMENTAL MONITORING AND ASSESSMENT 2016; 188:698. [PMID: 27896584 DOI: 10.1007/s10661-016-5708-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 11/18/2016] [Indexed: 06/06/2023]
Abstract
Improper disposal of mining waste is still considered a global problem, and further details on the contamination by potentially toxic metals are required for a proper assessment. In this context, it is important to have a combined view of the chemical and biological changes in the mining dump area. Thus, the objective of this study was to evaluate the Pb, Zn and Cd contamination in a slag disposal area using the integration of geochemical and microbiological data. Analyses of soil organic matter (SOM), pH, Eh, pseudo-total concentration of metals, sequential extraction and microbial community by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) were conducted. Metal availability was evaluated based on the geoaccumulation index (I geo), ecological risk ([Formula: see text]), Risk Assessment Code (RAC) and experimental data, and different reference values were tested to assist in the interpretation of the indices. The soil pH was slightly acidic to neutral, the Eh values indicated oxidized conditions and the average SOM content varied from 12.10 to 53.60 g kg-1. The average pseudo-total concentrations of metals were in the order of Zn > Pb > Cd. Pb and Zn were mainly bound to the residual fraction and Fe-Mn oxides, and a significant proportion of Cd was bound to the exchangeable and carbonate fractions. The topsoil (0-20 cm) is highly contaminated (I geo) with Cd and has a very high potential ecological risk ([Formula: see text]). Higher bacterial diversity was mainly associated with higher metal concentrations. It is concluded that the integration of geochemical and microbiological data can provide an appropriate evaluation of mining waste-contaminated areas.
Collapse
Affiliation(s)
- Mariana Consiglio Kasemodel
- Department of Geotechnical Engineering, University of São Paulo, 400 Trabalhador São Carlense Ave., São Carlos, 13566-590, Brazil
| | - Jacqueline Zanin Lima
- Department of Geotechnical Engineering, University of São Paulo, 400 Trabalhador São Carlense Ave., São Carlos, 13566-590, Brazil
| | - Isabel Kimiko Sakamoto
- Department of Hydraulics and Sanitary Engineering, University of São Paulo, 400 Trabalhador São Carlense Ave., São Carlos, 13566-590, Brazil
| | - Maria Bernadete Amancio Varesche
- Department of Hydraulics and Sanitary Engineering, University of São Paulo, 400 Trabalhador São Carlense Ave., São Carlos, 13566-590, Brazil
| | - Julio Cesar Trofino
- Department of Hydraulics and Sanitary Engineering, University of São Paulo, 400 Trabalhador São Carlense Ave., São Carlos, 13566-590, Brazil
| | | |
Collapse
|
31
|
Cavani L, Manici LM, Caputo F, Peruzzi E, Ciavatta C. Ecological restoration of a copper polluted vineyard: Long-term impact of farmland abandonment on soil bio-chemical properties and microbial communities. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2016; 182:37-47. [PMID: 27454095 DOI: 10.1016/j.jenvman.2016.07.050] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 07/11/2016] [Accepted: 07/15/2016] [Indexed: 06/06/2023]
Abstract
This study aimed at investigating the degree of interference of high soil copper (Cu) contamination when an old vineyard is converted into a protected area. This study was performed within an intensive agricultural system; it was organized into a two-factorial nested design to analyze the impact of management (conventional vs re-naturalized orchard) and position within each orchard (tree-rows and strips). Chemical and biochemical properties along with bacterial and fungal communities, evaluated with PCR-DGGE starting from total soil DNA, were analyzed. Total Cu was localized in tree rows in the old vineyard at 1000 mg kg(-1) of soil, whereas it did not exceed 80 mg kg(-1) soil in the other treatments. Total organic carbon and all biochemical properties significantly improved in re-naturalized compared to conventionally cultivated site, while no significant differences were observed between tree row and strip. Moreover, a higher extractable carbon-extractable nitrogen (Cext-to-Next) ratio in the re-naturalized (19.3) site than in the conventionally managed site (10.2) indicated a shift of soil system from C-limited to N-limited, confirming a successful ecological restoration. Deep improvement of soil biochemical properties exceeded the negative impact of Cu contamination. A shift of bacterial community composition as well as increased bacterial diversity in Cu contaminated treatment indicated a bacterial response to Cu stress; to the contrary, soil fungi were less susceptible than bacteria, though an overall reduction of fungal DNA was detected. Findings suggest that ecological restoration of highly polluted agricultural soils leads to overcoming the reduction of soil functionalities linked to Cu contamination and opens interesting perspectives for mitigating Cu stress in agricultural soils with strategies based on conservative agriculture.
Collapse
Affiliation(s)
- Luciano Cavani
- Department of Agricultural Sciences, Alma Mater Studiorum, University of Bologna, Viale Fanin 40, Bologna, Italy
| | - Luisa M Manici
- Council for Agricultural Research and Economics (CREA), Research Center for Agriculture and Environment, Via di Corticella 133, Bologna, Italy.
| | - Francesco Caputo
- Council for Agricultural Research and Economics (CREA), Research Center for Agriculture and Environment, Via di Corticella 133, Bologna, Italy
| | - Elisabetta Peruzzi
- Department of Agricultural Sciences, Alma Mater Studiorum, University of Bologna, Viale Fanin 40, Bologna, Italy; Council for Agricultural Research and Economics (CREA), Research Center for Agriculture and Environment, Via di Corticella 133, Bologna, Italy
| | - Claudio Ciavatta
- Department of Agricultural Sciences, Alma Mater Studiorum, University of Bologna, Viale Fanin 40, Bologna, Italy
| |
Collapse
|
32
|
Fashola MO, Ngole-Jeme VM, Babalola OO. Heavy Metal Pollution from Gold Mines: Environmental Effects and Bacterial Strategies for Resistance. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:ijerph13111047. [PMID: 27792205 PMCID: PMC5129257 DOI: 10.3390/ijerph13111047] [Citation(s) in RCA: 236] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 10/12/2016] [Accepted: 10/14/2016] [Indexed: 12/20/2022]
Abstract
Mining activities can lead to the generation of large quantities of heavy metal laden wastes which are released in an uncontrolled manner, causing widespread contamination of the ecosystem. Though some heavy metals classified as essential are important for normal life physiological processes, higher concentrations above stipulated levels have deleterious effects on human health and biota. Bacteria able to withstand high concentrations of these heavy metals are found in the environment as a result of various inherent biochemical, physiological, and/or genetic mechanisms. These mechanisms can serve as potential tools for bioremediation of heavy metal polluted sites. This review focuses on the effects of heavy metal wastes generated from gold mining activities on the environment and the various mechanisms used by bacteria to counteract the effect of these heavy metals in their immediate environment.
Collapse
Affiliation(s)
- Muibat Omotola Fashola
- Food Security and Safety Niche Area, Faculty of Agriculture, Science and Technology, North-West University, Private Bag X2046, Mmabatho 2735, South Africa.
| | - Veronica Mpode Ngole-Jeme
- Department of Environmental Sciences, College of Agriculture and Environmental Sciences, UNISA, Florida, Private Bag X6 Florida, Roodepoort 1710, South Africa.
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche Area, Faculty of Agriculture, Science and Technology, North-West University, Private Bag X2046, Mmabatho 2735, South Africa.
| |
Collapse
|
33
|
Nunes I, Jacquiod S, Brejnrod A, Holm PE, Johansen A, Brandt KK, Priemé A, Sørensen SJ. Coping with copper: legacy effect of copper on potential activity of soil bacteria following a century of exposure. FEMS Microbiol Ecol 2016; 92:fiw175. [DOI: 10.1093/femsec/fiw175] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2016] [Indexed: 12/18/2022] Open
|
34
|
Sharaff M, Archana G. Assessment of microbial communities in mung bean (Vigna radiata) rhizosphere upon exposure to phytotoxic levels of Copper. J Basic Microbiol 2015; 55:1299-307. [DOI: 10.1002/jobm.201400927] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/16/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Murali Sharaff
- Department of Microbiology & Biotechnology Centre; Faculty of Science; The Maharaja Sayajirao University of Baroda; Vadodara Gujarat India
| | - G. Archana
- Department of Microbiology & Biotechnology Centre; Faculty of Science; The Maharaja Sayajirao University of Baroda; Vadodara Gujarat India
| |
Collapse
|
35
|
Bacterial communities in the rhizosphere of Vitis vinifera L. cultivated under distinct agricultural practices in Argentina. Antonie van Leeuwenhoek 2014; 107:575-88. [PMID: 25527391 DOI: 10.1007/s10482-014-0353-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 12/08/2014] [Indexed: 10/24/2022]
Abstract
Plants interact with a myriad of microbial cells in the rhizosphere, an environment that is considered to be important for plant development. However, the differential structuring of rhizosphere microbial communities due to plant cultivation under differential agricultural practices remains to be described for most plant species. Here we describe the rhizosphere microbiome of grapevine cultivated under conventional and organic practices, using a combination of cultivation-independent approaches. The quantification of bacterial 16S rRNA and nifH genes, by quantitative PCR (qPCR), revealed similar amounts of these genes in the rhizosphere in both vineyards. PCR-DGGE was used to detect differences in the structure of bacterial communities, including both the complete whole communities and specific fractions, such as Alphaproteobacteria, Betaproteobacteria, Actinobacteria, and those harboring the nitrogen-fixing related gene nifH. When analyzed by a multivariate approach (redundancy analysis), the shifts observed in the bacterial communities were poorly explained by variations in the physical and chemical characteristics of the rhizosphere. These approaches were complemented by high-throughput sequencing (67,830 sequences) based on the V6 region of the 16S rRNA gene, identifying the major bacterial groups present in the rhizosphere of grapevines: Proteobacteria, Actinobacteria, Firmicutes, Bacteriodetes, Acidobacteria, Cloroflexi, Verrucomicrobia and Planctomycetes, which occur in distinct proportions in the rhizosphere from each vineyard. The differences might be related to the selection of plant metabolism upon distinct reservoirs of microbial cells found in each vineyard. The results fill a gap in the knowledge of the rhizosphere of grapevines and also show distinctions in these bacterial communities due to agricultural practices.
Collapse
|
36
|
Soler-Rovira P, Fernández-Calviño D, Arias-Estévez M, Plaza C, Polo A. Respiration parameters determined by the ISO-17155 method as potential indicators of copper pollution in vineyard soils after long-term fungicide treatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2013; 447:25-31. [PMID: 23376513 DOI: 10.1016/j.scitotenv.2012.12.077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 11/27/2012] [Accepted: 12/21/2012] [Indexed: 06/01/2023]
Abstract
This study seeks to determine the impact of copper-based fungicides on the respiration of vineyard soils. The ISO-17155 is an international standard recommended for monitoring soil quality by the evaluation of the effects of pollutants on soil microbial activity. Respiration curves and derived parameters [i.e., basal respiration (RB), substrate-induced respiration (RS), lag time (tlag), growth rate (μ), time to the peak maximum (tpeakmax), respiratory-activation quotient (QR), and the cumulative O2 consumption (CR)] were determined from 95 vineyard soils that covered a wide range of Cu contents. Statistical analyses showed that most of the variance of the ISO-17155 parameters was due to soil pH and organic C content, but not to the Cu pollution. When the parameters were expressed as a function of soil organic C content, the effect of soil Cu content was found to be significant on RS and tpeakmax but not on RB and CR. The results indicated that threshold values of total (CuT) and exchangeable (CuEX) contents indicative of soil Cu pollution cannot be established. However, adequate management practices resulting in soil organic C contents>2% and pH>5.5 are recommended for preserving vineyard soil quality.
Collapse
Affiliation(s)
- Pedro Soler-Rovira
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Serrano 115 dpdo., 28006 Madrid, Spain.
| | | | | | | | | |
Collapse
|
37
|
Altimira F, Yáñez C, Bravo G, González M, Rojas LA, Seeger M. Characterization of copper-resistant bacteria and bacterial communities from copper-polluted agricultural soils of central Chile. BMC Microbiol 2012; 12:193. [PMID: 22950448 PMCID: PMC3496636 DOI: 10.1186/1471-2180-12-193] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 08/27/2012] [Indexed: 12/20/2022] Open
Abstract
Background Copper mining has led to Cu pollution in agricultural soils. In this report, the effects of Cu pollution on bacterial communities of agricultural soils from Valparaiso region, central Chile, were studied. Denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA genes was used for the characterization of bacterial communities from Cu-polluted and non-polluted soils. Cu-resistant bacterial strains were isolated from Cu-polluted soils and characterized. Results DGGE showed a similar high number of bands and banding pattern of the bacterial communities from Cu-polluted and non-polluted soils. The presence of copA genes encoding the multi-copper oxidase that confers Cu-resistance in bacteria was detected by PCR in metagenomic DNA from the three Cu-polluted soils, but not in the non-polluted soil. The number of Cu-tolerant heterotrophic cultivable bacteria was significantly higher in Cu-polluted soils than in the non-polluted soil. Ninety two Cu-resistant bacterial strains were isolated from three Cu-polluted agricultural soils. Five isolated strains showed high resistance to copper (MIC ranged from 3.1 to 4.7 mM) and also resistance to other heavy metals. 16S rRNA gene sequence analyses indicate that these isolates belong to the genera Sphingomonas, Stenotrophomonas and Arthrobacter. The Sphingomonas sp. strains O12, A32 and A55 and Stenotrophomonas sp. C21 possess plasmids containing the Cu-resistance copA genes. Arthrobacter sp. O4 possesses the copA gene, but plasmids were not detected in this strain. The amino acid sequences of CopA from Sphingomonas isolates (O12, A32 and A55), Stenotrophomonas strain (C21) and Arthrobacter strain (O4) are closely related to CopA from Sphingomonas, Stenotrophomonas and Arthrobacter strains, respectively. Conclusions This study suggests that bacterial communities of agricultural soils from central Chile exposed to long-term Cu-pollution have been adapted by acquiring Cu genetic determinants. Five bacterial isolates showed high copper resistance and additional resistance to other heavy metals. Detection of copA gene in plasmids of four Cu-resistant isolates indicates that mobile genetic elements are involved in the spreading of Cu genetic determinants in polluted environments.
Collapse
Affiliation(s)
- Fabiola Altimira
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Center of Nanotechnology and Systems Biology, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | | | | | | | | | | |
Collapse
|
38
|
Selection for Cu-tolerant bacterial communities with altered composition, but unaltered richness, via long-term Cu exposure. Appl Environ Microbiol 2012; 78:7438-46. [PMID: 22904046 DOI: 10.1128/aem.01071-12] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Toxic metal pollution affects the composition and metal tolerance of soil bacterial communities. However, there is virtually no knowledge concerning the responses of members of specific bacterial taxa (e.g., phyla or classes) to metal toxicity, and contradictory results have been obtained regarding the impact of metals on operational taxonomic unit (OTU) richness. We used tag-coded pyrosequencing of the 16S rRNA gene to elucidate the impacts of copper (Cu) on bacterial community composition and diversity within a well-described Cu gradient (20 to 3,537 μg g(-1)) stemming from industrial contamination with CuSO(4) more than 85 years ago. DNA sequence information was linked to analysis of pollution-induced community tolerance (PICT) to Cu, as determined by the [(3)H]leucine incorporation technique, and to chemical characterization of the soil. PICT was significantly correlated to bioavailable Cu, as determined by the results seen with a Cu-specific bioluminescent biosensor strain, demonstrating a specific community response to Cu. The relative abundances of members of several phyla or candidate phyla, including the Proteobacteria, Bacteroidetes, Verrumicrobia, Chloroflexi, WS3, and Planctomycetes, decreased with increasing bioavailable Cu, while members of the dominant phylum, the Actinobacteria, showed no response and members of the Acidobacteria showed a marked increase in abundance. Interestingly, changes in the relative abundances of classes frequently deviated from the responses of the phyla to which they belong. Despite the apparent Cu impacts on Cu resistance and community structure, bioavailable Cu levels did not show any correlation to bacterial OTU richness (97% similarity level). Our report highlights several bacterial taxa responding to Cu and thereby provides new guidelines for future studies aiming to explore the bacterial domain for members of metal-responding taxa.
Collapse
|
39
|
Mackie KA, Müller T, Kandeler E. Remediation of copper in vineyards--a mini review. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2012; 167:16-26. [PMID: 22522314 DOI: 10.1016/j.envpol.2012.03.023] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 03/15/2012] [Accepted: 03/19/2012] [Indexed: 05/27/2023]
Abstract
Viticulturists use copper fungicide to combat Downy Mildew. Copper, a non-degradable heavy metal, can accumulate in soil or leach into water sources. Its accumulation in topsoil has impacted micro and macro organisms, spurring scientists to research in situ copper removal methods. Recent publications suggest that microorganism assisted phytoextraction, using plants and bacteria to actively extract copper, is most promising. As vineyards represent moderately polluted sites this technique has great potential. Active plant extraction and chelate assisted remediation extract too little copper or risk leaching, respectively. However, despite interesting pot experiment results using microorganism assisted phytoextraction, it remains a challenge to find plants that primarily accumulate copper in their shoots, a necessity in vineyards where whole plant removal would be time consuming and financially cumbersome. Vineyard remediation requires a holistic approach including sustainable soil management, proper plant selection, increasing biodiversity and microorganisms.
Collapse
Affiliation(s)
- K A Mackie
- Institute of Soil Science and Land Evaluation, Soil Biology Section, University of Hohenheim, 27 Emil-Wolff-Straße, 70599 Stuttgart, Germany.
| | | | | |
Collapse
|
40
|
Martins G, Miot-Sertier C, Lauga B, Claisse O, Lonvaud-Funel A, Soulas G, Masneuf-Pomarède I. Grape berry bacterial microbiota: Impact of the ripening process and the farming system. Int J Food Microbiol 2012; 158:93-100. [DOI: 10.1016/j.ijfoodmicro.2012.06.013] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 06/14/2012] [Accepted: 06/21/2012] [Indexed: 01/01/2023]
|
41
|
Andreazza R, Okeke BC, Pieniz S, Bortolon L, Lambais MR, Camargo FAO. Effects of stimulation of copper bioleaching on microbial community in vineyard soil and copper mining waste. Biol Trace Elem Res 2012; 146:124-33. [PMID: 21947860 DOI: 10.1007/s12011-011-9213-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 09/13/2011] [Indexed: 10/17/2022]
Abstract
Long-term copper application in vineyards and copper mining activities cause heavy metal pollution sites. Such sites need remediation to protect soil and water quality. Bioremediation of contaminated areas through bioleaching can help to remove copper ions from the contaminated soils. Thus, the aim of this work was to evaluate the effects of different treatments for copper bioleaching in two diverse copper-contaminated soils (a 40-year-old vineyard and a copper mining waste) and to evaluate the effect on microbial community by applying denaturing gradient gel electrophoresis (DGGE) of 16S ribosomal DNA amplicons and DNA sequence analysis. Several treatments with HCl, H(2)SO(4), and FeSO(4) were evaluated by stimulation of bioleaching of copper in the soils. Treatments and extractions using FeSO(4) and H(2)SO(4) mixture at 30°C displayed more copper leaching than extractions with deionized water at room temperature. Treatment with H(2)SO(4) supported bioleaching of as much as 120 mg kg(-1) of copper from vineyard soil after 115 days of incubation. DGGE analysis of the treatments revealed that some treatments caused greater diversity of microorganisms in the vineyard soil compared to the copper mining waste. Nucleotide Blast of PCR-amplified fragments of 16S rRNA gene bands from DGGE indicated the presence of Rhodobacter sp., Silicibacter sp., Bacillus sp., Paracoccus sp., Pediococcus sp., a Myxococcales, Clostridium sp., Thiomonas sp., a firmicute, Caulobacter vibrioides, Serratia sp., and an actinomycetales in vineyard soil. Contrarily, Sphingomonas was the predominant genus in copper mining waste in most treatments. Paracoccus sp. and Enterobacter sp. were also identified from DGGE bands of the copper mining waste. Paracoccus species is involved in the copper bioleaching by sulfur oxidation system, liberating the copper bounded in the soils and hence promoting copper bioremediation. Results indicate that stimulation of bioleaching with a combination of FeSO(4) and H(2)SO(4) promoted bioleaching in the soils and can be employed ex situ to remediate copper-impacted soils.
Collapse
Affiliation(s)
- Robson Andreazza
- Department of Soil Science, Faculty of Agronomy, Federal University of Rio Grande do Sul, 7712 Bento Gonçalves Ave., Porto Alegre, RS, 91541-000, Brazil.
| | | | | | | | | | | |
Collapse
|
42
|
de Boer TE, Taş N, Braster M, Temminghoff EJM, Röling WFM, Roelofs D. The influence of long-term copper contaminated agricultural soil at different pH levels on microbial communities and springtail transcriptional regulation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:60-8. [PMID: 21882881 DOI: 10.1021/es2013598] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Copper has long been applied for agricultural practises. Like other metals, copper is highly persistent in the environment and biologically active long after its use has ceased. Here we present a unique study on the long-term effects (27 years) of copper and pH on soil microbial communities and on the springtail Folsomia candida an important representative of the soil macrofauna, in an experiment with a full factorial, random block design. Bacterial communities were mostly affected by pH. These effects were prominent in Acidobacteria, while Actinobacteria and Gammaroteobacteria communities were affected by original and bioavailable copper. Reproduction and survival of the collembolan F. candida was not affected by the studied copper concentrations. However, the transcriptomic responses to copper reflected a mechanism of copper transport and detoxification, while pH exerted effects on nucleotide and protein metabolism and (acute) inflammatory response. We conclude that microbial community structure reflected the history of copper contamination, while gene expression analysis of F. candida is associated with the current level of bioavailable copper. The study is a first step in the development of a molecular strategy aiming at a more comprehensive assessment of various aspects of soil quality and ecotoxicology.
Collapse
Affiliation(s)
- Tjalf E de Boer
- Department of Ecological Sciences, VU University, de Boelelaan 1085, 1081HV, Amsterdam, The Netherlands
| | | | | | | | | | | |
Collapse
|
43
|
Choudhary S, Islam E, Kazy SK, Sar P. Uranium and other heavy metal resistance and accumulation in bacteria isolated from uranium mine wastes. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2012; 47:622-37. [PMID: 22375546 DOI: 10.1080/10934529.2012.650584] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Ten bacterial strains isolated from uranium mine wastes were characterized in terms of their uranium and other metal resistance and accumulation. 16S rRNA gene sequence analysis identified the strains as members of genera Bacillus, Serratia, and Arthrobacter. Strains were able to utilize various carbon sources, particularly aromatic hydrocarbons, grow at broad pH and temperature ranges and produce non specific acid phosphatase relevant for metal phosphate precipitation in contaminated environment. The isolates exhibited high uranium and other heavy metals (Ni, Co, Cu and Cd) resistance and accumulation capacities. Particularly, Arthrobacter sp. J001 and Bacillus sp. J003 were superior in terms of U resistance at low pH (pH 4.0) along with metals and actinides (U and Th) removal with maximum cell loading of 1088 μmol U, 1293 μmol Th, 425 μmol Cu, 305 μmol Cd, 377 μmol Zn, 250 μmol Ni g(-1) cell dry wt. Genes encoding P(1B)-type ATPases (Cu-CPx and Zn-CPx) and ABC transporters (nik) as catalytic tools for maintaining cellular metal homeostasis were detected within several Bacillus spp., with possible incidence of horizontal gene transfer for the later gene showing phylogenetic lineage to α Proteobacteria members. The study provides evidence on intrinsic abilities of indigenous bacteria from U-mine suitable for survival and cleaning up of contaminated mine sites.
Collapse
Affiliation(s)
- Sangeeta Choudhary
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, India
| | | | | | | |
Collapse
|
44
|
Alam MZ, Ahmad S, Malik A. Prevalence of heavy metal resistance in bacteria isolated from tannery effluents and affected soil. ENVIRONMENTAL MONITORING AND ASSESSMENT 2011; 178:281-291. [PMID: 20824329 DOI: 10.1007/s10661-010-1689-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Accepted: 08/23/2010] [Indexed: 05/29/2023]
Abstract
In the present study, a total of 198 bacteria were isolated, 88 from the tannery effluents and 110 from agricultural soil irrigated with the tannery effluents. Tannery effluents and soils were analyzed for metal concentrations by atomic absorption spectrophotometer. The tannery effluents and soil samples were found to be contaminated with chromium, nickel, zinc, copper, and cadmium. All isolates were tested for their resistance against Cr(6+ ), Cr(3+ ), Ni(2+ ), Zn(2+ ), Cu(2+ ), Cd(2+ ), and Hg(2+ ). From the total of 198 isolates, maximum bacterial isolates were found to be resistant to Cr(6+ ) 178 (89.9%) followed by Cr(3+ ) 146 (73.7%), Cd(2+ ) 86 (43.4%), Zn(2+ ) 83 (41.9%), Ni(2+ ) 61 (30.8%), and Cu(2+ ) 51 (25.6%). However, most of the isolates were sensitive to Hg(2+ ). Among the isolates from tannery effluents, 97.8% were resistant to Cr(6+ ) and 64.8% were resistant to Cr(3+ ). Most of the soil isolates were resistant against Cr(6+ ) (83.6%) and Cr(3+ ) (81.8%). All isolates were categorized into Gram-positive and Gram-negative bacteria. In a total of 114 Gram-positive isolates, 91.2% were resistant to Cr(6+ ) followed by 73.7% to Cr(3+ ), 42.1% to Zn(2+ ), 40.4% to Cd(2+ ), and 32.5% to Ni(2+ ). Among Gram-negative isolates, 88.1% were found showing resistance to Cr(6+ ), 75.0% to Cr(3+ ), and 47.6% were resistant to Cd(2+ ). Majority of these metal-resistant isolates were surprisingly found sensitive to the ten commonly used antibiotics. Out of 198 isolates, 114 were found sensitive to all antibiotics whereas only two isolates were resistant to maximum eight antibiotics at a time. Forty-one and 40 isolates which constitute 20.7% and 20.2% were resistant to methicilin and amoxicillin, respectively.
Collapse
Affiliation(s)
- Mohammad Zubair Alam
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh 202 002, India.
| | | | | |
Collapse
|
45
|
Ruggiero P, Terzano R, Spagnuolo M, Cavalca L, Colombo M, Andreoni V, Rao MA, Perucci P, Monaci E. Hg bioavailability and impact on bacterial communities in a long-term polluted soil. ACTA ACUST UNITED AC 2011; 13:145-56. [DOI: 10.1039/c0em00183j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
46
|
Vreulink JM, Stone W, Botha A. Effects of small increases in copper levels on culturable basidiomycetous yeasts in low-nutrient soils. J Appl Microbiol 2010; 109:1411-21. [PMID: 20522150 DOI: 10.1111/j.1365-2672.2010.04770.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS Investigating the effect of perturbations, with relatively low Cu concentrations, on yeast community composition in low-nutrient virgin soil. METHODS AND RESULTS Culturable soil yeast populations were monitored at an experimental site treated with the fungicide copper oxychloride (10 mg Cu per kg soil). Yeast numbers were unaffected by additional Cu; however, a shift in yeast community composition from Hymenomycetes to Urediniomycetes species occurred. Subsequent growth experiments conducted with a synthetic liquid medium revealed that hymenomycetous and urediniomycetous yeasts were affected differently by 1 and 10 mg l(-1) Cu. Soil microcosm experiments then indicated that additional 10 mg kg(-1) Cu may improve the competitive ability of urediniomycetous yeasts in the presence of hymenomycetous yeasts. CONCLUSIONS The shift from hymenomycetous to urediniomycetous yeasts, as a result of slightly increased soil Cu levels, may be because of hymenomycetous yeasts being more sensitive to elevated Cu levels and urediniomycetous yeasts having an improved competitive ability in the presence of elevated Cu levels. SIGNIFICANCE AND IMPACT OF THE STUDY Yeast community composition of pristine low-nutrient soils may change as a result of perturbations with relatively low concentrations of Cu. Urediniomycetous yeasts should be studied as potential bio-indicators of Cu perturbations.
Collapse
Affiliation(s)
- J-M Vreulink
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | | | | |
Collapse
|
47
|
Andreazza R, Pieniz S, Wolf L, Lee MK, Camargo FAO, Okeke BC. Characterization of copper bioreduction and biosorption by a highly copper resistant bacterium isolated from copper-contaminated vineyard soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2010; 408:1501-1507. [PMID: 20117823 DOI: 10.1016/j.scitotenv.2009.12.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2009] [Revised: 10/26/2009] [Accepted: 12/10/2009] [Indexed: 05/28/2023]
Abstract
Copper is an essential but toxic heavy metal that negatively impacts living systems at high concentration. This study presents factors affecting copper bioremoval (bioreduction and biosorption) by a highly copper resistant monoculture of Pseudomonas sp. NA and copper bioremoval from soil. Seven bacteria resistant to high concentration of Cu(II) were isolated from enrichment cultures of vineyard soils and mining wastes. Culture parameters influencing copper bioreduction and biosorption by one monoculture isolate were studied. The isolate was identified by 16S rRNA gene sequence analysis as a Pseudomonas sp. NA (98% similarity to Pseudomonas putida, Pseudomonas plecoglossicida and other Pseudomonas sp.). The optimal temperature for growth was 30 degrees C and bioremoval of Cu(II) was maximal at 35 degrees C. Considerable growth of the isolate was observed between pH 5.0 and 8.0 with the highest growth and biosorption recorded at pH 6.0. Maximal bioreduction was observed at pH 5.0. Cu(II) bioremoval was directly proportional to Cu(II) concentration in media. Pseudomonas sp. NA removed more than 110mg L(-1) Cu(II) in water within 24h through bioreduction and biosorption at initial concentration of 300mg L(-1). In cultures amended with 100mg L(-1), 20.7mg L(-1) of Cu(II) was biologically reduced and more than 23mg L(-1) of Cu(II) was biologically removed in 12h. The isolate strongly promoted copper bioleaching in soil. Results indicate that Pseudomonas sp. NA has good potential as an agent for removing copper from water and soil.
Collapse
Affiliation(s)
- Robson Andreazza
- Department of Biology, Auburn University at Montgomery, Montgomery, AL 36124, USA
| | | | | | | | | | | |
Collapse
|
48
|
Komárek M, Čadková E, Chrastný V, Bordas F, Bollinger JC. Contamination of vineyard soils with fungicides: a review of environmental and toxicological aspects. ENVIRONMENT INTERNATIONAL 2010; 36:138-151. [PMID: 19913914 DOI: 10.1016/j.envint.2009.10.005] [Citation(s) in RCA: 324] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Revised: 10/06/2009] [Accepted: 10/16/2009] [Indexed: 05/08/2023]
Abstract
The contamination of agricultural soils with inorganic (Cu-based) and organic pesticides (including their residues) presents a major environmental and toxicological concern. This review summarizes available studies published on the contamination of vineyard soils throughout the world with Cu-based and synthetic organic fungicides. It focuses on the behavior of these contaminants in vineyard soils and the associated environmental and toxicological risks. The concentrations of Cu in soils exceed the legislative limits valid in the EU in the vast majority of the studied vineyards. Regarding the environmental and toxicological hazards associated with the extensive use of fungicides, the choice of fungicides should be performed carefully according to the physico-chemical properties of the soils and climatic and hydrogeological characteristics of the vine-growing regions.
Collapse
Affiliation(s)
- Michael Komárek
- Department of Agro-Environmental Chemistry and Plant Nutrition, Czech University of Life Sciences Prague, Kamýcká 129, 165 21, Prague 6, Czech Republic; Groupement de Recherche Eau, Sol, Environnement (GRESE), Université de Limoges, 123, Av. Albert Thomas, 87060, Limoges, France.
| | - Eva Čadková
- Department of Agro-Environmental Chemistry and Plant Nutrition, Czech University of Life Sciences Prague, Kamýcká 129, 165 21, Prague 6, Czech Republic
| | - Vladislav Chrastný
- Czech Geological Survey, Geologická 6, 152 00, Prague 5, Czech Republic; Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - François Bordas
- Groupement de Recherche Eau, Sol, Environnement (GRESE), Université de Limoges, 123, Av. Albert Thomas, 87060, Limoges, France
| | - Jean-Claude Bollinger
- Groupement de Recherche Eau, Sol, Environnement (GRESE), Université de Limoges, 123, Av. Albert Thomas, 87060, Limoges, France
| |
Collapse
|
49
|
Occurrence of multiple metal-resistance in bacterial isolates associated with transgenic white poplars (Populus alba L.). ANN MICROBIOL 2009. [DOI: 10.1007/bf03175593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
|
50
|
Huang A, Chen H, Chen L, Dai Y, Zhao J. Effects of Cd(II) and cu(II) on microbial characteristics in 2-chlorophenol-degradation anaerobic bioreactors. J Environ Sci (China) 2008; 20:745-752. [PMID: 18763571 DOI: 10.1016/s1001-0742(08)62122-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The effects of Cd2+ and Cu2+ at 300 mg/L on anaerobic microbial communities that degrade 2-cholorophenol (2-CP) were examined. Based on the polymerase chain reaction (PCR) of 16S rDNA, bacterial community diversity and archaeal community structure were analyzed with denaturing gradient gel electrophoresis (DGGE) and cloning, respectively. Degradation capabilities of the anaerobic microbial community were drastically abated and the degradation efficiency of 2-CP was reduced to 60% after shock by Cu2+ and Cd2+, respectively. The bacterial community structure was disturbed and the biodiversity was reduced after shock by Cu2+ and Cd2+ for 3 d. Some new metal-resistant microbes which could cope with the new condition appeared. The sequence analysis showed that there existed common Archaea species in control sludge and systems when treated with Cu2+ and Cd2+, such as Methanothrix soehngenii, Methanosaeta concilii, uncultured euryarchaeote, and so on. Both the abundance and diversity of archaeal species were altered with addition of Cd2+ and Cu2+ at high concentration. Although the abundance of the predominant archaeal species decreased with Cd2+ and Cu2+ addition for 3 d, they recovered to some extent after 10 d. The diversity of archaeal species was remarkably reduced after recovery for 10 d and the shift in archaeal composition seemed to be irreversible. The 2-CP-degradation anaerobic system was more sensitive to Cu2+ than Cd2+.
Collapse
Affiliation(s)
- Aiqun Huang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| | | | | | | | | |
Collapse
|