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Sun S, Wei R, Hu S, Yang M, Ni J. Isolation and characterization of distinctive pyrene-degrading bacteria from an uncontaminated soil. Biodegradation 2024; 35:657-670. [PMID: 38279065 DOI: 10.1007/s10532-023-10065-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/13/2023] [Indexed: 01/28/2024]
Abstract
Considerable efforts that isolate and characterize degrading bacteria for polycyclic aromatic hydrocarbons (PAHs) have focused on contaminated environments so far. Here we isolated three distinctive pyrene (PYR)-degrading bacteria from a paddy soil that was not contaminated with PAHs. These included a novel Bacillus sp. PyB-9 and efficient degraders, Shigella sp. PyB-6 and Agromyces sp. PyB-10. All three strains could utilize naphthalene, phenanthrene, anthracene, fluoranthene and PYR as sole carbon sources, and degraded PYR in a range of temperatures (27-37 °C) and pH (5-8). Strains PyB-6 and PyB-10 almost completely degraded 50 mg L-1 PYR within 15 days, and 75.5% and 98.9% of 100 mg L-1 PYR in 27 days, respectively. The kinetics of PYR biodegradation was well represented by the Gompertz model. Ten and twelve PYR metabolites were identified in PYR degradation process by strains PyB-6 and PyB-10, respectively. Chemical analyses demonstrated that the degradation mechanisms of PYR were the same for strains PyB-6 and PyB-10 with initial dioxygenation mainly on C-4,5 positions of PYR. The degradation of 4,5-phenanthrenedicarboxylic acid was branched to 4-phenanthrenecarboxylic acid pathway and 5-hydroxy-4-phenanthrenecarboxylic acid pathway, both of which played important roles in PYR degradation by strains PyB-6 and PyB-10. To our knowledge, Shigella sp. and Agromyces sp. were found for the first time to possess the capability for PAHs degradation. These findings contributed to upgrading the bank of microbial resource and knowledge on PAH biodegradation.
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Affiliation(s)
- Shanshan Sun
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, College of Geographical Science, Fujian Normal University, Fuzhou, 350007, Fujian, China
- Department of Microbiology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Ran Wei
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, College of Geographical Science, Fujian Normal University, Fuzhou, 350007, Fujian, China.
| | - Siyi Hu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, College of Geographical Science, Fujian Normal University, Fuzhou, 350007, Fujian, China
| | - Meiyu Yang
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, College of Geographical Science, Fujian Normal University, Fuzhou, 350007, Fujian, China
| | - Jinzhi Ni
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, College of Geographical Science, Fujian Normal University, Fuzhou, 350007, Fujian, China
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2
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Kharey GS, Palace V, Whyte L, Greer CW. Influence of heavy Canadian crude oil on pristine freshwater boreal lake ecosystems in an experimental oil spill. FEMS Microbiol Ecol 2024; 100:fiae054. [PMID: 38650065 PMCID: PMC11065361 DOI: 10.1093/femsec/fiae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 02/29/2024] [Accepted: 04/18/2024] [Indexed: 04/25/2024] Open
Abstract
The overall impact of a crude oil spill into a pristine freshwater environment in Canada is largely unknown. To evaluate the impact on the native microbial community, a large-scale in situ model experimental spill was conducted to assess the potential role of the natural community to attenuate hydrocarbons. A small volume of conventional heavy crude oil (CHV) was introduced within contained mesocosm enclosures deployed on the shoreline of a freshwater lake. The oil was left to interact with the shoreline for 72 h and then free-floating oil was recovered using common oil spill response methods (i.e. freshwater flushing and capture on oleophilic absorptive media). Residual polycyclic aromatic hydrocarbon (PAH) concentrations returned to near preoiling concentrations within 2 months, while the microbial community composition across the water, soil, and sediment matrices of the enclosed oligotrophic freshwater ecosystems did not shift significantly over this period. Metagenomic analysis revealed key polycyclic aromatic and alkane degradation mechanisms also did not change in their relative abundance over the monitoring period. These trends suggest that for small spills (<2 l of oil per 15 m2 of surface freshwater), physical oil recovery reduces polycyclic aromatic hydrocarbon concentrations to levels tolerated by the native microbial community. Additionally, the native microbial community present in the monitored pristine freshwater ecosystem possesses the appropriate hydrocarbon degradation mechanisms without prior challenge by hydrocarbon substrates. This study corroborated trends found previously (Kharey et al. 2024) toward freshwater hydrocarbon degradation in an environmentally relevant scale and conditions on the tolerance of residual hydrocarbons in situ.
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Affiliation(s)
- Gurpreet S Kharey
- Department of Natural Resource Sciences, McGill University, 21111 Lakeshore Rd Ste-Anne-de-Bellevue, Quebec, H9X 3V9S, Canada
| | - Vince Palace
- International Institute for Sustainable Development – Experimental Lakes Area, Pine Rd, Kenora, Unorganized Ontario, P0V 2V0, Canada
| | - Lyle Whyte
- Department of Natural Resource Sciences, McGill University, 21111 Lakeshore Rd Ste-Anne-de-Bellevue, Quebec, H9X 3V9S, Canada
| | - Charles W Greer
- Department of Natural Resource Sciences, McGill University, 21111 Lakeshore Rd Ste-Anne-de-Bellevue, Quebec, H9X 3V9S, Canada
- National Research Council Canada, Energy, Mining and Environment Research Centre, 6100 Royalmount Ave., Montreal, Quebec, H4P 2R2, Canada
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Cao J, Zhao P, Wang D, Zhao Y, Wang Z, Zhong N. Effects of a Nanonetwork-Structured Soil Conditioner on Microbial Community Structure. BIOLOGY 2023; 12:biology12050668. [PMID: 37237482 DOI: 10.3390/biology12050668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/25/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023]
Abstract
Fertilizer application can increase yields, but nutrient runoff may cause environmental pollution and affect soil quality. A network-structured nanocomposite used as a soil conditioner is beneficial to crops and soil. However, the relationship between the soil conditioner and soil microbes is unclear. We evaluated the soil conditioner's impact on nutrient loss, pepper growth, soil improvement, and, especially, microbial community structure. High-throughput sequencing was applied to study the microbial communities. The microbial community structures of the soil conditioner treatment and the CK were significantly different, including in diversity and richness. The predominant bacterial phyla were Pseudomonadota, Actinomycetota, and Bacteroidota. Acidobacteriota and Chloroflexi were found in significantly higher numbers in the soil conditioner treatment. Ascomycota was the dominant fungal phylum. The Mortierellomycota phylum was found in significantly lower numbers in the CK. The bacteria and fungi at the genus level were positively correlated with the available K, available N, and pH, but were negatively correlated with the available P. Our results showed that the loss of nutrients controlled by the soil conditioner increased available N, which improved soil properties. Therefore, the microorganisms in the improved soil were changed. This study provides a correlation between improvements in microorganisms and the network-structured soil conditioner, which can promote plant growth and soil improvement.
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Affiliation(s)
- Jingjing Cao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Engineering Laboratory for Advanced Microbial Technology of Agriculture, Chinese Academy of Sciences, Beijing 100101, China
| | - Pan Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Engineering Laboratory for Advanced Microbial Technology of Agriculture, Chinese Academy of Sciences, Beijing 100101, China
- The Enterprise Key Laboratory of Advanced Technology for Potato Fertilizer and Pesticide, Hulunbuir 021000, China
| | - Dongfang Wang
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Yonglong Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Engineering Laboratory for Advanced Microbial Technology of Agriculture, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhiqin Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Engineering Laboratory for Advanced Microbial Technology of Agriculture, Chinese Academy of Sciences, Beijing 100101, China
| | - Naiqin Zhong
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Engineering Laboratory for Advanced Microbial Technology of Agriculture, Chinese Academy of Sciences, Beijing 100101, China
- The Enterprise Key Laboratory of Advanced Technology for Potato Fertilizer and Pesticide, Hulunbuir 021000, China
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Sola MCR, Santos AG, Nascimento MM, da Rocha GO, de Andrade JB. Occurrence, sources, and risk assessment of unconventional polycyclic aromatic compounds in marine sediments from sandy beach intertidal zones. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:152019. [PMID: 34856251 DOI: 10.1016/j.scitotenv.2021.152019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/23/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
This study investigated the concentrations of polycyclic aromatic compounds (PACs), including parent polyaromatic hydrocarbons (PAHs) and their nitrated and oxygenated derivatives, in 48 sediment samples from the intertidal region of sandy beaches in Baía de Todos os Santos (BTS), Salvador, State of Bahia, Brazil. The total PAH (∑PAH) concentration, total nitro-PAH (∑nitro-PAH) concentration, and total oxy-PAH (∑oxy-PAH) concentration ranged from 2.11 μg g-1 dry weight (dw) to 28.0 μg g-1 dw, 2.58 μg g-1 dw to 30.2 μg g-1 dw, and 0.34 μg g-1 dw to 3.65 μg g-1 dw, respectively. Elevated concentrations of parent PAHs and nitro-PAHs were found in samples from two sites in BTS, which were also characterized by high percentages of fine-medium sand and low organic matter contents. Potent mutagenic 3-nitrobenzanthrone (3-NBA) was found in 86% of the samples at concentrations ranging from 0.200 μg g-1 dw to 0.690 μg g-1 dw. Furthermore, calculations of the benzo[a]pyrene toxicity equivalency (BaPTEQ) indicated that three carcinogenic high-molecular-weight PAHs accounted for 98.7% of the total maximum PAH concentration. Finally, we assessed the possible environmental risks posed to benthic species living in the sediments of BTS. The results showed that the risk quotient for PAHs (RQPAHs) was ≥1. In turn, the summed RQ for all PACs (∑RQmixture) ranged from 1 to 30, but did not exceed the maximum allowable threshold; thus, the risks posed to benthic species were moderate for all sediment samples.
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Affiliation(s)
- Maria Claudia R Sola
- Centro Interdisciplinar de Energia e Ambiente - CIEnAm, Universidade Federal da Bahia, 40170-115 Salvador, BA, Brazil; Instituto Nacional de Ciência e Tecnologia em Energia e Ambiente - INCT E&A, UFBA, 40170-290 Salvador, BA, Brazil
| | - Aldenor G Santos
- Centro Interdisciplinar de Energia e Ambiente - CIEnAm, Universidade Federal da Bahia, 40170-115 Salvador, BA, Brazil; Instituto Nacional de Ciência e Tecnologia em Energia e Ambiente - INCT E&A, UFBA, 40170-290 Salvador, BA, Brazil; Universidade Federal da Bahia, Instituto de Química, Campus de Ondina, 40170-115 Salvador, BA, Brazil
| | - Madson M Nascimento
- Centro Interdisciplinar de Energia e Ambiente - CIEnAm, Universidade Federal da Bahia, 40170-115 Salvador, BA, Brazil; Instituto Nacional de Ciência e Tecnologia em Energia e Ambiente - INCT E&A, UFBA, 40170-290 Salvador, BA, Brazil; Universidade Federal da Bahia, Instituto de Química, Campus de Ondina, 40170-115 Salvador, BA, Brazil
| | - Gisele Olimpio da Rocha
- Centro Interdisciplinar de Energia e Ambiente - CIEnAm, Universidade Federal da Bahia, 40170-115 Salvador, BA, Brazil; Instituto Nacional de Ciência e Tecnologia em Energia e Ambiente - INCT E&A, UFBA, 40170-290 Salvador, BA, Brazil; Universidade Federal da Bahia, Instituto de Química, Campus de Ondina, 40170-115 Salvador, BA, Brazil
| | - Jailson Bittencourt de Andrade
- Centro Interdisciplinar de Energia e Ambiente - CIEnAm, Universidade Federal da Bahia, 40170-115 Salvador, BA, Brazil; Instituto Nacional de Ciência e Tecnologia em Energia e Ambiente - INCT E&A, UFBA, 40170-290 Salvador, BA, Brazil; Centro Universitário SENAI-CIMATEC, Av. Orlando Gomes, 1845 - Piatã, 41650-010 Salvador, BA, Brazil.
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Sun T, Li W, Yin K. Estimation of total flux of polycyclic aromatic hydrocarbons facilitated by methane ebullition into water column from global lake sediments. WATER RESEARCH 2021; 204:117611. [PMID: 34509869 DOI: 10.1016/j.watres.2021.117611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Methane ebullition and contamination are two typical characteristics from lakes, however, these two are generally studied independently. In fact, the exchange of matter and energy between methane bubbles and their surrounding environment can be very active to enhance the contaminant transport. There is limited research on understanding the characteristics and trends of gas ebullition facilitated contaminant emissions in large areas considering water and air as receptors. We herein estimate the transport capacity of methane ebullition for polycyclic aromatic hydrocarbons (PAHs) out of the sediment from global lakes, which may reach an average of 71 (up to 159) t yr-1. Methane bubbles could transfer one third of the total PAH flux from sediments, or equivalent of 1.3-3.0 ng L-1 of additional PAHs, into the water column with the rest going into air, offsetting from 52 to 118% of dry PAH deposition flux into global lakes sediment per year. Given the PAH concentration in lake water is often in the range of 0.1-100 ng L-1, ebullition facilitated PAH flux may increase PAH concentration by a factor of 1.4 to 2.4 until 2,100, being a significant contributor for the PAH increment in lake waters.
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Affiliation(s)
- Tingting Sun
- Department of Environmental Engineering, School of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037 China
| | - Wenxuan Li
- Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive, Singapore 117576
| | - Ke Yin
- Department of Environmental Engineering, School of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037 China.
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Yan Z, Wang L, Yan H, Dong Y, Zhang G, Wu H. Biodegradation potential of polycyclic aromatic hydrocarbons in Taihu Lake sediments. ENVIRONMENTAL TECHNOLOGY 2021; 43:1-9. [PMID: 34319863 DOI: 10.1080/09593330.2021.1961871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
ABSTRACTTo assess the biodegradation potential of polycyclic aromatic hydrocarbons (PAHs) in sediments, sediment microcosms were constructed with sediments collected from six lake zones with different trophic statuses in Taihu Lake. The presence and concentration of PAH-degrading bacteria (PDB) were estimated by the most probable number (MPN) method. After 85 d of aerobic and anaerobic incubation, spiked PAHs (phenanthrene, pyrene, and benzo[a]pyrene) were partially degraded by indigenous sediment microorganisms. Large differences in PAH degradation were observed depending on the molecular size of the PAHs. The PAH removal efficiency in sediments under aerobic conditions was higher than that under anaerobic conditions. MPN analyses showed a higher abundance of degrading microflora in the high PAH-contaminated sites than in the low PAH-contaminated sites. Moreover, the anaerobic PDB populations in the sediments from the six different sites were much higher than those of aerobic PDB. The PAH biodegradation capability in sediments was associated with the geochemical conditions and bacterial populations. PDB showed a broad spatial distribution, thereby implying that they played an important role in the natural attenuation and cycling of PAHs in Taihu Lake. This work indicates that PAHs remain a concern in Taihu Lake sediments and can provide useful information for further bioremediation of PAH-contaminated sediments.
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Affiliation(s)
- Zaisheng Yan
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, People's Republic of China
| | - Luming Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, People's Republic of China
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, People's Republic of China
| | - Haifeng Yan
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, People's Republic of China
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, People's Republic of China
| | - Yibo Dong
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, People's Republic of China
- College of Urban Construction, Nanjing University of Technology, Nanjing, People's Republic of China
| | - Guoqing Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, People's Republic of China
- College of Urban Construction, Nanjing University of Technology, Nanjing, People's Republic of China
| | - Huifang Wu
- College of Urban Construction, Nanjing University of Technology, Nanjing, People's Republic of China
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Ding Q, Gong X, Jin M, Yao X, Zhang L, Zhao Z. The biological pump effects of phytoplankton on the occurrence and benthic bioaccumulation of hydrophobic organic contaminants (HOCs) in a hypereutrophic lake. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 213:112017. [PMID: 33582414 DOI: 10.1016/j.ecoenv.2021.112017] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 01/18/2021] [Accepted: 01/31/2021] [Indexed: 06/12/2023]
Abstract
The distribution of hydrophobic organic contaminants (HOCs) in eutrophic ecosystems has been widely studied, but how phytoplankton blooms affect their occurrence and benthic bioaccumulation is poorly understood. To fill this knowledge gap, the biological pump effects of phytoplankton on the fate of organochlorine pesticides (OCPs) and polycyclic aromatic hydrocarbons (PAHs) in sediments and benthos (Corbicula fluminea) from Lake Taihu, a hypereutrophic lake in China, were identified. The spatial-temporal distribution of HOCs suggests that higher phytoplankton biomass, coupled with sediment organic matter (SOM) content, greatly increased the concentration of HOCs in sediments in both winter and summer seasons. This could be attributed to the biological pump effects sequestering more HOCs from water to sediments with settling phytoplankton, especially during the summer. The biological pump effects further promoted the uptake of sediment-bound HOCs by benthos. The significant positive relationships between concentrations of HOCs in sediments and benthos were observed during the winter dormancy phase of benthos. Furthermore, the benthic bioaccumulation of HOCs could be strengthened by phytoplankton, due to their contribution to SOM and the following increased bioavailability of HOCs in sediments. Further research is needed to elucidate the phytoplankton biological pump effects on the fate of HOCs in benthic food chain, especially for hypereutrophic waters.
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Affiliation(s)
- Qiqi Ding
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xionghu Gong
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Miao Jin
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Xiaolong Yao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Lu Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Zhonghua Zhao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China.
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Polycyclic Aromatic Hydrocarbons in Sediments from Typical Algae, Macrophyte Lake Bay and Adjoining River of Taihu Lake, China: Distribution, Sources, and Risk Assessment. WATER 2021. [DOI: 10.3390/w13040470] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental pollutants in sediments and pose a serious risk for freshwater ecosystems. In this study, sediment samples from 24 sites were collected from the cyanobacterial bloom-occurring, macrophyte-growing lake bay and adjoining river of Taihu Lake. Here, the concentration levels, sources, and risk assessment of 16 priority PAHs in the surface sediments from typical algae, macrophyte lake bay and adjoining river of Taihu Lake, were investigated, and the results were compared with those of previous studies. The total PAH (ΣPAH) concentrations ranged from 4900 to 16,800 ng·g−1 in sediments of the Taihu Lake bay and from 5736.2 to 69,362.8 ng·g−1 in sediments of the adjoining river. The level of PAHs in riverine sediments was significantly higher than those of the Taihu Lake bay, and that of the Dongshan River was significantly higher than that of the Mashan River, while there was no significant difference in the concentrations of PAHs between the cyanobacterial bloom-occurring and macrophyte-growing lake zone. The results indicated petroleum contamination was dominated in the cyanobacterial bloom-occurring, macrophyte-growing lake bay, while PAHs of the riverine sediments derived from petroleum contamination and the combined combustion including wood, coal combustion, and petroleum combustion according to the identification by the molecular diagnostic ratio and principal component analysis (PCA). Sediment risk assessment based on sediment quality guidelines (SQGs) suggested that partial regions of the Taihu Lake bay were subjected to the potential ecological risk of the 3-ring and 5-ring PAHs, and there existed negative effects related to naphthalene pollutant in all survey regions. The adjoining riverine sediments showed a high ecological risk.
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Yan Z, Song N, Wang C, Jiang H. Functional potential and assembly of microbes from sediments in a lake bay and adjoining river ecosystem for polycyclic aromatic hydrocarbon biodegradation. Environ Microbiol 2020; 23:628-640. [PMID: 32468666 DOI: 10.1111/1462-2920.15104] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/23/2020] [Accepted: 05/25/2020] [Indexed: 11/26/2022]
Abstract
Lake and adjoining river ecosystems are ecologically and economically valuable and are heavily threatened by anthropogenic activities. Determining the inherent capacity of ecosystems for polycyclic aromatic hydrocarbon (PAH) biodegradation can help quantify environmental impacts on the functioning of ecosystems, especially on that of the microbial community. Here, PAH biodegradation potential was compared between sediments collected from a lake bay (LS) and an adjoining river (RS) ecosystem. Microbial community composition, function, and their co-occurrence patterns were also explored. In the RS, the biodegradation rates (KD ) of pyrene or PAH were almost two orders of magnitude higher than those in the LS. Sediment functional community structure and network interactions were dramatically different between the LS and RS. Although PAH degradation genes (p450aro, quinoline, and qorl) were detected in the LS, the community activity of these genes needed to be biostimulated for accelerated bioremediation. In contrast, functional communities in the RS were capable of spontaneous natural attenuation of PAH. The degradation of PAH in the RS also required coordinated response of the complex functional community. Taken together, elucidating functions and network interactions in sediment microbial communities and their responses to environmental changes are very important for the bioremediation of anthropogenic toxic contaminants.
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Affiliation(s)
- Zaisheng Yan
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Na Song
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Changhui Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Helong Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
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10
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Idowu O, Carbery M, O'Connor W, Thavamani P. Speciation and source apportionment of polycyclic aromatic compounds (PACs) in sediments of the largest salt water lake of Australia. CHEMOSPHERE 2020; 246:125779. [PMID: 31927372 DOI: 10.1016/j.chemosphere.2019.125779] [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: 10/28/2019] [Revised: 12/25/2019] [Accepted: 12/27/2019] [Indexed: 06/10/2023]
Abstract
Great ecological and human health risks may arise from the presence of polycyclic aromatic hydrocarbons (PAHs) in aquatic environments and particularly in sediments, where they often partition. In spite of the apparent risk, knowledge about PAHs and their polar derivatives in sediments is limited. We, therefore, carried out an assessment of the concentrations of parent PAHs and their derivatives (polar PAHs) in sediments of Lake Macquarie: the largest saltwater lake in the southern hemisphere. A total of 31 sediment samples along the pollution prone western shoreline of the estuary were analysed. Multiple source apportionment methods were used to investigate PAH sources contributing to parent and polar PAH concentrations in the estuarine sediments. Concentration levels were highest for high molecular weight (HMW) PAHs compared to low molecular weight (LMW) PAHs. The highest PAH concentrations were recorded for oxygenated PAHs (oxy-PAHs) compared to parent and other polar PAHs. Polycyclic aromatic hydrocarbon diagnostic ratios and compositional analysis showed that PAHs in Lake Macquarie were predominantly pyrogenic exhibiting strong positive correlation (R2 = 0.972) with total PAH concentrations. Principal Component Analysis (PCA) identified three groupings of PAHs with oxy-PAHs and NPAHs dominating (40.2%). Carbazole, a heterocyclic PAH, was also a prominent contributor to sediment PAH concentrations. Atmospheric deposition, coal combustion and vehicular emissions were implicated as the major contributors to sediment pollution.
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Affiliation(s)
- Oluyoye Idowu
- Global Centre for Environmental Remediation (GCER), University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Maddison Carbery
- Global Centre for Environmental Remediation (GCER), University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Wayne O'Connor
- Port Stephens Fisheries Institute, NSW Department of Primary Industries, Port Stephens, NSW, 2316, Australia
| | - Palanisami Thavamani
- Global Centre for Environmental Remediation (GCER), University of Newcastle, Callaghan, NSW, 2308, Australia; Global Innovative Centre for Advanced Nanomaterials (GICAN), University of Newcastle, Callaghan, NSW, 2308, Australia.
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11
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Wu H, Wang M, Zhu S, Xie J, Preis S, Li F, Wei C. Structure and function of microbial community associated with phenol co-substrate in degradation of benzo[a]pyrene in coking wastewater. CHEMOSPHERE 2019; 228:128-138. [PMID: 31029958 DOI: 10.1016/j.chemosphere.2019.04.117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 04/04/2019] [Accepted: 04/14/2019] [Indexed: 06/09/2023]
Abstract
Coking wastewater (CWW) contains high contents of phenols and other toxic and refractory compounds including polycyclic aromatic hydrocarbons (PAHs) with the most carcinogenic benzo[a]pyrene (BaP) among them. The mechanism of PAHs/BaP degradation in activated sludge of CWW treatment with phenol as co-substrate was studied. For characterizing the structure and functions of microbial community associated with BaP degradation with phenol as co-substrate, high-throughput MiSeq sequencing was used to examine the 16S rRNA genes of microbiology, revealing noticeable shifts in CWW activated sludge bacterial populations. Major genera involved in anaerobic degradation were Tissierella_Soehngenia, Diaphorobacter and Geobacter, whereas in aerobic degradation Rhodanobacter, Dyella and Thauera prevailed. BaP degradation with phenol as co-substrate induced bacterial diversification in CWW activated sludge in opposite trends when anaerobic and aerobic conditions were applied. In order to predict the microbial community functional profiling, a bioinformatics software package of phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) was run to find that some dominant genera enriched in the BaP pathway may own the ability to degrade PAHs/BaP. Further experiments should focus on testing the dominant genera in BaP degradation at different oxygen levels.
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Affiliation(s)
- Haizhen Wu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, PR China
| | - Ming Wang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China
| | - Shuang Zhu
- Center for Bioresources & Drug Discovery and School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China.
| | - Junting Xie
- Center for Bioresources & Drug Discovery and School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Sergei Preis
- Department of Materials and Environmental Technology, Tallinn University of Technology, Tallinn, 19086, Estonia
| | - Fusheng Li
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China.
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12
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Molecular Biology-Based Analysis of the Interactive Effect of Nickel and Xanthates on Soil Bacterial Community Diversity and Structure. SUSTAINABILITY 2019. [DOI: 10.3390/su11143888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Metals and mineral flotation collector’s toxicity to the soil living system greatly compromise the sustainability of mining and ore processing. Their effects on the soil microbial community, the most active soil component, remain less understood and addressed particularly with regards to xanthates and their combination with metals. This study analyzed the interactive effects of Ni and xanthates, potassium ethyl xanthate and sodium isopropyl xanthate, on the soil bacterial community through an efficient molecular biology-based technique, the Miseq (Illumina). Both soil microbial community diversity and structure were more affected by xanthates than by Ni. The five most dominant phyla, representing 96.31% of the whole bacterial community, comprised Proteobacteria (54.16%), Firmicutes (17.51%), Actinobacteria (15.59%), Acidobacteria (4.87%), and Chloroflexi (4.16%). Different soil treatments exhibited greater difference in the species abundance/dominance than in the species numbers. Proteobacteria was the most dominant in the presence of xanthates, individually or in mixtures with nickel, while Firmicutes exhibited its highest proportion in the Ni/xanthate-treated samples. The most abundant and proportionally different bacterial species between different treatments were presented. The most abundant bacterial strains identified should be explored more for their potential application in biomining and for the prediction and biologically-based treatment and remediation of Ni and xanthate-contaminated systems.
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13
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Haleyur N, Shahsavari E, Jain SS, Koshlaf E, Ravindran VB, Morrison PD, Osborn AM, Ball AS. Influence of bioaugmentation and biostimulation on PAH degradation in aged contaminated soils: Response and dynamics of the bacterial community. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 238:49-58. [PMID: 30844545 DOI: 10.1016/j.jenvman.2019.02.115] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/31/2019] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) represent a group of hazardous compounds that are ubiquitous and persistent. The main aim of this study was to investigate the degradation of PAHs in chronically contaminated, aged and weathered soils obtained from a former gas plant of Australia. Biostimulation and bioaugmentation using individual isolates (Rhodococcus sp. (NH2), Achromobacter sp. (NH13), Oerskovia paurometabola (NH11), Pantoea sp. (NH15), Sejongia sp. (NH20), Microbacterium maritypicum (NH30) and Arthrobacter equi (NH21)) and a consortium of these isolates were tested during mesocosm studies. A significant reduction (99%) in PAH concentration was observed in all the treatments. In terms of the abundance of PAH-degrading genes and microbial community structure during PAH degradation, qPCR results revealed that Gram-positive bacteria were dominant over other bacterial communities in all the treatments. 16S sequencing results revealed that the inoculated organisms did not establish themselves during the treatment. However, substantial bacterial community changes during the treatments were observed, suggesting that the natural community exhibited sufficient resilience and diversity to enable an active, but changing degrading community at all stages of the degradation process. Consequently, biostimulation is proposed as the best strategy to remediate PAHs in aged, weathered and chronically contaminated soils.
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Affiliation(s)
- Nagalakshmi Haleyur
- School of Science, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia.
| | - Esmaeil Shahsavari
- School of Science, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia
| | - Sohni Singh Jain
- Department of Electrical and Biomedical Engineering, School of Engineering, RMIT University, Bundoora West, VIC, 3083, Australia
| | - Eman Koshlaf
- School of Science, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia
| | - Vivek B Ravindran
- School of Science, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia
| | - Paul D Morrison
- Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia
| | - A Mark Osborn
- School of Science, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia
| | - Andrew S Ball
- School of Science, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia.
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14
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Xu Y, Liu T, Zhu X, Ji G. Quantitative analysis of genetic associations in the biodegradative pathway of PAHs in wetland sediments of the Bohai coast region. CHEMOSPHERE 2019; 218:282-291. [PMID: 30472612 DOI: 10.1016/j.chemosphere.2018.11.059] [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: 07/11/2018] [Revised: 10/08/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
The present study characterized the distribution and sources of polycyclic aromatic hydrocarbons (PAHs) in 57 sediment cores collected from estuary and tidal flat wetlands in the Bohai coast region and investigated the molecular degradation mechanism of PAHs. The results showed that the PAH concentrations in estuary sediments were significantly higher than in tidal flat sediments. PAH patterns and pollutant sources were more complicated in estuary sediments. Quantitative response relationships showed that in estuary sediments, the key factors affecting PAH degradation changed from initial dioxygenase genes and C23O to salicylate hydroxylase genes and C23O with an increase in the PAH ring number. In contrast, for tidal flat sediments, the initial dioxygenase genes remained the key factors (nidA and nahAc/nagAc, except only nidA for 5-ring PAHs) related to PAHs with different ring numbers. Non-metric multidimensional scaling (NMDS) analysis revealed that the lower catechol dioxygenase pathway coupled with the upper pyrene dioxygenase pathway. The total polycyclic aromatic hydrocarbon (TPAH) level across the Bohai coast region was most affected by catechol dioxygenation (catA + C23O). Catechol dioxygenation was directly affected by naphthalene dioxygenation/nahG ((nahAc + nagAc)/nahG), indicating that the interaction within the upper pathway coupled with the lower pathway. In addition, TOC had direct positive effects on catechol dioxygenation and nidA. This study improves our understanding of the biodegradative pathway of PAHs with different ring numbers and the response of PAHs to biotic and abiotic factors.
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Affiliation(s)
- Yichan Xu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China
| | - Tiantian Liu
- Beijing Forestry University, Beijing 100083, China
| | - Xianfang Zhu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China.
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15
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Du J, Jing C. Anthropogenic PAHs in lake sediments: a literature review (2002-2018). ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2018; 20:1649-1666. [PMID: 30357191 DOI: 10.1039/c8em00195b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Lake sediments are an important reservoir for toxic and hydrophobic polycyclic aromatic hydrocarbons (PAHs). Monitoring of PAHs in sediment is helpful to understand pollution mechanisms and anthropogenic activities. This study reviews studies of PAHs in lake sediments published during 2002-2018. The studies' findings are analyzed, distributions of PAHs in lake sediments are summarized, and the applicability of lake sediments for tracking changes in PAH emission sources is emphasized. Lake sediments heavily polluted with PAHs are distributed in China, Egypt, the USA, and some urban lakes in Africa. The high levels of PAHs are predominantly associated with human activities such as anthropogenic combustion, petroleum industries, road traffic, and socioeconomic factors. However, the concentrations of sedimentary PAHs in most lakes were below the international guideline values.
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Affiliation(s)
- Jingjing Du
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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16
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Liang B, Ma C, Fan L, Wang Y, Yuan Y. Soil amendment alters soil physicochemical properties and bacterial community structure of a replanted apple orchard. Microbiol Res 2018; 216:1-11. [PMID: 30269849 DOI: 10.1016/j.micres.2018.07.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/14/2018] [Accepted: 07/19/2018] [Indexed: 11/30/2022]
Abstract
Compost amendment reportedly improved apple tree growth in replant soils. However, its effects should be evaluated at different soil depths and locations. This study investigated the impact of soil improvement with compost on soil physicochemical properties and bacterial community structure of a replanted apple orchard in comparison with the original orchard without compost improvement. The V1-V3 region of the bacterial 16S rRNA gene was subjected to high-throughput 454 pyrosequencing, and data were analyzed using the Mothur pipeline. The results showed that the soil improvement benefited tree growth and fruit quality during the study period. The compost amendment markedly increased tree height and stem diameter by a range of 6.1%-21.0% and 4.0%-14.0%, respectively. Fruit yield (9.5%), average weight (9.6%), and soluble solid content (5.6%) were also increased by compost amendment compared to those of the unimproved treatment. The pH, organic matter, and available N, P, and K contents were significantly increased by 5.7%-21.9%, 0.2%-62.9%, 9.3%-29.3%, 36.7%-64.5%, and 17.2%-100.3% in the compost improved soil. The pyrosequencing data showed that the soil improvement changed the bacterial community structure at all soil depths (0-20 cm and 20-40 cm) and locations (in-row and inter-row) considered; e.g., the relative abundance of Proteobacteria (20.2%), Bacteroidetes (2.5%), and Cyanobacteria (1.0%) was increased while that of Chloroflexi (5.5%), Acidobacteria (5.2%), Nitrospirae (4.5%), Gemmatimonadetes (3.8%), and Actinobacteria (1.8%) was decreased. The relative abundance of some dominant genera Burkholderia (2.3%), Pseudomonas (1.0%), and Paenibacillus (0.5%) were enhanced in the compost improved soil. Moreover, other dominant genera such as Nitrospira (6.4%), Gemmatimonas (2.2%), and Phenylobacterium (0.3%) were reduced by the application of compost. Our results indicate that soil improvement benefits the growth of tree and fruit quality, and is likely mediated by increased soil pH, organic matter, and available nutrient contents and beneficial bacterial community composition.
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Affiliation(s)
- Bowen Liang
- Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, Qingdao Agricultural University, Qingdao, China; College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Changqing Ma
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Lianmei Fan
- Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, Qingdao Agricultural University, Qingdao, China; College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Yongzhang Wang
- Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, Qingdao Agricultural University, Qingdao, China; College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Yongbing Yuan
- Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, Qingdao Agricultural University, Qingdao, China; College of Horticulture, Qingdao Agricultural University, Qingdao, China.
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17
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Roguet A, Therial C, Catherine A, Bressy A, Varrault G, Bouhdamane L, Tran V, Lemaire BJ, Vincon-Leite B, Saad M, Moulin L, Lucas FS. Importance of Local and Regional Scales in Shaping Mycobacterial Abundance in Freshwater Lakes. MICROBIAL ECOLOGY 2018; 75:834-846. [PMID: 29063147 DOI: 10.1007/s00248-017-1088-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 10/09/2017] [Indexed: 06/07/2023]
Abstract
Biogeographical studies considering the entire bacterial community may underestimate mechanisms of bacterial assemblages at lower taxonomic levels. In this context, the study aimed to identify factors affecting the spatial and temporal dynamic of the Mycobacterium, a genus widespread in aquatic ecosystems. Nontuberculous mycobacteria (NTM) density variations were quantified in the water column of freshwater lakes at the regional scale (annual monitoring of 49 lakes in the Paris area) and at the local scale (2-year monthly monitoring in Créteil Lake) by real-time quantitative PCR targeting the atpE gene. At the regional scale, mycobacteria densities in water samples ranged from 6.7 × 103 to 1.9 × 108 genome units per liter. Density variations were primarily explained by water pH, labile iron, and dispersal processes through the connection of the lakes to a river. In Créteil Lake, no spatial variation of mycobacterial densities was noticed over the 2-year monthly survey, except after large rainfall events. Indeed, storm sewer effluents locally and temporarily increased NTM densities in the water column. The temporal dynamic of the NTM densities in Créteil Lake was associated with suspended solid concentrations. No clear seasonal variation was noticed despite a shift in NTM densities observed over the 2012-2013 winter. Temporal NTM densities fluctuations were well predicted by the neutral community model, suggesting a random balance between loss and gain of mycobacterial taxa within Créteil Lake. This study highlights the importance of considering multiple spatial scales for understanding the spatio-temporal dynamic of bacterial populations in natural environments.
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Affiliation(s)
- Adélaïde Roguet
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France.
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53204, USA.
| | - Claire Therial
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | - Arnaud Catherine
- Unité Molécules de Communication et Adaptation des Micro-organismes (MCAM UMR 7245), Sorbonne Université, Muséum National d'Histoire Naturelle, Case 39, 57 rue Cuvier, FR 75005, Paris, France
| | - Adèle Bressy
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | - Gilles Varrault
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | - Lila Bouhdamane
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | - Viet Tran
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | - Bruno J Lemaire
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | | | - Mohamed Saad
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
| | - Laurent Moulin
- Eau de Paris, Direction Recherche et Développement Qualité de l'Eau (DRDQE), 33 avenue Jean Jaurès, FR 94200, Ivry-sur-Seine, France
| | - Françoise S Lucas
- Leesu, UMR-MA 102, UPEC, École des Ponts, AgroParisTech, 94000, Créteil, France
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18
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Chen SC, Duan GL, Ding K, Huang FY, Zhu YG. DNA stable-isotope probing identifies uncultivated members of Pseudonocardia associated with biodegradation of pyrene in agricultural soil. FEMS Microbiol Ecol 2018; 94:4862470. [DOI: 10.1093/femsec/fiy026] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/14/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Song-Can Chen
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Gui-Lan Duan
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Kai Ding
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
| | - Fu-Yi Huang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
| | - Yong-Guan Zhu
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
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19
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Yan Z, He Y, Cai H, Van Nostrand JD, He Z, Zhou J, Krumholz LR, Jiang HL. Interconnection of Key Microbial Functional Genes for Enhanced Benzo[a]pyrene Biodegradation in Sediments by Microbial Electrochemistry. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:8519-8529. [PMID: 28677976 DOI: 10.1021/acs.est.7b00209] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Sediment microbial fuel cells (SMFCs) can stimulate the degradation of polycyclic aromatic hydrocarbons in sediments, but the mechanism of this process is poorly understood at the microbial functional gene level. Here, the use of SMFC resulted in 92% benzo[a]pyrene (BaP) removal over 970 days relative to 54% in the controls. Sediment functions, microbial community structure, and network interactions were dramatically altered by the SMFC employment. Functional gene analysis showed that c-type cytochrome genes for electron transfer, aromatic degradation genes, and extracellular ligninolytic enzymes involved in lignin degradation were significantly enriched in bulk sediments during SMFC operation. Correspondingly, chemical analysis of the system showed that these genetic changes resulted in increases in the levels of easily oxidizable organic carbon and humic acids which may have resulted in increased BaP bioavailability and increased degradation rates. Tracking microbial functional genes and corresponding organic matter responses should aid mechanistic understanding of BaP enhanced biodegradation by microbial electrochemistry and development of sustainable bioremediation strategies.
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Affiliation(s)
- Zaisheng Yan
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences , Nanjing 210008, China
| | - Yuhong He
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences , Nanjing 210008, China
| | - Haiyuan Cai
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences , Nanjing 210008, China
| | - Joy D Van Nostrand
- Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Zhili He
- Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States
- Earth Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
- Department of Environmental Science and Engineering, Tsinghua University , Beijing 100084, China
| | - Lee R Krumholz
- Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - He-Long Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences , Nanjing 210008, China
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20
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Gupta G, Kumar V, Pal AK. Microbial Degradation of High Molecular Weight Polycyclic Aromatic Hydrocarbons with Emphasis on Pyrene. Polycycl Aromat Compd 2017. [DOI: 10.1080/10406638.2017.1293696] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Gauri Gupta
- Laboratory of Applied Microbiology, Department of Environmental Science & Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, India
| | - Vipin Kumar
- Laboratory of Applied Microbiology, Department of Environmental Science & Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, India
| | - A. K. Pal
- Laboratory of Applied Microbiology, Department of Environmental Science & Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, India
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21
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Wang L, Li J, Yang F, E Y, Raza W, Huang Q, Shen Q. Application of Bioorganic Fertilizer Significantly Increased Apple Yields and Shaped Bacterial Community Structure in Orchard Soil. MICROBIAL ECOLOGY 2017; 73:404-416. [PMID: 27670433 DOI: 10.1007/s00248-016-0849-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 08/25/2016] [Indexed: 05/20/2023]
Abstract
Application of bioorganic fertilizers has been reported to improve crop yields and change soil bacterial community structure; however, little work has been done in apple orchard soils where the biological properties of the soils are being degraded due to long-term application of chemical fertilizers. In this study, we used Illumina-based sequencing approach to characterize the bacterial community in the 0-60-cm soil profile under different fertilizer regimes in the Loess Plateau. The experiment includes three treatments: (1) control without fertilization (CK); (2) application of chemical fertilizer (CF); and (3) application of bioorganic fertilizer and organic-inorganic mixed fertilizer (BOF). The results showed that the treatment BOF increased the apple yields by 114 and 67 % compared to the CK and CF treatments, respectively. The treatment BOF also increased the soil organic matter (SOM) by 22 and 16 % compared to the CK and CF treatments, respectively. The Illumina-based sequencing showed that Acidobacteria and Proteobacteria were the predominant phyla and Alphaproteobacteria and Gammaproteobacteria were the most abundant classes in the soil profile. The bacterial richness for ACE was increased after the addition of BOF. Compared to CK and CF treatments, BOF-treated soil revealed higher abundance of Proteobacteria, Alphaproteobacteria and Gammaproteobacteria, Rhizobiales, and Xanthomonadales while Acidobacteria, Gp7, Gp17, and Sphaerobacter were found in lower abundance throughout the soil profile. Bacterial community structure varied with soil depth under different fertilizer treatments, e.g., the bacterial richness, diversity, and the relative abundance of Verruccomicrobia, Candidatus Brocadiales, and Skermanella were decreased with the soil depth in all three treatments. Permutational multivariate analysis showed that the fertilizer regime was the major factor than soil depth in the variations of the bacterial community composition. Two groups, Lysobacter and Rhodospirillaceae, were found to be the significantly increased by the BOF addition and the genus Lysobacter may identify members of this group effective in biological control-based plant disease management and the members of family Rhodospirillaceae had an important role in fixing molecular nitrogen. These results strengthen the understanding of responses to the BOF and possible interactions within bacterial communities in soil that can be associated with disease suppression and the accumulation of carbon and nitrogen. The increase of apple yields after the application of BOF might be attributed to the fact that the application of BOF increased SOM, and soil total nitrogen, and changed the bacterial community by enriching Rhodospirillaceae, Alphaprotreobateria, and Proteobacteria.
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Affiliation(s)
- Lei Wang
- Jiangsu Key Laboratory for Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jing Li
- Jiangsu Key Laboratory for Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fang Yang
- Jiangsu Key Laboratory for Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yaoyao E
- Jiangsu Key Laboratory for Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Waseem Raza
- Jiangsu Key Laboratory for Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qiwei Huang
- Jiangsu Key Laboratory for Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China.
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Qirong Shen
- Jiangsu Key Laboratory for Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
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Hoostal MJ, Bouzat JL. Spatial Patterns of bphA Gene Diversity Reveal Local Adaptation of Microbial Communities to PCB and PAH Contaminants. MICROBIAL ECOLOGY 2016; 72:559-570. [PMID: 27430632 DOI: 10.1007/s00248-016-0812-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 06/29/2016] [Indexed: 06/06/2023]
Abstract
Biphenyl dioxygenases, encoded by the bphA gene, initiate the oxidation of polychlorinated biphenyls (PCBs) and specify the substrate range of PCB congeners metabolized by bacteria. Increased bphA gene diversity within microbial communities may allow a broader range of PCB congeners to be catabolized, thus resulting in greater PCB degradation. To assess the role of PCBs in modulating bphA gene diversity, 16S ribosomal RNA (rRNA) gene and bphA environmental DNA libraries were generated from bacterial communities in sediments with a steep gradient of PCB contamination. Multiple measures of sequence diversity revealed greater heterogeneity of bphA sequences in polluted compared to unpolluted locations. Codon-based signatures of selection in bphA sequences provided evidence of purifying selection. Unifrac analysis of 16S rRNA sequences revealed independent taxonomic lineages from polluted and unpolluted locations, consistent with the presence of locally adapted bacterial communities. Phylogenetic analysis of bphA sequences indicated that dioxygenases from sediments were closely related to previously characterized dioxygenases that metabolize PCBs and polynuclear aromatic hydrocarbons (PAHs), consistent with high levels of these contaminants within the studied sediments. Structural analyses indicated that the BphA protein of Rhodococcus jostii, capable of metabolizing both PCBs and PAHs, provided a more optimal modeling template for bphA sequences reported in this study than a BphA homologue with more restricted substrate specificity. Results from this study suggest that PCBs and PAHs may drive local adaptation of microbial communities by acting as strong selective agents for biphenyl dioxygenases capable of metabolizing a wide range of congeners.
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Affiliation(s)
- Matthew J Hoostal
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - Juan L Bouzat
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA.
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Chen B, Huang J, Yuan K, Lin L, Wang X, Yang L, Luan T. Direct evidences on bacterial growth pattern regulating pyrene degradation pathway and genotypic dioxygenase expression. MARINE POLLUTION BULLETIN 2016; 105:73-80. [PMID: 26952991 DOI: 10.1016/j.marpolbul.2016.02.054] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 02/17/2016] [Accepted: 02/19/2016] [Indexed: 06/05/2023]
Abstract
Pyrene degradation by Mycobacterium sp. strain A1-PYR was investigated in the presence of nutrient broth, phenanthrene and fluoranthene, respectively. Fast bacterial growth in the nutrient broth considerably enhanced pyrene degradation rate, whereas degradation efficiency per cell was substantially decreased. The addition of nutrient broth could not alter the transcription levels of all dioxygenase genotypes. In the PAH-only substrates, bacterial growth completely relied on biological conversion of PAHs into the effective carbon sources, which led to a higher degradation efficiency of pyrene per cell than the case of nutrient broth. Significant correlations were only observed between nidA-related dioxygenase expression and pyrene degradation or bacterial growth. The highest pyrene degradation rate in the presence of phenanthrene was consistent with the highest transcription level of nidA and 4,5-pyrenediol as the sole initial metabolite. This study reveals that bacterial growth requirement can invigorate degradation of PAHs by regulating metabolic pathway and genotypic enzyme expression.
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Affiliation(s)
- Baowei Chen
- MOE Key Laboratory of Aquatic Product Safety, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, School of Marine Sciences, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
| | - Jinyin Huang
- MOE Key Laboratory of Aquatic Product Safety, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, School of Marine Sciences, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
| | - Ke Yuan
- MOE Key Laboratory of Aquatic Product Safety, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, School of Marine Sciences, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
| | - Li Lin
- MOE Key Laboratory of Aquatic Product Safety, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, School of Marine Sciences, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
| | - Xiaowei Wang
- MOE Key Laboratory of Aquatic Product Safety, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, School of Marine Sciences, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
| | - Lihua Yang
- MOE Key Laboratory of Aquatic Product Safety, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, School of Marine Sciences, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
| | - Tiangang Luan
- MOE Key Laboratory of Aquatic Product Safety, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, School of Marine Sciences, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China.
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High mycobacterial diversity in recreational lakes. Antonie van Leeuwenhoek 2016; 109:619-31. [PMID: 26873594 DOI: 10.1007/s10482-016-0665-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 02/03/2016] [Indexed: 10/22/2022]
Abstract
Although nontuberculous mycobacteria (NTM) are natural inhabitants of freshwater ecosystems, few studies have focused on their distribution in these habitats. Thus, the knowledge about the abundance as well as the composition of NTM remains limited and patchy in these environments. In this context, a prospective study was performed to identify favourable habitats for mycobacteria in two recreational lakes. Mycobacterial density and diversity were measured using quantitative real-time PCR and the MiSeq Illumina platform. For both lakes, five compartments were investigated, i.e. water column, air-water interface, sediment, epilithon and epiphyton biofilms. Nontuberculous mycobacteria were detected in all compartments in large densities and displayed a remarkable diversity. NTM were dominated by fast-growing species. Lakes and compartments appeared to shape mycobacteria assemblage composition as well as their densities. In both lakes, some OTUs assigned to the species level were identified as related to known opportunistic pathogens.
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Ren G, Ren W, Teng Y, Li Z. Evident bacterial community changes but only slight degradation when polluted with pyrene in a red soil. Front Microbiol 2015; 6:22. [PMID: 25688237 PMCID: PMC4311681 DOI: 10.3389/fmicb.2015.00022] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 01/08/2015] [Indexed: 11/13/2022] Open
Abstract
Understanding the potential for Polycyclic aromatic hydrocarbons (PAH) degradation by indigenous microbiota and the influence of PAHs on native microbial communities is of great importance for bioremediation and ecological evaluation. Various studies have focused on the bacterial communities in the environment where obvious PAH degradation was observed, little is known about the microbiota in the soil where poor degradation was observed. Soil microcosms were constructed with a red soil by supplementation with a high-molecular-weight PAH (pyrene) at three dosages (5, 30, and 70 mg ⋅ kg(-1)). Real-time PCR was used to evaluate the changes in bacterial abundance and pyrene dioxygenase gene (nidA) quantity. Illumina sequencing was used to investigate changes in diversity, structure, and composition of bacterial communities. After 42 days of incubation, no evident degradation was observed. The poor degradation ability was associated with the stability or significant decrease of abundance of the nidA gene. Although the abundance of the bacterial 16S rRNA gene was not affected by pyrene, the bacterial richness and diversity were decreased with increasing dosage of pyrene and the community structure was changed. Phylotypes affected by pyrene were comprehensively surveyed: (1) at the high taxonomic level, seven of the abundant phyla/classes (relative abundance >1.0%) including Chloroflexi, AD3, WPS-2, GAL5, Alphaproteobacteria, Actinobacteria, and Deltaproteobacteria and one rare phylum Crenarchaeota were significantly decreased by at least one dosage of pyrene, while three phyla/classes (Acidobacteria, Betaproteobacteria, and Gammaproteobacteria) were significantly increased; and (2) at the lower taxonomic level, the relative abundances of twelve orders were significantly depressed, whereas those of nine orders were significantly increased. This work enhanced our understanding of the biodegradation potential of pyrene in red soil and the effect of pyrene on soil ecosystems at the microbial community level.
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Affiliation(s)
- Gaidi Ren
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science - Chinese Academy of Sciences Nanjing, China
| | - Wenjie Ren
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science - Chinese Academy of Sciences Nanjing, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science - Chinese Academy of Sciences Nanjing, China
| | - Zhengao Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science - Chinese Academy of Sciences Nanjing, China
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Korosi JB, Cheng W, Blais JM. Organic Pollutants in Sediment Core Archives. ENVIRONMENTAL CONTAMINANTS 2015. [DOI: 10.1007/978-94-017-9541-8_8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Bacosa HP, Inoue C. Polycyclic aromatic hydrocarbons (PAHs) biodegradation potential and diversity of microbial consortia enriched from tsunami sediments in Miyagi, Japan. JOURNAL OF HAZARDOUS MATERIALS 2014; 283:689-697. [PMID: 25464311 DOI: 10.1016/j.jhazmat.2014.09.068] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 09/22/2014] [Accepted: 09/27/2014] [Indexed: 06/04/2023]
Abstract
The Great East Japan Earthquake caused tsunamis and resulted in widespread damage to human life and infrastructure. The disaster also resulted in contamination of the environment by chemicals such as polycyclic aromatic hydrocarbons (PAHs). This study was conducted to investigate the degradation potential and describe the PAH-degrading microbial communities from tsunami sediments in Miyagi, Japan. PAH-degrading bacteria were cultured by enrichment using PAH mixture or pyrene alone as carbon and energy sources. Among the ten consortia tested for PAH mixture, seven completely degraded fluorene and more than 95% of phenanthrene in 10 days, while only four consortia partially degraded pyrene. Six consortia partially degraded pyrene as a single substrate. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) revealed that each sample was dominated by unique microbial populations, regardless of sampling location. The consortia were dominated by known PAHs degraders including Sphingomonas, Pseudomonas, and Sphingobium; and previously unknown degraders such as Dokdonella and Luteimonas. A potentially novel and PAH-degrading Dokdonella was detected for the first time. PAH-ring hydroxylating dioxygenase (PAH-RHDα) gene was shown to be more effective than nidA in estimating pyrene-degrading bacteria in the enriched consortia. The consortia obtained in this study are potential candidates for remediation of PAHs contaminated soils.
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Affiliation(s)
- Hernando Pactao Bacosa
- Graduate School of Environmental Studies, Tohoku University, Aoba 6-6-20, Aramaki, Aoba-ku, Sendai 980-8579, Japan; Marine Science Institute, The University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX 78373, United States.
| | - Chihiro Inoue
- Graduate School of Environmental Studies, Tohoku University, Aoba 6-6-20, Aramaki, Aoba-ku, Sendai 980-8579, Japan
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Wilhelm SW, LeCleir GR, Bullerjahn GS, McKay RM, Saxton MA, Twiss MR, Bourbonniere RA. Seasonal changes in microbial community structure and activity imply winter production is linked to summer hypoxia in a large lake. FEMS Microbiol Ecol 2013; 87:475-85. [PMID: 24164471 DOI: 10.1111/1574-6941.12238] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 09/25/2013] [Accepted: 10/18/2013] [Indexed: 11/29/2022] Open
Abstract
Carbon and nutrient cycles in large temperate lakes such as Lake Erie are primarily driven by phototrophic and heterotrophic microorganisms, although our understanding of these is often constrained to late spring through summer due to logistical constraints. During periods of > 90% ice cover in February of 2008, 2009, and 2010, we collected samples from an icebreaker for an examination of bacterial production as well as microbial community structure. In comparison with summer months (August 2002 and 2010), we tested hypotheses concerning seasonal changes in microbial community diversity and production. Bacterial production estimates were c. 2 orders of magnitude higher (volume normalized) in summer relative to winter. Our observations further demonstrate that the microbial community, including single-celled phototrophs, varied in composition between August and February. Sediment traps deployed and collected over a 3 year period (2008-2011) confirmed that carbon export was ongoing and not limiting winter production. The results support the notion that active primary producers in winter months export carbon to the sediments that is not consumed until the warmer seasons. The establishment of this linkage is a critical observation in efforts to understand the extent and severity of annual summertime formations of a zone of regional hypoxia in Lake Erie.
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Affiliation(s)
- Steven W Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, TN, USA
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29
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Zhang Q, Sun J, Liu S, Wei Q. Manure refinement affects apple rhizosphere bacterial community structure: a study in sandy soil. PLoS One 2013; 8:e76937. [PMID: 24155909 PMCID: PMC3796563 DOI: 10.1371/journal.pone.0076937] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 09/04/2013] [Indexed: 11/19/2022] Open
Abstract
We used DNA-based pyrosequencing to characterize the bacterial community structure of the sandy soil of an apple orchard with different manure ratios. Five manure percentages (5%, 10%, 15%, 20% and 25%) were examined. More than 10,000 valid reads were obtained for each replicate. The communities were composed of five dominant groups (Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria and Bacteroidetes), of which Proteobacteria content gradually decreased from 41.38% to 37.29% as manure ratio increased from 0% to 25%, respectively. Redundancy analysis showed that 37 classes were highly correlated with manure ratio, 18 of which were positively correlated. Clustering revealed that the rhizosphere samples were grouped into three components: low manure (control, 5%) treatment, medium manure (10%, 15%) treatment and high manure (20%, 25%) treatment. Venn analysis of species types of these three groups revealed that the bacteria community difference was primarily reflected by quantity ratio rather than species variety. Although greater manure content led to higher soil organic matter content, the medium manure improved soil showed the highest urease activity and saccharase activity, while 5% to 20% manure ratio improvement also resulted in higher bacteria diversity than control and 25% manure ratio treatment. Our experimental results suggest that the use of a proper manure ratio results in significantly higher soil enzyme activity and different bacteria community patterns, whereas the use of excessive manure amounts has negative effect on soil quality.
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Affiliation(s)
- Qiang Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Jian Sun
- Institute of Forestry and Pomology, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Songzhong Liu
- Institute of Forestry and Pomology, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Qinping Wei
- Institute of Forestry and Pomology, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
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Thureborn P, Lundin D, Plathan J, Poole AM, Sjöberg BM, Sjöling S. A metagenomics transect into the deepest point of the Baltic Sea reveals clear stratification of microbial functional capacities. PLoS One 2013; 8:e74983. [PMID: 24086414 PMCID: PMC3781128 DOI: 10.1371/journal.pone.0074983] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 08/06/2013] [Indexed: 11/27/2022] Open
Abstract
The Baltic Sea is characterized by hyposaline surface waters, hypoxic and anoxic deep waters and sediments. These conditions, which in turn lead to a steep oxygen gradient, are particularly evident at Landsort Deep in the Baltic Proper. Given these substantial differences in environmental parameters at Landsort Deep, we performed a metagenomic census spanning surface to sediment to establish whether the microbial communities at this site are as stratified as the physical environment. We report strong stratification across a depth transect for both functional capacity and taxonomic affiliation, with functional capacity corresponding most closely to key environmental parameters of oxygen, salinity and temperature. We report similarities in functional capacity between the hypoxic community and hadal zone communities, underscoring the substantial degree of eutrophication in the Baltic Proper. Reconstruction of the nitrogen cycle at Landsort deep shows potential for syntrophy between archaeal ammonium oxidizers and bacterial denitrification at anoxic depths, while anaerobic ammonium oxidation genes are absent, despite substantial ammonium levels below the chemocline. Our census also reveals enrichment in genetic prerequisites for a copiotrophic lifestyle and resistance mechanisms reflecting adaptation to prevalent eutrophic conditions and the accumulation of environmental pollutants resulting from ongoing anthropogenic pressures in the Baltic Sea.
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Affiliation(s)
- Petter Thureborn
- School of Natural Sciences and Environmental Studies, Södertörn University, Huddinge, Sweden
- Department of Molecular Biology and Functional Genomics, Stockholm University, Stockholm, Sweden
- * E-mail:
| | - Daniel Lundin
- School of Natural Sciences and Environmental Studies, Södertörn University, Huddinge, Sweden
- Science for Life Laboratories, Royal Institute of Technology, Solna, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Josefin Plathan
- Department of Molecular Biology and Functional Genomics, Stockholm University, Stockholm, Sweden
| | - Anthony M. Poole
- Department of Molecular Biology and Functional Genomics, Stockholm University, Stockholm, Sweden
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Britt-Marie Sjöberg
- Department of Molecular Biology and Functional Genomics, Stockholm University, Stockholm, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Sara Sjöling
- School of Natural Sciences and Environmental Studies, Södertörn University, Huddinge, Sweden
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31
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In silico bioremediation of polycyclic aromatic hydrocarbon: A frontier in environmental chemistry. J Mol Graph Model 2013; 44:1-8. [DOI: 10.1016/j.jmgm.2013.04.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 04/24/2013] [Accepted: 04/27/2013] [Indexed: 11/23/2022]
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32
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Exploring the potential environmental functions of viable but non-culturable bacteria. World J Microbiol Biotechnol 2013; 29:2213-8. [PMID: 23733177 DOI: 10.1007/s11274-013-1390-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 05/28/2013] [Indexed: 12/25/2022]
Abstract
A conventional plate count is the most commonly employed method to estimate the number of living bacteria in environmental samples. In fact, judging the level of viable culture by plate count is limited, because it is often several orders of magnitude less than the number of living bacteria actually present. Most of the bacteria are in "viable but non-culturable" (VBNC) state, whose cells are intact and alive and can resuscitate when surrounding conditions are more favorable. The most exciting recent development in resuscitating VBNC bacteria is a bacterial cytokine, namely, the resuscitation-promoting factor (Rpf), secreted by Micrococcus luteus, which promotes the resuscitation and growth of high G+C Gram-positive organisms, including some species of the genus Mycobacterium. However, most of studies deal with VBNC bacteria only from the point of view of medicine and epidemiology. It is therefore of great significance to research whether these VBNC state bacteria also possess some useful environmental capabilities, such as degradation, flocculation, etc. Further studies are needed to elucidate the possible environmental role of the VBNC bacteria, rather than only considering their role as potential pathogens from the point view of epidemiology and public health. We have studied the resuscitation of these VBNC bacteria in polluted environments by adding culture supernatant containing Rpf from M. luteus, and it was found that, as a huge microbial resource, VBNC bacteria could provide important answers to dealing with existing problems of environmental pollution. This mini-review will provide new insight for considering the potentially environmental functions of VBNC bacteria.
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Pratt B, Riesen R, Johnston CG. PLFA analyses of microbial communities associated with PAH-contaminated riverbank sediment. MICROBIAL ECOLOGY 2012; 64:680-691. [PMID: 22584297 DOI: 10.1007/s00248-012-0060-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 04/12/2012] [Indexed: 05/31/2023]
Abstract
Sediment contaminated with polycyclic aromatic hydrocarbons (PAHs) is widely distributed in aquatic ecosystems. The microbial community structure of riverbank PAH-contaminated sediments was investigated using phospholipid-derived fatty acid (PLFA) analysis. Surface and subsurface riverbank sediment was collected from a highly contaminated site and from an uncontaminated site along the Mahoning River, OH. PAH concentrations, physical sediment characteristics, and other microbial community parameters (biomass as phospholipid phosphate (PLP) and activity) were also measured. PAHs were detected in all samples but were only quantifiable in the contaminated (250 μg/g g(-1)) subsurface sediment. Subsurface samples from both locations showed very similar PLP values and distribution of PLFAs, with 27-37 % of the microbial community structure being composed of sulfate reducing and other anaerobic bacteria. Principal components analysis indicated no correlation between PAH contamination and PLFA diversity. Although PLP and phospholipid fatty acid measurements of bacterial communities did not reflect the environmental differences among sites, the highly PAH-contaminated sediment showed the highest measured microbial activity (reduction of 1,200 nmol INT g(-1) h(-1)), likely from a population adapted to environmental pollutants, rates that are much higher than measured in many uncontaminated soil and sediment systems. These data warrant further investigation into community structure at the genetic level and indicate potential for bioremediation by indigenous microbes.
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DeBruyn JM, Mead TJ, Sayler GS. Horizontal transfer of PAH catabolism genes in Mycobacterium: evidence from comparative genomics and isolated pyrene-degrading bacteria. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:99-106. [PMID: 21899303 DOI: 10.1021/es201607y] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Biodegradation of high molecular weight polycyclic aromatic hydrocarbons (PAHs), such as pyrene and benzo[a]pyrene, has only been observed in a few genera, namely fast-growing Mycobacterium and Rhodococcus. In M. vanbaalenii PYR-1, multiple aromatic ring hydroxylating dioxygenase (ARHDOs) genes including pyrene dioxygenases nidAB and nidA3B3 are localized in one genomic region. Here we examine the homologous genomic regions in four other PAH-degrading Mycobacterium (strains JLS, KMS, and MCS, and M. gilvum PYR-GCK), presenting evidence for past horizontal gene transfer events. Seven distinct types of ARHDO genes are present in all five genomes, and display conserved syntenic architecture with respect to gene order, orientation, and association with other genes. Duplications and putative integrase and transposase genes suggest past gene shuffling. To corroborate these observations, pyrene-degrading strains were isolated from two PAH-contaminated sediments: Chattanooga Creek (Tennessee) and Lake Erie (western basin). Some were related to fast-growing Mycobacterium spp. and carried both nidA and nidA3 genes. Other isolates belonged to Microbacteriaceae and Intrasporangiaceae presenting the first evidence of pyrene degradation in these families. These isolates had nidA (and some, nidA3) genes that were homologous to Mycobacterial ARHDO genes, suggesting that horizontal gene transfer events have occurred.
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Affiliation(s)
- Jennifer M DeBruyn
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Tennessee, United States
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35
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Liu X, Jing J, Li S, Zhang G, Zou T, Xia X, Huang W. Measurement of pyrene in the gills of exposed fish using synchronous fluorescence spectroscopy. CHEMOSPHERE 2012; 86:198-201. [PMID: 22071375 DOI: 10.1016/j.chemosphere.2011.10.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 10/11/2011] [Accepted: 10/14/2011] [Indexed: 05/31/2023]
Abstract
A synchronous fluorescence spectroscopy (SFS) method was developed for determination of pyrene in the gills of exposed fish. The wavelength differences (Δλ) of 50 nm was maintained between excitation and emission wavelengths and it was found to be suitable for the effective determination of pyrene in fish gills; the peak were observed at λ(ex) 334.5 nm. Linear relationships between SFS intensity and the concentration of pyrene in n-hexane solution were established. It was demonstrated that the SFS method was effective, simple, and less expensive, providing an attractive alternative for the rapid analysis of pyrene in fish gills.
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Affiliation(s)
- Xianli Liu
- Hubei Key Laboratory of Mine Environmental Pollution Control & Remediation, Huangshi Institute of Technology, Huangshi 435003, PR China
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36
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Mikac I, Fiket Z, Terzić S, Barešić J, Mikac N, Ahel M. Chemical indicators of anthropogenic impacts in sediments of the pristine karst lakes. CHEMOSPHERE 2011; 84:1140-1149. [PMID: 21531436 DOI: 10.1016/j.chemosphere.2011.04.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 04/03/2011] [Accepted: 04/07/2011] [Indexed: 05/30/2023]
Abstract
The anthropogenic impact on the pristine karst lakes was investigated using combination of specific parameters, including multielemental analysis of major inorganic constituents (Al, K, Fe) and trace metals (Li, Ag, Cd, Sn, Pb, Bi, Cr, Co, Ni, Cu, Zn and Sb), polycyclic aromatic hydrocarbons (PAHs) and anionic surfactants of linear alkylbenzene sulfonate (LAS) type. The study was performed in the Plitvice Lakes National Park, situated in a sparsely populated area of the northwestern Dinarides, central Croatia. Dated cores of recent sediments from the two biggest lakes, Lake Prosce and Lake Kozjak, were analysed for the selected contaminants using highly specific methods, involving inductively coupled plasma mass spectrometry (ICP/MS), gas chromatography/mass spectrometry (GC/MS) and liquid chromatography/tandem mass spectrometry (LC/MS/MS). The concentration of inorganic constituents reflected primarily the geological background of the area as well as geomorphological and geochemical characteristics of the Plitvice Lakes. Due to the higher terrigenous input, the concentration of all elements was significantly higher in the Lake Prosce. The concentration of toxic metals was relatively low in both lakes, except for Cd (>1 mg kg(-1)) and Pb (up to 40 mg kg(-1)). The vertical profiles of these metals suggested that elevated concentrations of Cd were of natural origin, derived from the erosion of the Jurassic dolomite bedrock, while Pb was predominately of recent anthropogenic origin. A similar distribution pattern, suggesting the same prevailing mechanism of input, was observed for pyrolytic PAHs. The characteristic diagnostic PAH ratios revealed that higher PAHs prevailingly originated from the combustion of biomass and fossil fuels. LAS, which represent highly specific indicators of untreated wastewaters, were found in rather high concentrations in the recent sediment layers (up to 4.7 mg kg(-1)), suggesting that contaminated household and hotel wastewaters reach the Lakes, very probably by leaking through the porous karst rocks.
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Affiliation(s)
- I Mikac
- Division for Marine and Environmental Research, Rudjer Boskovic Institute, Bijenicka 54, Zagreb, Croatia
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Radomski N, Betelli L, Moilleron R, Haenn S, Moulin L, Cambau E, Rocher V, Gonçalves A, Lucas FS. Mycobacterium behavior in wastewater treatment plant, a bacterial model distinct from Escherichia coli and Enterococci. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2011; 45:5380-6. [PMID: 21591688 DOI: 10.1021/es104084c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Mycobacteria are waterborne emerging pathogens causing infections in human. Mycobacteria have been previously isolated from wastewater and sludge, but their densities were not estimated due to cultural biases. In order to evaluate the impact of wastewater treatment processes on mycobacteria removal, we used a real time PCR method. First we compared six DNA extraction methods and second we used the more efficient DNA extraction procedure (i.e., enzymatic lysis combined with hexadecyltrimethylammonium bromide-NaCl procedure) in order to quantify Mycobacterium. With the aim to identify parameters that could serve as indicator of mycobacterial behavior, mycobacterial densities were measured in parallel to those of Escherichia coli and enterococci, and to concentrations of chemical parameters usually monitored in wastewater. Mycobacterium reached 5.5 × 10⁵ ± 3.9 × 10⁵ copies/L in the influent, but was not detected in the effluent after decantation and biofiltration. Most mycobacteria (98.6 ± 2.7%, i.e. 2.4 ± 0.7 log₁₀) were removed by the physical-chemical decantation, and the remaining mycobacteria were removed by biofiltration. In contrast, enterococci and E. coli were lightly removed by decantation step and mainly removed by biofiltration. Our results showed that Mycobacterium corresponds to a hydrophobic behavior linked to insoluble compound removal, whereas enterococci and E. coli refer to hydrophilic behaviors linked to soluble compound removals.
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Affiliation(s)
- Nicolas Radomski
- Laboratoire Eau Environnement Systèmes Urbains UMR MA 102 AgroParisTech, Université Paris-Est, FR 77455 Champs sur Marne.
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Achten C, Cheng S, Straub KL, Hofmann T. The lack of microbial degradation of polycyclic aromatic hydrocarbons from coal-rich soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2011; 159:623-629. [PMID: 21050626 DOI: 10.1016/j.envpol.2010.09.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Revised: 09/23/2010] [Accepted: 09/25/2010] [Indexed: 05/30/2023]
Abstract
Analytical techniques used to assess the environmental risk of contamination from polycyclic aromatic hydrocarbons (PAHs) typically consider only abiotic sample parameters. Supercritical fluid extraction and sorption enthalpy experiments previously suggested slow desorption rates for PAH compounds in two coal-contaminated floodplain soils. In this study, the actual PAH availability for aerobic soil microorganisms was tested in two series of soil-slurry experiments. The experimental conditions supported microbial degradation of phenanthrene if it was weakly sorbed onto silica gel. Native coals and coal-derived particles in two soils effectively acted as very strong sorbents and prevented microbial PAH degradation. The long history of PAH exposure and degree of coal contamination apparently had no influence on the capability of the microbial soil community to overcome constraints of PAH availability. Within the context of the experimental conditions and the compounds chosen, our results confirm that coal-bound PAHs are not bioavailable and hence of low environmental concern.
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Affiliation(s)
- Christine Achten
- University of Vienna, Department of Environmental Geosciences, Althanstr. 14, 1090 Vienna, Austria
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Toyama T, Furukawa T, Maeda N, Inoue D, Sei K, Mori K, Kikuchi S, Ike M. Accelerated biodegradation of pyrene and benzo[a]pyrene in the Phragmites australis rhizosphere by bacteria-root exudate interactions. WATER RESEARCH 2011; 45:1629-1638. [PMID: 21196023 DOI: 10.1016/j.watres.2010.11.044] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 09/06/2010] [Accepted: 11/30/2010] [Indexed: 05/30/2023]
Abstract
We investigated the biodegradation of pyrene and benzo[a]pyrene in Phragmites australis rhizosphere sediment. We collected P. australis plants, rhizosphere sediments, and unvegetated sediments from natural aquatic sites and conducted degradation experiments using sediments spiked with pyrene or benzo[a]pyrene. Accelerated removal of pyrene and benzo[a]pyrene was observed in P. australis rhizosphere sediments with plants, whereas both compounds persisted in unvegetated sediments without plants and in autoclaved rhizosphere sediments with sterilized plants, suggesting that the accelerated removal resulted largely from biodegradation by rhizosphere bacteria. Initial densities of pyrene-utilizing bacteria were substantially higher in the rhizosphere than in unvegetated sediments, but benzo[a]pyrene-utilizing bacteria were not detected in rhizosphere sediments. Mycobacterium gilvum strains isolated from rhizosphere sediments utilized pyrene aerobically as a sole carbon source and were able to degrade benzo[a]pyrene when induced with pyrene. Phragmites australis root exudates containing phenolic compounds supported growth as a carbon source for the one Mycobacterium strain tested, and induced benzo[a]pyrene-degrading activity of the strain. The stimulatory effect on benzo[a]pyrene biodegradation and the amounts of phenolic compounds in root exudates increased when P. australis was exposed to pyrene. Our results show that Mycobacterium-root exudate interactions can accelerate biodegradation of pyrene and benzo[a]pyrene in P. australis rhizosphere sediments.
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Affiliation(s)
- Tadashi Toyama
- Department of Research, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
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Bacteria-mediated PAH degradation in soil and sediment. Appl Microbiol Biotechnol 2011; 89:1357-71. [PMID: 21210104 DOI: 10.1007/s00253-010-3072-7] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 12/09/2010] [Accepted: 12/09/2010] [Indexed: 10/18/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous in the natural environment and easily accumulate in soil and sediment due to their low solubility and high hydrophobicity, rendering them less available for biological degradation. However, microbial degradation is a promising mechanism which is responsible for the ecological recovery of PAH-contaminated soil and sediment for removing these recalcitrant compounds compared with chemical degradation of PAHs. The goal of this review is to provide an outline of the current knowledge of biodegradation of PAHs in related aspects. Over 102 publications related to PAH biodegradation in soil and sediment are compiled, discussed, and analyzed. This review aims to discuss PAH degradation under various redox potential conditions, the factors affecting the biodegradation rates, degrading bacteria, the relevant genes in molecular monitoring methods, and some recent-year bioremediation field studies. The comprehensive understanding of the bioremediation kinetics and molecular means will be helpful for optimizing and monitoring the process, and overcoming its limitations in practical projects.
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Peng JJ, Cai C, Qiao M, Li H, Zhu YG. Dynamic changes in functional gene copy numbers and microbial communities during degradation of pyrene in soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2010; 158:2872-2879. [PMID: 20615597 DOI: 10.1016/j.envpol.2010.06.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 06/01/2010] [Accepted: 06/10/2010] [Indexed: 05/29/2023]
Abstract
This study investigates the dynamics of pyrene degradation rates, microbial communities, and functional gene copy numbers during the incubation of pyrene-spiked soils. Spiking pyrene to the soil was found to have negligible effects on the bacterial community present. Our results demonstrated that there was a significant difference in nidA gene copy numbers between sampling dates in QZ soil. Mycobacterium 16S rDNA clone libraries showed that more than 90% mycobacteria detected were closely related to fast-growing PAH-degrading Mycobacterium in pyrene-spiked soil, while other sequences related to slow-growing Mycobacterium were only detected in the control soil. It is suggested that nidA gene copy number and fast-growing PAH-degrading Mycobacterium could be used as indicators to predict pyrene contamination and its degradation activity in soils.
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Affiliation(s)
- Jing-Jing Peng
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
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