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Shi J, Jiang J, Chen Q, Wang L, Nian K, Long T. Production of higher toxic intermediates of organic pollutants during chemical oxidation processes: A review. ARAB J CHEM 2023. [DOI: 10.1016/j.arabjc.2023.104856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
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Bokade P, Gaur VK, Tripathi V, Bobate S, Manickam N, Bajaj A. Bacterial remediation of pesticide polluted soils: Exploring the feasibility of site restoration. JOURNAL OF HAZARDOUS MATERIALS 2023; 441:129906. [PMID: 36088882 DOI: 10.1016/j.jhazmat.2022.129906] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
For decades, reclamation of pesticide contaminated sites has been a challenging avenue. Due to increasing agricultural demand, the application of synthetic pesticides could not be controlled in its usage, and it has now adversely impacted the soil, water, and associated ecosystems posing adverse effects on human health. Agricultural soil and pesticide manufacturing sites, in particular, are one of the most contaminated due to direct exposure. Among various strategies for soil reclamation, ecofriendly microbial bioremediation suffers inherent challenges for large scale field application as interaction of microbes with the polluted soil varies greatly under climatic conditions. Methodically, starting from functional or genomic screening, enrichment isolation; functional pathway mapping, production of tensioactive metabolites for increasing the bioavailability and bio-accessibility, employing genetic engineering strategies for modifications in existing catabolic genes to enhance the degradation activity; each step-in degradation study has challenges and prospects which can be addressed for successful application. The present review critically examines the methodical challenges addressing the feasibility for restoring and reclaiming pesticide contaminated sites along with the ecotoxicological risk assessments. Overall, it highlights the need to fine-tune the available processes and employ interdisciplinary approaches to make microbe assisted bioremediation as the method of choice for reclamation of pesticide contaminated sites.
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Affiliation(s)
- Priyanka Bokade
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Vivek Kumar Gaur
- Environmental Biotechnology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; School of Energy and Chemical Engineering, UNIST, Ulsan 44919, South Korea
| | - Varsha Tripathi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India; Environmental Biotechnology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
| | - Shishir Bobate
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Natesan Manickam
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India; Environmental Biotechnology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
| | - Abhay Bajaj
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
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Unveiling the Wheat Microbiome under Varied Agricultural Field Conditions. Microbiol Spectr 2022; 10:e0263322. [PMID: 36445165 PMCID: PMC9769940 DOI: 10.1128/spectrum.02633-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Wheat being the important staple food crop plays a significant role in nutritional security. A wide variety of microbial communities beneficial to plants and contributing to plant health and production are found in the rhizosphere. The wheat microbiome encompasses an extensive variety of microbial species playing a key role in sustaining the physiology of the crop, nutrient uptake, and biotic/abiotic stress resilience. This report presents wheat microbiome analysis under six different farm practices, namely, organic (Org), timely sown (TS), wheat after pulse crop (WAPC), temperature-controlled phenotyping facility (TCPF), maize-wheat cropping system (MW), and residue burnt field (Bur), using 16S rRNA sequencing methodology. The soil samples collected from either side of the wheat row were mixed to get a final sample set for DNA extraction under each condition. After the data preprocessing, microbial community analysis was performed, followed by functional analysis and annotation. An abundance of the phylum Proteobacteria was observed, followed by Acidobacteria, Actinobacteria, and Gemmatimonadetes in the majority of the samples, while relative abundance was found to vary at the genus level. Analysis against the Carbohydrate-Active Enzymes (CAZy) database showed a high number of glycoside hydrolase genes in the TS, TCPF, and WAPC samples, while the Org, MW, and Bur samples predominantly had glycosyltransferase genes and carbohydrate esterase genes were in the lowest numbers. Also, the Org and TCPF samples showed lower diversity, while rare and abundant species ranged from 12 to 25% and 20 to 32% of the total bacterial species in all the sets, respectively. These variations indicate that the different cropping sequence had a significant impact on soil microbial diversity and community composition, which characterizes its economic and environmental value as a sustainable agricultural approach to maintaining food security and ecosystem health. IMPORTANCE This investigation examined the wheat microbiome under six different agricultural field conditions to understand the role of cropping pattern on soil microbial diversity. This study also elaborated the community composition, which has importance in economic (role of beneficial community leading to higher production) and environmental (role of microbial diversity/community in safeguarding the soil health, etc.) arenas. This could lead to a sustainable farming approach for food security and improved ecosystem health. Also, the majority of the microbes are unculturable; hence, technology-based microcultivation will be a potential approach for harnessing other cultured microorganisms, leading to unique species for commercial production. The outcome of this research-accelerated work can provide an idea to the scientists/breeders/agronomists/pathologists under the mentioned field conditions regarding their influence over their crops.
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Microbial Degradation of Azo Dyes: Approaches and Prospects for a Hazard-Free Conversion by Microorganisms. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19084740. [PMID: 35457607 PMCID: PMC9026373 DOI: 10.3390/ijerph19084740] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 11/16/2022]
Abstract
Azo dyes have become a staple in various industries, as colors play an important role in consumer choices. However, these dyes pose various health and environmental risks. Although different wastewater treatments are available, the search for more eco-friendly options persists. Bioremediation utilizing microorganisms has been of great interest to researchers and industries, as the transition toward greener solutions has become more in demand through the years. This review tackles the health and environmental repercussions of azo dyes and its metabolites, available biological approaches to eliminate such dyes from the environment with a focus on the use of different microorganisms, enzymes that are involved in the degradation of azo dyes, and recent trends that could be applied for the treatment of azo dyes.
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Liu S, Wang P, Wang C, Chen J, Wang X, Hu B, Yuan Q. Ecological insights into the disturbances in bacterioplankton communities due to emerging organic pollutants from different anthropogenic activities along an urban river. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 796:148973. [PMID: 34274679 DOI: 10.1016/j.scitotenv.2021.148973] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
Emerging organic pollutants (EOPs) in urban rivers have raised concerns regarding their eco-toxicological effects. However, the bacterioplankton community disturbances caused by EOPs in urban rivers and the associated ecological mechanisms remain unclear. This study provided profiles of the spatial distribution of a bacterioplankton community disturbed by human activity along an urban river. The results showed that EOP concentration and composition were differently distributed in residential and industrial areas, which significantly influenced bacterioplankton community structure. Based on redundancy analysis, parabens (methylparaben and propylparaben) were the major factors driving bacterioplankton community changes. Parabens inhibited gram-positive bacteria and promoted oxidative stress-tolerant bacteria in the river ecosystem. Parabens also disturbed ecological processes of bacterioplankton community assembly, shifting from a homogeneous selection (consistent selection pressure under similar environmental condition) to stochastic processes (random changes due to birth, death, immigration, and emigration) with changing in paraben concentrations. Heterogeneous selection was predicted to dominate microbial community assembly with paraben concentration changes exceeding 61.6 ng/L, which could deteriorate the river ecosystem. Furthermore, specific bacterial genera were identified as potential bioindicators to assess the condition of EOP contaminants in the river. Overall, this study highlights significant disturbances in bacterioplankton communities by EOPs at environmental concentrations, and our results could facilitate generation of appropriate management strategies aimed at EOPs in urban rivers.
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Affiliation(s)
- Sheng Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China.
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Xun Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Bin Hu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Qiusheng Yuan
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
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Abdulsada Z, Kibbee R, Princz J, DeRosa M, Örmeci B. Transformation of Silver Nanoparticles (AgNPs) during Lime Treatment of Wastewater Sludge and Their Impact on Soil Bacteria. NANOMATERIALS 2021; 11:nano11092330. [PMID: 34578645 PMCID: PMC8465233 DOI: 10.3390/nano11092330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 11/16/2022]
Abstract
This study investigated the impact of lime stabilization on the fate and transformation of AgNPs. It also evaluated the changes in the population and diversity of the five most relevant bacterial phyla in soil after applying lime-stabilized sludge containing AgNPs. The study was performed by spiking an environmentally relevant concentration of AgNPs (2 mg AgNPs/g TS) in sludge, applying lime stabilization to increase pH to above 12 for two hours, and applying lime-treated sludge to soil samples. Transmission electron microscopy (TEM) and energy-dispersive X-ray spectroscopy (EDS) were used to investigate the morphological and compositional changes of AgNPs during lime stabilization. After the application of lime stabilized sludge to the soil, soil samples were periodically analyzed for total genomic DNA and changes in bacterial phyla diversity using quantitative polymerase chain reaction (qPCR). The results showed that lime treatment effectively removed AgNPs from the aqueous phase, and AgNPs were deposited on the lime molecules. The results revealed that AgNPs did not significantly impact the presence and diversity of the assessed phyla in the soil. However, lime stabilized sludge with AgNPs affected the abundance of each phylum over time. No significant effects on the soil total organic carbon (TOC), heterotrophic plate count (HPC), and percentage of the live cells were observed.
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Affiliation(s)
- Zainab Abdulsada
- Department of Civil and Environmental Engineering, Carleton University, Ottawa, ON K1S 5B6, Canada; (Z.A.); (R.K.)
- Department of Environmental Engineering, University of Baghdad, Karrada, Al-Jadriya, Baghdad, Iraq
| | - Richard Kibbee
- Department of Civil and Environmental Engineering, Carleton University, Ottawa, ON K1S 5B6, Canada; (Z.A.); (R.K.)
| | - Juliska Princz
- Environment and Climate Change Canada, 335 River Road South, Ottawa, ON K1V 1C7, Canada;
| | - Maria DeRosa
- Department of Chemistry, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Banu Örmeci
- Department of Civil and Environmental Engineering, Carleton University, Ottawa, ON K1S 5B6, Canada; (Z.A.); (R.K.)
- Correspondence: ; Tel.: +1-613-520-2600 (ext. 4144)
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Rong L, Wu X, Xu J, Dong F, Liu X, Xu H, Cao J, Zheng Y. Clomazone improves the interactions between soil microbes and affects C and N cycling functions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 770:144730. [PMID: 33736380 DOI: 10.1016/j.scitotenv.2020.144730] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Clomazone, a widely used herbicide, is mainly used in soybean fields. We previously found that clomazone alters Proteobacteria and Nitrospirae abundances and also alters urease activity, which result in changes in NH4+ and NO3- contents in soil nitrogen cycling. It remains unknown, however, how the co-occurrence patterns of species and functions of soil ecosystems change in response to clomazone applications in soil. We designed a 3-month greenhouse experiment to investigate soil microorganism dynamics in response to clomazone. Clomazone was applied at three doses (e.g., T1, T10, T100), which significantly increased bacterial abundance at days 15 and 60. Fungal abundance was stimulated at day 30 in T10-treated soils, whereas fungal abundances decreased in T100-treated soils at day 15. Clomazone altered bacterial and fungal community structures. Network analyses showed more complex and highly connected microbial communities in clomazone-treated soils. Moreover, an Acidobacteria-dominated cluster was identified within each network of clomazone-treated soils. Clomazone applied at the recommended rate decreased the functional groups that were associated with denitrification and hydrogen oxidation at days 15 and 60, and enhanced photoheterotrophy from days 30 to 60. High clomazone inputs increased trophic types (e.g., chemoheterotrophy, phototrophy, photoautotrophy and cyanobacteria) and C cycling functional groups (e.g., fermentation and cellulolysis). The half-life of clomazone ranged from 40.1 to 93.5 days in three cases. Our results provide important information for use of this herbicide.
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Affiliation(s)
- Lili Rong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Xiaohu Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jun Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fengshou Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xingang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hanqing Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Junli Cao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yongquan Zheng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Pino-Otín MR, Ballestero D, Navarro E, Mainar AM, Val J. Effects of the insecticide fipronil in freshwater model organisms and microbial and periphyton communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 764:142820. [PMID: 33121789 DOI: 10.1016/j.scitotenv.2020.142820] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 05/24/2023]
Abstract
Fipronil is a broad-spectrum insecticide whose release in the environment damages many non-target organisms. This study evaluated the toxicity of fipronil at two biological levels using in vivo conditions and environmentally relevant concentrations: the first based on two model organisms (aquatic invertebrate Daphnia magna and the unicellular freshwater alga Chlamydomonas reinhardtii) and a second based on three natural communities (river periphyton and freshwater and soil microbial communities). The physicochemical properties of fipronil make it apparently unstable in the environment, so its behaviour was followed with high performance liquid chromatography (HPLC) under the different test conditions. The most sensitive organism to fipronil was D. magna, with median lethal dose (LC50) values from 0.07 to 0.38 mg/L (immobilisation test). Toxicity was not affected by the media used (MOPS or river water), but it increased with temperature. Fipronil produced effects on the photosynthetic activity of C. reinhardtii at 20 °C in MOPS (EC50 = 2.44 mg/L). The freshwater periphyton presented higher sensitivity to fipronil (photosynthetic yield EC50 of 0.74 mg/L) in MOPS and there was a time-dependent effect (toxicity increased with time). Toxicity was less evident when periphyton and C. reinhardtii tests were performed in river water, where the solubility of fipronil is poor. Finally, the assessment of the metabolic profiles using Biolog EcoPlates showed that bacteria communities were minimally affected by fipronil. The genetic identification of these communities based on 16S rRNA gene sequencing revealed that many of the taxa are specialists in degrading high molecular weight compounds, including pesticides. This work allows us to better understand the impact of fipronil on the environment at different levels of the food chain and in different environmental conditions, a necessary point given its presence in the environment and the complex behaviour of this compound.
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Affiliation(s)
| | - Diego Ballestero
- Universidad San Jorge, Villanueva de Gállego, 50830 Zaragoza, Spain.
| | - Enrique Navarro
- Pyrenean Institute of Ecology, CSIC, Av. Montañana 1005, Zaragoza 50059, Spain.
| | - Ana M Mainar
- I3A, Universidad de Zaragoza, c/ Mariano Esquillor s/n, 50018 Zaragoza, Spain.
| | - Jonatan Val
- Universidad San Jorge, Villanueva de Gállego, 50830 Zaragoza, Spain; Pyrenean Institute of Ecology, CSIC, Av. Montañana 1005, Zaragoza 50059, Spain.
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Bhatt P, Bhatt K, Sharma A, Zhang W, Mishra S, Chen S. Biotechnological basis of microbial consortia for the removal of pesticides from the environment. Crit Rev Biotechnol 2021; 41:317-338. [PMID: 33730938 DOI: 10.1080/07388551.2020.1853032] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The application of microbial strains as axenic cultures has frequently been employed in a diverse range of sectors. In the natural environment, microbes exist as multispecies and perform better than monocultures. Cell signaling and communication pathways play a key role in engineering microbial consortia, because in a consortium, the microorganisms communicate via diffusible signal molecules. Mixed microbial cultures have gained little attention due to the lack of proper knowledge about their interactions with each other. Some ideas have been proposed to deal with and study various microbes when they live together as a community, for biotechnological application purposes. In natural environments, microbes can possess unique metabolic features. Therefore, microbial consortia divide the metabolic burden among strains in the group and robustly perform pesticide degradation. Synthetic microbial consortia can perform the desired functions at naturally contaminated sites. Therefore, in this article, special attention is paid to the microbial consortia and their function in the natural environment. This review comprehensively discusses the recent applications of microbial consortia in pesticide degradation and environmental bioremediation. Moreover, the future directions of synthetic consortia have been explored. The review also explores the future perspectives and new platforms for these approaches, besides highlighting the practical understanding of the scientific information behind consortia.
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Affiliation(s)
- Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Kalpana Bhatt
- Department of Botany and Microbiology, Gurukula Kangri University, Haridwar, Uttarakhand, India
| | - Anita Sharma
- Department of Microbiology, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Wenping Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Sandhya Mishra
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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Pinto OHB, Costa FS, Rodrigues GR, da Costa RA, da Rocha Fernandes G, Júnior ORP, Barreto CC. Soil Acidobacteria Strain AB23 Resistance to Oxidative Stress Through Production of Carotenoids. MICROBIAL ECOLOGY 2021; 81:169-179. [PMID: 32617619 DOI: 10.1007/s00248-020-01548-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
Metagenomic studies revealed the prevalence of Acidobacteria in soils, but the physiological and ecological reasons for their success are not well understood. Many Acidobacteria exhibit carotenoid-related pigments, which may be involved in their tolerance of environmental stress. The aim of this work was to investigate the role of the orange pigments produced by Acidobacteria strain AB23 isolated from a savannah-like soil and to identify putative carotenoid genes in Acidobacteria genomes. Phylogenetic analysis revealed that strain AB23 belongs to the Occallatibacter genus from the class Acidobacteriia (subdivision 1). Strain AB23 produced carotenoids in the presence of light and vitamins; however, the growth rate and biomass decreased when cells were exposed to light. The presence of carotenoids resulted in tolerance to hydrogen peroxide. Comparative genomics revealed that all members of Acidobacteriia with available genomes possess the complete gene cluster for phytoene production. Some Acidobacteriia members have an additional gene cluster that may be involved in the production of colored carotenoids. Both colored and colorless carotenoids are involved in tolerance to oxidative stress. These results show that the presence of carotenoid genes is widespread among Acidobacteriia. Light and atmospheric oxygen stimulate carotenoid synthesis, but there are other natural sources of oxidative stress in soils. Tolerance to environmental oxidative stress provided by carotenoids may offer a competitive advantage for Acidobacteria in soils.
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Affiliation(s)
- Otávio Henrique Bezerra Pinto
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, SGAN 916 Módulo B Avenida W5 - Asa Norte, Brasília, 70790-160, Brazil
- Laboratory of Enzymology, Institute of Biological Sciences, Department of Cell Biology, University of Brasília, Brasília, 70910-900, Brazil
| | - Flávio Silva Costa
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, SGAN 916 Módulo B Avenida W5 - Asa Norte, Brasília, 70790-160, Brazil
- Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
| | - Gisele Regina Rodrigues
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, SGAN 916 Módulo B Avenida W5 - Asa Norte, Brasília, 70790-160, Brazil
| | - Rosiane Andrade da Costa
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, SGAN 916 Módulo B Avenida W5 - Asa Norte, Brasília, 70790-160, Brazil
| | - Gabriel da Rocha Fernandes
- Research Center René Rachou, Oswaldo Cruz Foundation (Fiocruz), Avenida Augusto de Lima 1715, Barro Preto, Belo Horizonte, 30190-002, Brazil
| | - Osmindo Rodrigues Pires Júnior
- Department of Physiological Sciences, Institute of Biological Sciences, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Cristine Chaves Barreto
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, SGAN 916 Módulo B Avenida W5 - Asa Norte, Brasília, 70790-160, Brazil.
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Hamid H, Li LY, Grace JR. Effect of substrate concentrations on aerobic biotransformation of 6:2 fluorotelomer sulfonate (6:2 FTS) in landfill leachate. CHEMOSPHERE 2020; 261:128108. [PMID: 33113640 DOI: 10.1016/j.chemosphere.2020.128108] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 08/05/2020] [Accepted: 08/20/2020] [Indexed: 06/11/2023]
Abstract
Biotransformation of 6:2 fluorotelomer sulfonate (FTS) results in the formation of short-chain (C4 - C6) perfluorocarboxylic acids (PFCAs) in landfill leachate. Although leachate substrate concentrations (i.e., organic carbon, ammonia) vary widely, their effects on 6:2 FTS biotransformation and PFCAs formation are unknown. This study investigated the effect of organic carbon and ammonia concentration in 6:2 FTS aerobic biotransformation and PFCA formation in leachate. Biotransformation experiments were conducted with sediment collected from a landfill leachate ditch, to which deionized (DI) water and various amounts of leachate were added. Microbial community analysis using 16S rRNA indicated that while phylum Proteobacteria dominated the bacterial composition throughout the 60 days, Actinobacteria increased with time. Many genera from Proteobacteria and Actinobacteria can synthesize a wide array of enzymes, indicating that these phyla are likely to play an important role in 6:2 FTS biotransformation. Higher biotransformation of 6:2 FTS was observed in leachate-added microcosms (∼21%), compared to DI water microcosm (∼14%), likely reflecting the substrate dependency of 6:2 FTS biotransformation. Substrate limiting conditions in DI water microcosm resulted in slightly greater formation of ∑(C4 - C6) PFCAs (∼14 mol%), compared with leachate added microcosms (10-13 mol%). The findings suggest that dilution of landfill leachate, (e.g., during wet seasons), likely results in reduced 6:2 FTS biotransformation and increased PFCAs formation compared to dry conditions. Observed formation of C7 - C8 PFCAs in the live microcosms suggested that landfills act as secondary sources of legacy PFCAs (e.g., perfluorooctanoic acid) in the environment.
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Affiliation(s)
- Hanna Hamid
- Civil Engineering, University of British Columbia, 6250 Applied Science Lane, Vancouver, BC, V6T 1Z4, Canada
| | - Loretta Y Li
- Civil Engineering, University of British Columbia, 6250 Applied Science Lane, Vancouver, BC, V6T 1Z4, Canada.
| | - John R Grace
- Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, BC, V6T 1Z3, Canada
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12
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Wang CN, Wu RL, Li YY, Qin YF, Li YL, Meng FQ, Wang LG, Xu FL. Effects of pesticide residues on bacterial community diversity and structure in typical greenhouse soils with increasing cultivation years in Northern China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 710:136321. [PMID: 31923679 DOI: 10.1016/j.scitotenv.2019.136321] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/18/2019] [Accepted: 12/22/2019] [Indexed: 06/10/2023]
Abstract
The understanding of soil microbiome is important for sustainable cultivation, especially under greenhouse conditions. Here, we investigated the changes in soil pesticide residues and microbial diversity and community structure at different cultivation years under a greenhouse system. The 9-to-14 years sites were found to have the least diversity/rich microbial population as compared to sites under 8 years and over 16 years, as analyzed with alpha diversity index. In total, 42 bacterial phyla were identified across soils with different pesticide residues and cultivation ages. Proteobacteria, Acidobacteria, and Bacteroidetes represented the dominant phyla, that accounted for 34.2-43.4%, 9.7-19.3% and 9.2-16.5% of the total population, respectively. Our data prove that certain pesticides contribute to variation in soil microbial community and that soil bacteria respond differently to cultivation years under greenhouse conditions. Thus, this study provides an insight into microbial community structure changes by pesticides under greenhouse systems and natural biodegradation may have an important part in pesticides soil decontamination.
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Affiliation(s)
- Chao-Nan Wang
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Rui-Lin Wu
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yu-Yan Li
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yi-Fan Qin
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yi-Long Li
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Fan-Qiao Meng
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Li-Gang Wang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Key Laboratory of Agricultural Non-point Source Pollution Control, Ministry of Agriculture, Beijing 100081, China
| | - Fu-Liu Xu
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China.
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13
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Baćmaga M, Wyszkowska J, Kucharski J. Response of soil microorganisms and enzymes to the foliar application of Helicur 250 EW fungicide on Horderum vulgare L. CHEMOSPHERE 2020; 242:125163. [PMID: 31677518 DOI: 10.1016/j.chemosphere.2019.125163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/17/2019] [Accepted: 10/20/2019] [Indexed: 06/10/2023]
Abstract
The use of fungicides bears the risk of many undesirable outcomes that are manifested in, among other things, changes in the structure and activity of microorganisms. This study aimed at determining the effect of a Helicur 250 EW preparation, used to protect crops against fungal diseases, on the microbiological and biochemical activity of soil and on the development of Horderum vulgare L. The fungicide was sprayed on leaves of spring barley in the following doses (per active substance, i.e. tebuconazole, TEB): 0.046, 0.093, 0.139, 1.395, and 2.790 mg TEB plant-1. The following indices were analyzed in the study: index of microorganisms resistance (RS) to the effects of fungicide, microorganisms colony development index (CD), microorganisms ecophysiological diversity index (EP), genetic diversity of bacteria, enzymatic activity, and effect of the fungicide on spring barley development (IFH). The most susceptible to the effects of the fungicide turned out to be fungi. The metagenomic analysis demonstrated that the bacterial community differed in terms of structure and percentage contribution in the soil exposed to the fungicide from the control soil even at the Phylum level. However, Proteobacteria appeared to be the prevailing taxon in both soils. Bacillus arabhattai, B. soli, and B. simplex occurred exclusively in the control soil, whereas Ramlibacter tataounensis, Azospirillum palatum, and Kaistobacter terrae - exclusively in the soil contaminated with the fungicide. Helicur 250 EW suppressed activities of all soil enzymes except for arylsulfatase. In addition, it proved to be a strong inhibitor of spring barley growth and development.
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Affiliation(s)
- Małgorzata Baćmaga
- Department of Microbiology, University of Warmia and Mazury in Olsztyn, Plac Łódzki 3, 10-727, Olsztyn, Poland
| | - Jadwiga Wyszkowska
- Department of Microbiology, University of Warmia and Mazury in Olsztyn, Plac Łódzki 3, 10-727, Olsztyn, Poland.
| | - Jan Kucharski
- Department of Microbiology, University of Warmia and Mazury in Olsztyn, Plac Łódzki 3, 10-727, Olsztyn, Poland
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14
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Romero IA, van Dillewijn P, Nesme J, Sørensen SJ, Romero E. Improvement of pesticide removal in contaminated media using aqueous extracts from contaminated biopurification systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 691:749-759. [PMID: 31325872 DOI: 10.1016/j.scitotenv.2019.07.087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/02/2019] [Accepted: 07/06/2019] [Indexed: 06/10/2023]
Abstract
Despite certain limitations, bioaugmentation enhances the efficiency of bioremediation systems. In this study, three aqueous extracts (APE, ACE and APE) from aged residual biomixtures in three biopurification systems (BPSs) exposed to pesticides at a pilot scale were found to improve pesticide removal. The addition of ACEs and AVEs to solutions containing the model compound diuron increased removal rates 6- and 17-fold, respectively, as compared to APEs. These extracts also increased the removal of the metabolite 3,4-dichloroaniline, while AVEs, in particular, were found to remove all pesticides within 9 days. Three metabolites less hazardous than 3,4-dichloroaniline were identified by SPME/GC/MS. AVEs, which also enhance linuron removal in liquid media, were found to increase diuron removal 6-fold in BPSs. We observed an increase in the relative abundance of taxa, such as Chloroflexi, Acidobacteria, Gemmatimonadetes, Firmicutes, Deinococcus-Thermus and especially Proteobacteria (10%), in AV biomixtures, as well as an enrichment of γ-proteobacteria and the actinobacterial genus Dokdonella in AVEs with respect to initial noncontaminated IV biomixture. We demonstrate that extracts containing a pollutant-acclimatized microbiome could be used as part of a bioaugmentation strategy to improve the functioning of on-farm BPSs and contaminated systems.
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Affiliation(s)
- Inés Aguilar Romero
- Department of Environmental Protection, Estación Experimental del Zaidín. Consejo Superior de Investigaciones Científicas (EEZ-CSIC), C/ Profesor Albareda 1, 18008 Granada, Spain.
| | - Pieter van Dillewijn
- Department of Environmental Protection, Estación Experimental del Zaidín. Consejo Superior de Investigaciones Científicas (EEZ-CSIC), C/ Profesor Albareda 1, 18008 Granada, Spain.
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Esperanza Romero
- Department of Environmental Protection, Estación Experimental del Zaidín. Consejo Superior de Investigaciones Científicas (EEZ-CSIC), C/ Profesor Albareda 1, 18008 Granada, Spain.
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15
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Hemmat-Jou MH, Safari-Sinegani AA, Mirzaie-Asl A, Tahmourespour A. Analysis of microbial communities in heavy metals-contaminated soils using the metagenomic approach. ECOTOXICOLOGY (LONDON, ENGLAND) 2018; 27:1281-1291. [PMID: 30242595 DOI: 10.1007/s10646-018-1981-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/01/2018] [Indexed: 06/08/2023]
Abstract
Soil pollution occurring at mining sites has adverse impacts on soil microbial diversity. New approaches, such as metagenomics approach, have become a powerful tool to investigate biodiversity of soil microbial communities. In the current study, metagenomics approach was used to investigate the microbial diversity of soils contaminated with different concentrations of lead (Pb) and zinc (Zn). The contaminated soils were collected from a Pb and Zn mine. The soil total DNA was extracted and 16S rDNA genes were amplified using universal primers. The PCR amplicons were sequenced and bioinformatic analysis of metagenomes was conducted to identify prokaryotic diversity in the Pb- and Zn-contaminated soils. The results indicated that the ten most abundant bacteria in all samples were Solirubrobacter (Actinobacteria), Geobacter (Proteobacteria), Edaphobacter (Acidobacteria), Pseudomonas (Proteobacteria), Gemmatiomonas (Gemmatimonadetes), Nitrosomonas, Xanthobacter, and Sphingomonas (Proteobacteria), Pedobacter (Bacterioidetes), and Ktedonobacter (Chloroflexi), descendingly. Archaea were also numerous, and Nitrososphaerales which are important in the nitrogen cycle had the highest abundance in the samples. Although, alpha and beta diversity showed negative effects of Pb and Zn contamination on soil microbial communities, microbial diversity of the contaminated soils was not subjected to a significant change. This study provided valuable insights into microbial composition in heavy metals-contaminated soils.
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Affiliation(s)
- M H Hemmat-Jou
- Department of Soil Science, College of Agriculture, Bu-Ali Sina University, Hamedan, 6517838695, Iran.
| | - A A Safari-Sinegani
- Department of Soil Science, College of Agriculture, Bu-Ali Sina University, Hamedan, 6517838695, Iran
| | - A Mirzaie-Asl
- Department of Biotechnology, College of Agriculture, Bu-Ali Sina University, Hamedan, 6517838695, Iran
| | - A Tahmourespour
- Department of Basic Medical Sciences, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan, Iran
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16
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Bergsveinson J, Perry B, Sheedy C, Braul L, Reedyk S, Gossen B, Yost C. Identifying the core bacterial and fungal communities within four agricultural biobeds used for the treatment of pesticide rinsates. J Appl Microbiol 2018; 125:1333-1342. [DOI: 10.1111/jam.14051] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 06/29/2018] [Accepted: 07/13/2018] [Indexed: 11/29/2022]
Affiliation(s)
- J. Bergsveinson
- Department of Biology; University of Regina; Regina SK Canada
| | - B.J. Perry
- Department of Biology; University of Regina; Regina SK Canada
| | - C. Sheedy
- Agriculture and Agri-Food Canada; Lethbridge AB Canada
| | - L. Braul
- Agriculture and Agri-Food Canada; Regina SK Canada
| | - S. Reedyk
- Agriculture and Agri-Food Canada; Edmonton AB Canada
| | - B.D. Gossen
- Agriculture and Agri-Food Canada; Saskatoon SK Canada
| | - C.K. Yost
- Department of Biology; University of Regina; Regina SK Canada
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17
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Roberto AA, Van Gray JB, Leff LG. Sediment bacteria in an urban stream: Spatiotemporal patterns in community composition. WATER RESEARCH 2018; 134:353-369. [PMID: 29454907 DOI: 10.1016/j.watres.2018.01.045] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/04/2018] [Accepted: 01/20/2018] [Indexed: 05/25/2023]
Abstract
Sediment bacterial communities play a critical role in biogeochemical cycling in lotic ecosystems. Despite their ecological significance, the effects of urban discharge on spatiotemporal distribution of bacterial communities are understudied. In this study, we examined the effect of urban discharge on the spatiotemporal distribution of stream sediment bacteria in a northeast Ohio stream. Water and sediment samples were collected after large storm events (discharge > 100 m) from sites along a highly impacted stream (Tinkers Creek, Cuyahoga River watershed, Ohio, USA) and two reference streams. Although alpha (α) diversity was relatively constant spatially, multivariate analysis of bacterial community 16S rDNA profiles revealed significant spatial and temporal effects on beta (β) diversity and community composition and identified a number of significant correlative abiotic parameters. Clustering of upstream and reference sites from downstream sites of Tinkers Creek combined with the dominant families observed in specific locales suggests that environmentally-induced species sorting had a strong impact on the composition of sediment bacterial communities. Distinct groupings of bacterial families that are often associated with nutrient pollution (i.e., Comamonadaceae, Rhodobacteraceae, and Pirellulaceae) and other contaminants (i.e., Sphingomonadaceae and Phyllobacteriaceae) were more prominent at sites experiencing higher degrees of discharge associated with urbanization. Additionally, there were marked seasonal changes in community composition, with individual taxa exhibiting different seasonal abundance patterns. However, spatiotemporal variation in stream conditions did not affect bacterial community functional profiles. Together, these results suggest that local environmental drivers and niche filtering from discharge events associated with urbanization shape the bacterial community structure. However, dispersal limitations and interactions among other species likely play a role as well.
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Affiliation(s)
- Alescia A Roberto
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA.
| | - Jonathon B Van Gray
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA.
| | - Laura G Leff
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA.
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18
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Isolation of the (+)-Pinoresinol-Mineralizing Pseudomonas sp. Strain SG-MS2 and Elucidation of Its Catabolic Pathway. Appl Environ Microbiol 2018; 84:AEM.02531-17. [PMID: 29222099 DOI: 10.1128/aem.02531-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 11/28/2017] [Indexed: 11/20/2022] Open
Abstract
Pinoresinol is a dimer of two β-β'-linked coniferyl alcohol molecules. It is both a plant defense molecule synthesized through the shikimic acid pathway and a representative of several β-β-linked dimers produced during the microbial degradation of lignin in dead plant material. Until now, little has been known about the bacterial catabolism of such dimers. Here we report the isolation of the efficient (+)-pinoresinol-mineralizing Pseudomonas sp. strain SG-MS2 and its catabolic pathway. Degradation of pinoresinol in this strain is inducible and proceeds via a novel oxidative route, which is in contrast to the previously reported reductive transformation by other bacteria. Based on enzyme assays and bacterial growth, cell suspension, and resting cell studies, we provide conclusive evidence that pinoresinol degradation in strain SG-MS2 is initiated by benzylic hydroxylation, generating a hemiketal via a quinone methide intermediate, which is then hydrated at the benzylic carbon by water. The hemiketal, which stays in equilibrium with the corresponding keto alcohol, undergoes an aryl-alkyl cleavage to generate a lactone and 2-methoxyhydroquinone. While the fate of 2-methoxyhydroquinone is not investigated further, it is assumed to be assimilated by ring cleavage. The lactone is further metabolized via two routes, namely, lactone ring cleavage and benzylic hydroxylation via a quinone methide intermediate, as described above. The resulting hemiketal again exists in equilibrium with a keto alcohol. Our evidence suggests that both routes of lactone metabolism lead to vanillin and vanillic acid, which we show can then be mineralized by strain SG-MS2.IMPORTANCE The oxidative catabolism of (+)-pinoresinol degradation elucidated here is fundamentally different from the reductive cometabolism reported for two previously characterized bacteria. Our findings open up new opportunities to use lignin for the biosynthesis of vanillin, a key flavoring agent in foods, beverages, and pharmaceuticals, as well as various new lactones. Our work also has implications for the study of new pinoresinol metabolites in human health. The enterodiol and enterolactone produced through reductive transformation of pinoresinol by gut microbes have already been associated with decreased risks of cancer and cardiovascular diseases. The metabolites from oxidative metabolism we find here also deserve attention in this respect.
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19
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Holmsgaard PN, Dealtry S, Dunon V, Heuer H, Hansen LH, Springael D, Smalla K, Riber L, Sørensen SJ. Response of the bacterial community in an on-farm biopurification system, to which diverse pesticides are introduced over an agricultural season. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 229:854-862. [PMID: 28734695 DOI: 10.1016/j.envpol.2017.07.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 07/06/2017] [Accepted: 07/08/2017] [Indexed: 06/07/2023]
Abstract
A biopurification system (BPS) is used on-farm to clean pesticide-contaminated wastewater. Due to high pesticide loads, a BPS represents a hot spot for the proliferation and selection as well as the genetic adaptation of discrete pesticide degrading microorganisms. However, while considerable knowledge exists on the biodegradation of specific pesticides in BPSs, the bacterial community composition of these systems has hardly been explored. In this work, the Shannon diversity, the richness and the composition of the bacterial community within an operational BPS receiving wastewater contaminated with various pesticides was, for the first time, elucidated over the course of an agricultural season, using DGGE profiling and pyrosequencing of 16S rRNA gene fragments amplified from total community DNA. During the agricultural season, an increase in the concentration of pesticides in the BPS was observed along with the detection of significant community changes including a decrease in microbial diversity. Additionally, a significant increase in the relative abundance of Proteobacteria, mainly the Gammaproteobacteria, was found, and OTUs (operational taxonomic units) affiliated to Pseudomonas responded positively during the course of the season. Furthermore, a banding-pattern analysis of 16S rRNA gene-based DGGE fingerprinting, targeting the Alpha- and Betaproteobacteria as well as the Actinobacteria, indicated that the Betaproteobacteria might play an important role. Interestingly, a decrease of Firmicutes and Bacteroidetes was observed, indicating their selective disadvantage in a BPS, to which pesticides have been introduced.
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Affiliation(s)
- Peter N Holmsgaard
- Section for Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Simone Dealtry
- Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany; Civil Engineering Department, Catholic University of Rio de Janeiro, Rua Marquês de São Vicente 225/301-L, Gávea, 22453-900 Rio de Janeiro, RJ, Brazil
| | - Vincent Dunon
- Division of Soil and Water Management, KULeuven, 3001 Leuven, Belgium
| | - Holger Heuer
- Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany
| | - Lars H Hansen
- Section for Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark; Department of Environmental Science, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark
| | - Dirk Springael
- Division of Soil and Water Management, KULeuven, 3001 Leuven, Belgium
| | - Kornelia Smalla
- Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany
| | - Leise Riber
- Section for Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark.
| | - Søren J Sørensen
- Section for Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
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20
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Characterization of novel Acidobacteria exopolysaccharides with potential industrial and ecological applications. Sci Rep 2017; 7:41193. [PMID: 28117455 PMCID: PMC5259719 DOI: 10.1038/srep41193] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 12/15/2016] [Indexed: 01/19/2023] Open
Abstract
Acidobacteria have been described as one of the most abundant and ubiquitous bacterial phyla in soil. However, factors contributing to this ecological success are not well elucidated mainly due to difficulties in bacterial isolation. Acidobacteria may be able to survive for long periods in soil due to protection provided by secreted extracellular polymeric substances that include exopolysaccharides (EPSs). Here we present the first study to characterize EPSs derived from two strains of Acidobacteria from subdivision 1 belonging to Granulicella sp. EPS are unique heteropolysaccharides containing mannose, glucose, galactose and xylose as major components, and are modified with carboxyl and methoxyl functional groups that we characterized by Fourier transform infrared (FTIR) spectroscopy. Both EPS compounds we identified can efficiently emulsify various oils (sunflower seed, diesel, and liquid paraffin) and hydrocarbons (toluene and hexane). Moreover, the emulsions are more thermostable over time than those of commercialized xanthan. Acidobacterial EPS can now be explored as a source of biopolymers that may be attractive and valuable for industrial applications due to their natural origin, sustainability, biodegradability and low toxicity.
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21
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22
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Kielak AM, Barreto CC, Kowalchuk GA, van Veen JA, Kuramae EE. The Ecology of Acidobacteria: Moving beyond Genes and Genomes. Front Microbiol 2016; 7:744. [PMID: 27303369 PMCID: PMC4885859 DOI: 10.3389/fmicb.2016.00744] [Citation(s) in RCA: 437] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 05/03/2016] [Indexed: 12/01/2022] Open
Abstract
The phylum Acidobacteria is one of the most widespread and abundant on the planet, yet remarkably our knowledge of the role of these diverse organisms in the functioning of terrestrial ecosystems remains surprisingly rudimentary. This blatant knowledge gap stems to a large degree from the difficulties associated with the cultivation of these bacteria by classical means. Given the phylogenetic breadth of the Acidobacteria, which is similar to the metabolically diverse Proteobacteria, it is clear that detailed and functional descriptions of acidobacterial assemblages are necessary. Fortunately, recent advances are providing a glimpse into the ecology of members of the phylum Acidobacteria. These include novel cultivation and enrichment strategies, genomic characterization and analyses of metagenomic DNA from environmental samples. Here, we couple the data from these complementary approaches for a better understanding of their role in the environment, thereby providing some initial insights into the ecology of this important phylum. All cultured acidobacterial type species are heterotrophic, and members of subdivisions 1, 3, and 4 appear to be more versatile in carbohydrate utilization. Genomic and metagenomic data predict a number of ecologically relevant capabilities for some acidobacteria, including the ability to: use of nitrite as N source, respond to soil macro-, micro nutrients and soil acidity, express multiple active transporters, degrade gellan gum and produce exopolysaccharide (EPS). Although these predicted properties allude to a competitive life style in soil, only very few of these prediction shave been confirmed via physiological studies. The increased availability of genomic and physiological information, coupled to distribution data in field surveys and experiments, should direct future progress in unraveling the ecology of this important but still enigmatic phylum.
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Affiliation(s)
- Anna M Kielak
- Department of Microbial Ecology, The Netherlands Institute of Ecology - Koninklijke Nederlandse Akademie van Wetenschappen Wageningen, Netherlands
| | - Cristine C Barreto
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília Brasília, Brazil
| | - George A Kowalchuk
- Ecology and Biodiversity Group, University of Utrecht Utrecht, Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, The Netherlands Institute of Ecology - Koninklijke Nederlandse Akademie van Wetenschappen Wageningen, Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, The Netherlands Institute of Ecology - Koninklijke Nederlandse Akademie van Wetenschappen Wageningen, Netherlands
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23
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Jałowiecki Ł, Chojniak JM, Dorgeloh E, Hegedusova B, Ejhed H, Magnér J, Płaza GA. Microbial Community Profiles in Wastewaters from Onsite Wastewater Treatment Systems Technology. PLoS One 2016; 11:e0147725. [PMID: 26807728 PMCID: PMC4725721 DOI: 10.1371/journal.pone.0147725] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 01/07/2016] [Indexed: 11/18/2022] Open
Abstract
The aim of the study was to determine the potential of community-level physiological profiles (CLPPs) methodology as an assay for characterization of the metabolic diversity of wastewater samples and to link the metabolic diversity patterns to efficiency of select onsite biological wastewater facilities. Metabolic fingerprints obtained from the selected samples were used to understand functional diversity implied by the carbon substrate shifts. Three different biological facilities of onsite wastewater treatment were evaluated: fixed bed reactor (technology A), trickling filter/biofilter system (technology B), and aerated filter system (the fluidized bed reactor, technology C). High similarities of the microbial community functional structures were found among the samples from the three onsite wastewater treatment plants (WWTPs), as shown by the diversity indices. Principal components analysis (PCA) showed that the diversity and CLPPs of microbial communities depended on the working efficiency of the wastewater treatment technologies. This study provided an overall picture of microbial community functional structures of investigated samples in WWTPs and discerned the linkages between microbial communities and technologies of onsite WWTPs used. The results obtained confirmed that metabolic profiles could be used to monitor treatment processes as valuable biological indicators of onsite wastewater treatment technologies efficiency. This is the first step toward understanding relations of technology types with microbial community patterns in raw and treated wastewaters.
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Affiliation(s)
- Łukasz Jałowiecki
- Department of Environmental Microbiology, Institute for Ecology of Industrial Areas, Katowice, Poland
| | | | - Elmar Dorgeloh
- Development and Assessment Institute in Waste Water Technology at RWTH Aachen University, Aachen, Germany
| | - Berta Hegedusova
- Development and Assessment Institute in Waste Water Technology at RWTH Aachen University, Aachen, Germany
| | - Helene Ejhed
- Natural resources &Environmental Effects, IVL Swedish Environmental Research Institute, Stockholm, Sweden
| | - Jörgen Magnér
- Natural resources &Environmental Effects, IVL Swedish Environmental Research Institute, Stockholm, Sweden
| | - Grażyna Anna Płaza
- Department of Environmental Microbiology, Institute for Ecology of Industrial Areas, Katowice, Poland
- * E-mail:
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24
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Delineating bacterial community structure of polluted soil samples collected from cancer prone belt of Punjab, India. 3 Biotech 2015; 5:727-734. [PMID: 28324527 PMCID: PMC4569629 DOI: 10.1007/s13205-014-0270-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/13/2014] [Indexed: 11/01/2022] Open
Abstract
16S rRNA gene analysis has emerged as one of the valuable tools that are being utilized in investigating the molecular phylogenetic structure of the particular environment. Here, we embarked upon understanding and delineating the molecular phylogeny structure of microbes in polluted soil samples from cancer prone belt of the Punjab, India, which is highly contaminated with herbicide, pesticide and heavy metals. To investigate the bacterial phylogeny structure, a high-molecular weight metagenomic DNA was extracted from the soil samples, followed by PCR amplification, cloning and analysis of the 16S rRNA genes. Study employing 16S rRNA profiling of the community DNA revealed the presence of two major phylums: the Proteobacteria (26.7 %), the Bacteroidetes (11.2 %), and several minor groups, i.e., Acidobacteria (4.2 %), Actinobacteria (4.2 %), Firmicutes (2.8 %), Verrucomicrobia (2.8 %), Gemmatimonadetes (1.4 %) and Chloroflexi (1.4 %). Among the Proteobacteria, we mainly observed the α-Proteobacteria (18.3 %). Nearly, 38 % of the recovered 16S rRNA gene sequences in this study do not share similarity with known culturable bacterial sequences reported in the genebank data base and hence considered to be novel. More interestingly, 16S rRNA gene sequences of archaeal origin (7.0 %) were also recovered that primarily indicate change in their evolution pattern. A phylogenetic tree constructed based on alignment-dependent method revealed the extent of similarity these clones shared with each other, followed by alignment-independent methods that statistically confirmed the sequence variation among the clones. Despite the high level of contamination in the study area, we observed remarkable microbial diversity that mainly includes the Gram-negative bacteria. The presence of more Gram-negative bacteria indicates that they have evolved a robust mechanism to resist and cope up with these pollutants compared to Gram-positive groups. Investigation of the polluted soil samples employing culture-independent approach revealed important bacterial groups which could be engineered for future bioremediation studies.
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Subha B, Song YC, Woo JH. Optimization of biostimulant for bioremediation of contaminated coastal sediment by response surface methodology (RSM) and evaluation of microbial diversity by pyrosequencing. MARINE POLLUTION BULLETIN 2015; 98:235-246. [PMID: 26139459 DOI: 10.1016/j.marpolbul.2015.06.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 06/10/2015] [Accepted: 06/24/2015] [Indexed: 06/04/2023]
Abstract
The present study aims to optimize the slow release biostimulant ball (BSB) for bioremediation of contaminated coastal sediment using response surface methodology (RSM). Different bacterial communities were evaluated using a pyrosequencing-based approach in contaminated coastal sediments. The effects of BSB size (1-5cm), distance (1-10cm) and time (1-4months) on changes in chemical oxygen demand (COD) and volatile solid (VS) reduction were determined. Maximum reductions of COD and VS, 89.7% and 78.8%, respectively, were observed at a 3cm ball size, 5.5cm distance and 4months; these values are the optimum conditions for effective treatment of contaminated coastal sediment. Most of the variance in COD and VS (0.9291 and 0.9369, respectively) was explained in our chosen models. BSB is a promising method for COD and VS reduction and enhancement of SRB diversity.
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Affiliation(s)
- Bakthavachallam Subha
- Department of Environmental Engineering, Korea Maritime and Ocean University, Busan, South Korea
| | - Young Chae Song
- Department of Environmental Engineering, Korea Maritime and Ocean University, Busan, South Korea.
| | - Jung Hui Woo
- Nuclear Power Equipment Research Center, Korea Maritime and Ocean University, Busan, South Korea
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Cray JA, Bell ANW, Bhaganna P, Mswaka AY, Timson DJ, Hallsworth JE. The biology of habitat dominance; can microbes behave as weeds? Microb Biotechnol 2013; 6:453-92. [PMID: 23336673 PMCID: PMC3918151 DOI: 10.1111/1751-7915.12027] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 12/03/2012] [Indexed: 02/06/2023] Open
Abstract
Competition between microbial species is a product of, yet can lead to a reduction in, the microbial diversity of specific habitats. Microbial habitats can resemble ecological battlefields where microbial cells struggle to dominate and/or annihilate each other and we explore the hypothesis that (like plant weeds) some microbes are genetically hard-wired to behave in a vigorous and ecologically aggressive manner. These 'microbial weeds' are able to dominate the communities that develop in fertile but uncolonized--or at least partially vacant--habitats via traits enabling them to out-grow competitors; robust tolerances to habitat-relevant stress parameters and highly efficient energy-generation systems; avoidance of or resistance to viral infection, predation and grazers; potent antimicrobial systems; and exceptional abilities to sequester and store resources. In addition, those associated with nutritionally complex habitats are extraordinarily versatile in their utilization of diverse substrates. Weed species typically deploy multiple types of antimicrobial including toxins; volatile organic compounds that act as either hydrophobic or highly chaotropic stressors; biosurfactants; organic acids; and moderately chaotropic solutes that are produced in bulk quantities (e.g. acetone, ethanol). Whereas ability to dominate communities is habitat-specific we suggest that some microbial species are archetypal weeds including generalists such as: Pichia anomala, Acinetobacter spp. and Pseudomonas putida; specialists such as Dunaliella salina, Saccharomyces cerevisiae, Lactobacillus spp. and other lactic acid bacteria; freshwater autotrophs Gonyostomum semen and Microcystis aeruginosa; obligate anaerobes such as Clostridium acetobutylicum; facultative pathogens such as Rhodotorula mucilaginosa, Pantoea ananatis and Pseudomonas aeruginosa; and other extremotolerant and extremophilic microbes such as Aspergillus spp., Salinibacter ruber and Haloquadratum walsbyi. Some microbes, such as Escherichia coli, Mycobacterium smegmatis and Pseudoxylaria spp., exhibit characteristics of both weed and non-weed species. We propose that the concept of nonweeds represents a 'dustbin' group that includes species such as Synodropsis spp., Polypaecilum pisce, Metschnikowia orientalis, Salmonella spp., and Caulobacter crescentus. We show that microbial weeds are conceptually distinct from plant weeds, microbial copiotrophs, r-strategists, and other ecophysiological groups of microorganism. Microbial weed species are unlikely to emerge from stationary-phase or other types of closed communities; it is open habitats that select for weed phenotypes. Specific characteristics that are common to diverse types of open habitat are identified, and implications of weed biology and open-habitat ecology are discussed in the context of further studies needed in the fields of environmental and applied microbiology.
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Affiliation(s)
- Jonathan A Cray
- School of Biological Sciences, MBC, Queen's University BelfastBelfast, BT9 7BL, Northern Ireland, UK
| | - Andrew N W Bell
- School of Biological Sciences, MBC, Queen's University BelfastBelfast, BT9 7BL, Northern Ireland, UK
| | - Prashanth Bhaganna
- School of Biological Sciences, MBC, Queen's University BelfastBelfast, BT9 7BL, Northern Ireland, UK
| | - Allen Y Mswaka
- School of Biological Sciences, MBC, Queen's University BelfastBelfast, BT9 7BL, Northern Ireland, UK
| | - David J Timson
- School of Biological Sciences, MBC, Queen's University BelfastBelfast, BT9 7BL, Northern Ireland, UK
| | - John E Hallsworth
- School of Biological Sciences, MBC, Queen's University BelfastBelfast, BT9 7BL, Northern Ireland, UK
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Muturi EJ, Orindi BO, Kim CH. Effect of leaf type and pesticide exposure on abundance of bacterial taxa in mosquito larval habitats. PLoS One 2013; 8:e71812. [PMID: 23940789 PMCID: PMC3733839 DOI: 10.1371/journal.pone.0071812] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 07/03/2013] [Indexed: 10/29/2022] Open
Abstract
Lentic freshwater systems including those inhabited by aquatic stages of mosquitoes derive most of their carbon inputs from terrestrial organic matter mainly leaf litter. The leaf litter is colonized by microbial communities that provide the resource base for mosquito larvae. While the microbial biomass associated with different leaf species in container aquatic habitats is well documented, the taxonomic composition of these microbes and their response to common environmental stressors is poorly understood. We used indoor aquatic microcosms to determine the abundances of major taxonomic groups of bacteria in leaf litters from seven plant species and their responses to low concentrations of four pesticides with different modes of action on the target organisms; permethrin, malathion, atrazine and glyphosate. We tested the hypotheses that leaf species support different quantities of major taxonomic groups of bacteria and that exposure to pesticides at environmentally relevant concentrations alters bacterial abundance and community structure in mosquito larval habitats. We found support for both hypotheses suggesting that leaf litter identity and chemical contamination may alter the quality and quantity of mosquito food base (microbial communities) in larval habitats. The effect of pesticides on microbial communities varied significantly among leaf types, suggesting that the impact of pesticides on natural microbial communities may be highly complex and difficult to predict. Collectively, these findings demonstrate the potential for detritus composition within mosquito larval habitats and exposure to pesticides to influence the quality of mosquito larval habitats.
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Affiliation(s)
- Ephantus J Muturi
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Illinois, United States of America.
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Xie S, Wan R, Wang Z, Wang Q. Atrazine biodegradation by Arthrobacter strain DAT1: effect of glucose supplementation and change of the soil microbial community. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:4078-4084. [PMID: 23224504 DOI: 10.1007/s11356-012-1356-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 11/21/2012] [Indexed: 06/01/2023]
Abstract
The objective of this study was to investigate the impact of glucose supplementation on the soil microbiota inoculated with the atrazine-degrading Arthrobacter strain DAT1. Soil microcosms with different treatments were constructed for biodegradation tests. The impact of glucose supplementation on atrazine degradation capacity of the strain DAT1 and the strain's survival and growth were assessed. The densities of the 16S rRNA gene and the atrazine-metabolic trzN gene were determined using quantitative PCR. The growth of the strain DAT1 and the bacterial community structure were characterized using terminal restriction fragment length polymorphism. Glucose supplementation could affect atrazine degradation by the strain DAT1 and the strain's trzN gene density and growth. The density of the16S rRNA gene decreased during the incubation period. Glucose supplementation could alter the bacterial community structure during the bioaugmentation process. Glucose supplementation could promote the growth of the autochthonous soil degraders that harbored novel functional genes transforming atrazine. Further study will be necessary in order to elucidate the impact of exogenous carbon on autochthonous and inoculated degraders. This study could add some new insights on atrazine bioremediation.
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Affiliation(s)
- Shuguang Xie
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing, 100871, China.
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Liu J, Peng M, Li Y. Phylogenetic diversity of nitrogen-fixing bacteria and the nifH gene from mangrove rhizosphere soil. Can J Microbiol 2012; 58:531-9. [PMID: 22455729 DOI: 10.1139/w2012-016] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nine types of nitrogen-fixing bacterial strains were isolated from 3 rhizosphere soil samples taken from mangrove plants in the Dongzhaigang National Mangrove Nature Reserve of China. Most isolates belonged to Gammaproteobacteria Pseudomonas, showing that these environments constituted favorable niches for such abundant nitrogen-fixing bacteria. New members of the diazotrophs were also found. Using a soil DNA extraction and PCR-cloning-sequencing approach, 135 clones were analyzed by restriction fragment length polymorphism (RFLP) analysis, and 27 unique nifH sequence phylotypes were identified, most of which were closely related to sequences from uncultured bacteria. The diversity of nitrogen-fixing bacteria was assessed by constructing nifH phylogenetic trees from sequences of all isolates and clones in this work, together with related nifH sequences from other mangrove ecosystems in GenBank. The nifH diversity varied among soil samples, with distinct biogeochemical properties within a mangrove ecosystem. When comparing different mangrove ecosystems, the nifH gene sequences from a specific site tended to cluster as individual groups. The results provided interesting data and novel information on our understanding of diazotroph community diversity in the mangrove ecosystems.
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Affiliation(s)
- Jianyin Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
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Renault D, Vallance J, Déniel F, Wery N, Godon JJ, Barbier G, Rey P. Diversity of bacterial communities that colonize the filter units used for controlling plant pathogens in soilless cultures. MICROBIAL ECOLOGY 2012; 63:170-187. [PMID: 22015683 DOI: 10.1007/s00248-011-9961-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 09/29/2011] [Indexed: 05/31/2023]
Abstract
In recent years, increasing the level of suppressiveness by the addition of antagonistic bacteria in slow filters has become a promising strategy to control plant pathogens in the recycled solutions used in soilless cultures. However, knowledge about the microflora that colonize the filtering columns is still limited. In order to get information on this issue, the present study was carried out over a 4-year period and includes filters inoculated or not with suppressive bacteria at the start of the filtering process (two or three filters were used each year). After 9 months of filtration, polymerase chain reaction (PCR)-single strand conformation polymorphism analyses point out that, for the same year of experiment, the bacterial communities from control filters were relatively similar but that they were significantly different between the bacteria-amended and control filters. To characterize the changes in bacterial communities within the filters, this microflora was studied by quantitative PCR, community-level physiological profiles, and sequencing 16SrRNA clone libraries (filters used in year 1). Quantitative PCR evidenced a denser bacterial colonization of the P-filter (amended with Pseudomonas putida strains) than control and B-filter (amended with Bacillus cereus strains). Functional analysis focused on the cultivable bacterial communities pointed out that bacteria from the control filter metabolized more carbohydrates than those from the amended filters whose trophic behaviors were more targeted towards carboxylic acids and amino acids. The bacterial communities in P- and B-filters both exhibited significantly more phylotype diversity and markedly distinct phylogenetic compositions than those in the C-filter. Although there were far fewer Proteobacteria in B- and P-filters than in the C-filter (22% and 22% rather than 69% of sequences, respectively), the percentages of Firmicutes was much higher (44% and 55% against 9%, respectively). Many Pseudomonas species were also found in the bacterial communities of the control filter. The persistence of the amended suppressive-bacteria in the filters is discussed with regards to the management of suppressive microflora in soilless culture.
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Affiliation(s)
- David Renault
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, ESMISAB, Université Européenne de Bretagne/Université de Brest, 29280, Plouzané, France
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Kolekar YM, Nemade HN, Markad VL, Adav SS, Patole MS, Kodam KM. Decolorization and biodegradation of azo dye, reactive blue 59 by aerobic granules. BIORESOURCE TECHNOLOGY 2012; 104:818-822. [PMID: 22153293 DOI: 10.1016/j.biortech.2011.11.046] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Revised: 11/10/2011] [Accepted: 11/11/2011] [Indexed: 05/31/2023]
Abstract
The present study deals with development of aerobic granules from textile wastewater sludge and challenged with different concentration of reactive blue 59 (RB59) to test their dye degradation potential. The granules efficiently degraded reactive blue 59 and also sustained higher dye loading of up to 5.0 g l(-1). The significant induction of enzymes azoreductase and cytochrome P-450 indicated their prominent role in the dye degradation while genotoxicity studies demonstrated that the biotransformed product of the dye as non-toxic. The microbial community of the textile dyes degrading aerobic sludge granules analyzed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), revealed significantly diverse dye degrading microbial community belonging to alpha-, beta-, and gamma-proteobacteria.
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Affiliation(s)
- Yogesh M Kolekar
- Biochemistry Division, Department of Chemistry, University of Pune, Ganeshkhind, Pune 411007, India
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Petrić I, Bru D, Udiković-Kolić N, Hršak D, Philippot L, Martin-Laurent F. Evidence for shifts in the structure and abundance of the microbial community in a long-term PCB-contaminated soil under bioremediation. JOURNAL OF HAZARDOUS MATERIALS 2011; 195:254-260. [PMID: 21885188 DOI: 10.1016/j.jhazmat.2011.08.036] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 07/22/2011] [Accepted: 08/11/2011] [Indexed: 05/31/2023]
Abstract
Although the impact of bioremediation of PCB-contaminated sites on the indigenous microbial community is a key question for soil restoration, it remains poorly understood. Therefore, a small-scale bioremediation assay made of (a) a biostimulation treatment with carvone, soya lecithin and xylose and (b) two bioaugmentation treatments, one with a TSZ7 mixed culture and another with a Rhodococcus sp. Z6 pure strain was set up. Changes in the structure of the global soil microbial community and in the abundances of different taxonomic phyla were monitored using ribosomal intergenic spacer analysis (RISA) and real-time PCR. After an 18-month treatment, the structure of the bacterial community in the bioremediated soils was significantly different from that of the native soil. The shift observed in the bacterial community structure using RISA analysis was in accordance with the monitored changes in the abundances of 11 targeted phyla and classes. Actinobacteria, Bacteriodetes and α- and γ-Proteobacteria were more abundant under all three bioremediation treatments, with Actinobacteria representing the dominant phylum. Altogether, our results indicate that bioremediation of PCB-contaminated soil induces significant changes in the structure and abundance of the total microbial community, which must be addressed to implement bioremediation practices in order to restore soil functions.
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Affiliation(s)
- I Petrić
- Rudjer Boskovic Institute, Division for Marine and Environmental Research, 10002 Zagreb, Croatia.
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Inoue D, Yamazaki Y, Tsutsui H, Sei K, Soda S, Fujita M, Ike M. Impacts of gene bioaugmentation with pJP4-harboring bacteria of 2,4-D-contaminated soil slurry on the indigenous microbial community. Biodegradation 2011; 23:263-76. [DOI: 10.1007/s10532-011-9505-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 08/06/2011] [Indexed: 10/17/2022]
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Udiković-Kolić N, Devers-Lamrani M, Petrić I, Hršak D, Martin-Laurent F. Evidence for taxonomic and functional drift of an atrazine-degrading culture in response to high atrazine input. Appl Microbiol Biotechnol 2011; 90:1547-54. [DOI: 10.1007/s00253-011-3198-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 02/28/2011] [Accepted: 03/01/2011] [Indexed: 10/18/2022]
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Arteau M, Labrie S, Roy D. Terminal-restriction fragment length polymorphism and automated ribosomal intergenic spacer analysis profiling of fungal communities in Camembert cheese. Int Dairy J 2010. [DOI: 10.1016/j.idairyj.2010.02.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ellegaard-Petersen L, Selck H, Priemé A, Salvito D, Forbes V. Investigation of the fate and effects of acetyl cedrene on Capitella teleta and sediment bacterial community. ECOTOXICOLOGY (LONDON, ENGLAND) 2010; 19:1046-1058. [PMID: 20339914 DOI: 10.1007/s10646-010-0486-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/11/2010] [Indexed: 05/29/2023]
Abstract
The fate of the fragrance material, acetyl cedrene (AC), in sediment was examined in a 16 day laboratory experiment using the sediment microbial community subjected to the following treatments: AC (nominal concentration; 0 and 50 microg g(-1) dw sediment) and macrofaunal worms (with/without Capitella teleta (formerly Capitella sp. I)). Furthermore effects of AC on microbial respiration in the system were determined by examining CO(2) flux. T-RFLP (terminal restriction fragment length polymorphism) was used to analyze PCR (polymerase chain reaction) amplified 16S DNA gene fragments from the sediments to detect changes in the structure and diversity of the bacterial community. In addition, survival of C. teleta in sediment was determined. Lastly, we examined how the interactions between microbes and C. teleta in the sediment affected the above-mentioned parameters. The results showed that there was an interaction between worm treatment and time of sampling on the loss of AC from the sediment. This was caused by AC loss initially being fastest in the sediment with C. teleta present, but at experimental termination there was no significant difference between the two treatments (i.e., with/without worms) in the amount of AC remaining in the sediment. Survival of C. teleta was significantly reduced by AC at experimental termination, but neither microbial respiration nor structure and diversity of the bacterial community were significantly affected.
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Affiliation(s)
- Lea Ellegaard-Petersen
- Department of Microbiology, Institute of Biology, Copenhagen University, Sølvgade 83H, 1307 Copenhagen K, Denmark.
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Yu SL, Tang YQ, Li Y, Zhang H, Wu XL. Gradient decrement of annealing time can improve PCR with fluorescent-labeled primers. J Biosci Bioeng 2010; 110:500-4. [PMID: 20646958 DOI: 10.1016/j.jbiosc.2010.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Revised: 05/08/2010] [Accepted: 05/12/2010] [Indexed: 10/19/2022]
Abstract
The influences of fluorescence labeling on PCR amplification and T-RFLP analysis were examined by the analyses of a soil bacterial and archaeal community using both clone library and T-RFLP methods. The PCR amplification and microbial community structure patterns were compared among the primers labeled with and without fluorescent groups. PCR amplification was negatively affected by the labeling groups of the primers, which may be caused by the increment of primer molecular weight. It is known that thermodynamic movement of molecules will be slowed as molecular weight increased. Therefore it is understandable that the reaction of primer-DNA template hybridization will be inhibited with the fluorescent groups added to the primer(s). An effective "Gradient-Decreasing Annealing Time Program," in which the annealing time was initially set long and reduced cycle by cycle, can improve PCR efficiency under comparable amplification specificity with the fluorescent-labeled primers. No significant negative impact was observed in the altered conditions.
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Affiliation(s)
- Su-Lin Yu
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, China
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Biodegradation: gaining insight through proteomics. Biodegradation 2010; 21:861-79. [DOI: 10.1007/s10532-010-9361-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Accepted: 04/13/2010] [Indexed: 10/19/2022]
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Morgante V, López-López A, Flores C, González M, González B, Vásquez M, Rosselló-Mora R, Seeger M. Bioaugmentation with Pseudomonas sp. strain MHP41 promotes simazine attenuation and bacterial community changes in agricultural soils. FEMS Microbiol Ecol 2010; 71:114-26. [PMID: 19889033 DOI: 10.1111/j.1574-6941.2009.00790.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Bioremediation is an important technology for the removal of persistent organic pollutants from the environment. Bioaugmentation with the encapsulated Pseudomonas sp. strain MHP41 of agricultural soils contaminated with the herbicide simazine was studied. The experiments were performed in microcosm trials using two soils: soil that had never been previously exposed to s-triazines (NS) and soil that had >20 years of s-triazine application (AS). The efficiency of the bioremediation process was assessed by monitoring simazine removal by HPLC. The simazine-degrading microbiota was estimated using an indicator for respiration combined with most-probable-number enumeration. The soil bacterial community structures and the effect of bioaugmentation on these communities were determined using 16S RNA gene clone libraries and FISH analysis. Bioaugmentation with MHP41 cells enhanced simazine degradation and increased the number of simazine-degrading microorganisms in the two soils. In highly contaminated NS soil, bioaugmentation with strain MHP41 was essential for simazine removal. Comparative analysis of 16S rRNA gene clone libraries from NS and AS soils revealed high bacterial diversity. Bioaugmentation with strain MHP41 promoted soil bacterial community shifts. FISH analysis revealed that bioaugmentation increased the relative abundances of two phylogenetic groups (Acidobacteria and Planctomycetes) in both soils. Although members of the Archaea were metabolically active in these soils, their relative abundance was not altered by bioaugmentation.
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Affiliation(s)
- Verónica Morgante
- Departamento de Química, Universidad Técnica Federico Santa María, Valparaíso, Chile
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Sánchez-Peinado MDM, González-López J, Martínez-Toledo MV, Pozo C, Rodelas B. Influence of linear alkylbenzene sulfonate (LAS) on the structure of Alphaproteobacteria, Actinobacteria, and Acidobacteria communities in a soil microcosm. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2010; 17:779-790. [PMID: 19484283 DOI: 10.1007/s11356-009-0180-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Accepted: 04/05/2009] [Indexed: 05/27/2023]
Abstract
BACKGROUND, AIM, AND SCOPE Linear alkylbenzene sulfonate (LAS) is the most used anionic surfactant in a worldwide scale and is considered a high-priority pollutant. LAS is regarded as a readily biodegradable product under aerobic conditions in aqueous media and is mostly removed in wastewater treatment plants, but an important fraction (20-25%) is immobilized in sewage sludge and persists under anoxic conditions. Due to the application of the sludge as a fertilizer, LAS reaches agricultural soil, and therefore, microbial toxicity tests have been widely used to evaluate the influence of LAS on soil microbial ecology. However, molecular-based community-level analyses have been seldom applied in studies regarding the effects of LAS on natural or engineered systems, and, to our knowledge, there are no reports of their use for such appraisals in agricultural soil. In this study, a microcosm system is used to evaluate the effects of a commercial mixture of LAS on the community structure of Alphaproteobacteria, Actinobacteria, and Acidobacteria in an agricultural soil. MATERIAL AND METHODS The microcosms consisted of agricultural soil columns (800 g) fed with sterile water (8 ml h(-1)) added of different concentration of LAS (10 or 50 mg l(-1)) for periods of time up to 21 days. Sterile water was added to control columns for comparison. The structures of Alphaproteobacteria, Actinobacteria, and Acidobacteria communities were analyzed by a cultivation independent method (temperature gradient gel electrophoresis (TGGE) separation of polymerase chain reaction (PCR)-amplified partial 16S rRNA genes). Relevant populations were identified by subsequent reamplification, DNA sequencing, and database comparisons. RESULTS Cluster analysis of the TGGE fingerprints taking into consideration both the number of bands and their relative intensities revealed that the structure of the Alphaproteobacteria community was significantly changed in the presence of LAS, at both concentrations tested. The average number of bands was significantly lower in the microcosms receiving 50 mg l(-1) LAS and in the lower portion of soil cores. The clear differentiation of the samples of the upper portion of the soil columns amended with LAS was specifically related to the presence and intensity of a distinctive major band (named band class 7). There was a statistically significant positive correlation between the concentrations of LAS detected in soil portions taken from LAS 10 mg l(-1) and LAS 50 mg l(-1) microcosms and the relative intensity of band class 7 in the corresponding TGGE profiles. Prevalent Alphaproteobacteria populations in the soil microcosms had close similarity (>99%) to cultivated species affiliated to genera of the Rhizobiaceae, Methylocystaceae, Hyphomicrobiaceae, Rhodospirillaceae, Brucellaceae, Bradyrhizobiaceae, and Caulobacteraceae families. The population represented by band class 7 was found closely related to the genus Phenylobacterium (Caulobacteraceae). According to cluster analysis of TGGE profiles, the structure of both Actinobacteria and Acidobacteria communities in the soil microcosms was remarkably stable in the presence of LAS at the two concentrations tested, as most bands were universally present in all samples and displayed fairly similar relative intensities. DISCUSSION Previous studies by others authors, based on biological and chemical tests, concluded that LAS toxicity was not an important microbial selection factor in sludge amended soil, while work based on the use of molecular fingerprinting to evaluate the impact of LAS in aqueous media and marine sediments showed that concentrations as low as 1 mg l(-1) significantly influence the development of the bacterial community structure. Although TGGE is not a strictly quantitative method due to the bias introduced by the PCR reaction, changes of band intensity through experiments are a consequence of a change in the relative abundance of the corresponding populations in the community and can be used as a semiquantitative measure of bacterial diversity. Our results evidence that the Phenylobacterium population represented by band class 7 was favored by the presence of increasing concentrations of LAS in the soil and turned into a dominant population, suggesting its possible ability to use LAS in soil as a source of nutrients. As studies with pure cultures are required to confirm the ability of this population to degrade LAS, isolation strategies are currently under development in our laboratory. The weak effect of LAS on the structure of Actinobacteria and Acidobacteria communities is particularly interesting, as to our knowledge, there are no previous reports regarding the effects of LAS on these bacterial groups in soil. CONCLUSIONS, RECOMMENDATIONS, AND PERSPECTIVES: The Phenylobacterium-related alphaproteobacterial population identified in this work was selectively enriched in LAS polluted soil and is a plausible candidate to play a relevant role in the biotransformation of the surfactant under the conditions tested. The surfactant had no remarkable effects on the Actinobacteria and Acidobacteria fingerprints in soil, even when present at concentrations widely exceeding those reached in soil immediately after sludge application. TGGE fingerprinting provides a reliable and low time-consuming method for the monitoring of the bacterial community structure and dynamics, and we recommend its integration with the biological and chemical analyses usually applied in risk assessment of LAS in the environment.
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Kapur M, Bhatia R, Pandey G, Pandey J, Paul D, Jain RK. A case study for assessment of microbial community dynamics in genetically modified Bt cotton crop fields. Curr Microbiol 2010; 61:118-24. [PMID: 20098990 DOI: 10.1007/s00284-010-9585-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Accepted: 01/07/2010] [Indexed: 11/25/2022]
Abstract
Bt cotton was the first genetically modified crop approved for use in India. However, only a few studies have been conducted to assess the feasibility of its commercial application. Bt cotton is genetically modified to express a proteinaceous endotoxin (Cry) encoded by cry gene of Bacillus thuringiensis that has specific insecticidal activity against bollworms. Therefore, the amount of pesticides used for growing Bt cotton is postulated to be considerably low as compared to their non-Bt counterparts. Alternatively, it is also speculated that application of a genetically modified crop may alter the bio-geochemical balance of the agriculture field(s). Microbial community composition and dynamics is an important descriptor for assessment of such alterations. In the present study, we have assessed the culturable and non-culturable microbial diversities in Bt cotton and non-Bt cotton soils to determine the ecological consequences of application of Bt cotton. The analyses of microbial community structures indicated that cropping of Bt cotton did not adversely affect the diversity of the microbial communities.
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Affiliation(s)
- Manisha Kapur
- Institute of Microbial Technology, Chandigarh, India
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Pandey J, Chauhan A, Jain RK. Integrative approaches for assessing the ecological sustainability ofin situbioremediation. FEMS Microbiol Rev 2009; 33:324-75. [PMID: 19178567 DOI: 10.1111/j.1574-6976.2008.00133.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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Rani A, Porwal S, Sharma R, Kapley A, Purohit HJ, Kalia VC. Assessment of microbial diversity in effluent treatment plants by culture dependent and culture independent approaches. BIORESOURCE TECHNOLOGY 2008; 99:7098-7107. [PMID: 18280146 DOI: 10.1016/j.biortech.2008.01.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Revised: 12/26/2007] [Accepted: 01/03/2008] [Indexed: 05/25/2023]
Abstract
Microbial community structure of two distinct effluent treatment plants (ETPs) of pesticide and pharmaceutical industries was assessed and defined by (i) culture dependent and culture independent approaches on the basis of 16S rRNA gene sequencing, (ii) diversity index analysis - operational taxonomic units (OTUs). A total of 38 and 44 bacterial OTUs having 85-99% similarity with the closest match in the database were detected among pharmaceutical and pesticide sludge samples, respectively. Fifty percent of the OTUs were related to uncultured bacteria. These OTUs had a Shannon diversity index value of 2.09-2.33 for culturables and in the range of 3.25-3.38 for unculturables. The high species evenness values of 0.86 and 0.95 indicated the vastness of microbial diversity retrieved by these approaches. The dominant cultured bacteria indicative of microbial diversity in functional ETPs were Alcaligenes, Bacillus and Pseudomonas. Brevundimonas, Citrobacter, Pandoraea and Stenotrophomonas were specific to pesticide ETP and Agrobacterium, Brevibacterium, Micrococcus, Microbacterium, Paracoccus and Rhodococcus were specific to pharmaceutical ETP. These microbes can thus be maintained and exploited for efficient functioning and maintenance of ETPs.
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Affiliation(s)
- Asha Rani
- Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Mall Road, Delhi - 110007, India
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Meier C, Wehrli B, van der Meer JR. Seasonal fluctuations of bacterial community diversity in agricultural soil and experimental validation by laboratory disturbance experiments. MICROBIAL ECOLOGY 2008; 56:210-222. [PMID: 18038213 DOI: 10.1007/s00248-007-9337-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Revised: 10/22/2007] [Accepted: 10/25/2007] [Indexed: 05/25/2023]
Abstract
Natural fluctuations in soil microbial communities are poorly documented because of the inherent difficulty to perform a simultaneous analysis of the relative abundances of multiple populations over a long time period. Yet, it is important to understand the magnitudes of community composition variability as a function of natural influences (e.g., temperature, plant growth, or rainfall) because this forms the reference or baseline against which external disturbances (e.g., anthropogenic emissions) can be judged. Second, definition of baseline fluctuations in complex microbial communities may help to understand at which point the systems become unbalanced and cannot return to their original composition. In this paper, we examined the seasonal fluctuations in the bacterial community of an agricultural soil used for regular plant crop production by using terminal restriction fragment length polymorphism profiling (T-RFLP) of the amplified 16S ribosomal ribonucleic acid (rRNA) gene diversity. Cluster and statistical analysis of T-RFLP data showed that soil bacterial communities fluctuated very little during the seasons (similarity indices between 0.835 and 0.997) with insignificant variations in 16S rRNA gene richness and diversity indices. Despite overall insignificant fluctuations, between 8 and 30% of all terminal restriction fragments changed their relative intensity in a significant manner among consecutive time samples. To determine the magnitude of community variations induced by external factors, soil samples were subjected to either inoculation with a pure bacterial culture, addition of the herbicide mecoprop, or addition of nutrients. All treatments resulted in statistically measurable changes of T-RFLP profiles of the communities. Addition of nutrients or bacteria plus mecoprop resulted in bacteria composition, which did not return to the original profile within 14 days. We propose that at less than 70% similarity in T-RFLP, the bacterial communities risk to drift apart to inherently different states.
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Affiliation(s)
- Christoph Meier
- Swiss Federal Institute for Aquatic Science and Technology (Eawag), CH-8600, Dübendorf, Switzerland
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Terminal restriction fragment length polymorphism (T-RFLP) analysis: Characterizing the unseen. Indian J Microbiol 2007; 47:90-1. [PMID: 23100647 DOI: 10.1007/s12088-007-0017-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2006] [Revised: 01/17/2007] [Accepted: 01/18/2007] [Indexed: 10/23/2022] Open
Abstract
The golden era of microbiology during early 1900s was based on the isolation and characterization of purified single cultures. However, since the understanding of limitations of culturing methods to decipher the majority of the microbial diversity, microbiologists have been keen to assess the abundance and distribution of microbial diversity by alternative methods(1). The quest has been further fueled by the idea of relating such information about the community structure to the ecosystem function. Therefore, the goal of new cohort of modern day microbiologists is to understand microbial community structure and dynamics within their natural habitats. Consequently, a wide variety of culture independent approaches and methods for microbial community structure determination have been developed and applied to varied ecosystems. By far the majority of such methods use direct isolation of genetic content from the environmental samples and PCR amplification of genes of interest for bypassing the culturing biases. Existing methods include Amplified Ribosomal DNA Restriction Analysis (ARDRA), Single Stranded Conformation Polymorphism (SSCP), Thermal and Denaturing Gradient Gel Electrophoresis (TGGE and DGGE), Amplified Length Heterogeneity (ALH) analysis and Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis(2).
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Pandey J, Ganesan K, Jain RK. Variations in T-RFLP profiles with differing chemistries of fluorescent dyes used for labeling the PCR primers. J Microbiol Methods 2006; 68:633-8. [PMID: 17196691 DOI: 10.1016/j.mimet.2006.11.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2006] [Revised: 11/07/2006] [Accepted: 11/20/2006] [Indexed: 11/27/2022]
Abstract
Culture independent molecular methods have emerged as indispensable tools for studying microbial community structure and dynamics in natural habitats, since they allow a closer look at microbial diversity that is not reflected by culturing techniques. Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis is one of the informative and widely used techniques for such studies. However, the method has a few limitations to predict microbial community structure with significant accuracy. One of the major limitations is variation in real Terminal Restriction Fragment (TRF) length and observed TRF length. In the present study we report the generation of TRF length variations using different fluorescent dyes to label the PCR primers. T-RFLP profiles generated from primers labeled with different dyes varied significantly and led to inconsistent microbial species identification. Occurrence of such variations can have serious consequences on interpretation of the T-RFLP profiles from environmental samples representing complex microbial community. Therefore, in a T-RFLP study, the primers and labeling dye system should be carefully evaluated and optimized for an individual community under investigation. Further, it would be recommended to establish a target gene library in parallel with T-RFLP analysis to facilitate the accurate prediction of microbial community structure.
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Affiliation(s)
- Janmejay Pandey
- Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India
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