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Sugiyama A, Nakata K, Hirano SI, Hasegawa T. Identification of groundwater microbes that decrease the concentration of the conservative tracer uranine. Heliyon 2024; 10:e27397. [PMID: 38496874 PMCID: PMC10944235 DOI: 10.1016/j.heliyon.2024.e27397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/20/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
Fluorescent dyes are commonly used as conservative groundwater tracers to track the migration of water. Over- or underestimation of important parameters such as the water flow rate can occur if the concentration of a dye is changed by unexpected reactions. Because such errors may seriously affect the results of experiments, the reactions and processes that change fluorescent dye concentrations need to be understood. In this study, we focused on the widely used fluorescent dye uranine (UR) and aimed to identify microbes contributing to decreases in UR concentrations in groundwater. First, we identified the conditions (water temperature, pH, and salinity) under which significant decreases in UR concentrations occurred to show that the decrease in UR concentrations were caused by the effects of microbes in the groundwater. Next, we obtained information about the metabolism of organic matter by potential contributing microbes. These results were used to narrow down possible microbes that could decrease the UR concentration. Analysis of the microbial community in groundwater using 16S rRNA gene sequencing was then used to further identify contributing microbes. Finally, a verification experiment was conducted using a strain of one of the identified microbes (Parapontixanthobacter aurantiacus). Our results showed that conservation of the concentration of fluorescent dye solutions prepared with on-site groundwater was affected by several microbes with different metabolic characteristics, including P. aurantiacus. When fluorescent dye solutions prepared with on-site groundwater are used in field investigations or tracer tests, the pros and cons of using fluorescent dyes should be carefully evaluated because of the potential effects of microbes in the groundwater.
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Affiliation(s)
- Ayumi Sugiyama
- Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry (CRIEPI), 1646 Abiko, Abiko-shi, Chiba 270-1194, Japan
| | - Kotaro Nakata
- Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry (CRIEPI), 1646 Abiko, Abiko-shi, Chiba 270-1194, Japan
| | - Shin-Ichi Hirano
- Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry (CRIEPI), 1646 Abiko, Abiko-shi, Chiba 270-1194, Japan
| | - Takuma Hasegawa
- Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry (CRIEPI), 1646 Abiko, Abiko-shi, Chiba 270-1194, Japan
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Genitsaris S, Stefanidou N, Hatzinikolaou D, Kourkoutmani P, Michaloudi E, Voutsa D, Gros M, García-Gómez E, Petrović M, Ntziachristos L, Moustaka-Gouni M. Marine Microbiota Responses to Shipping Scrubber Effluent Assessed at Community Structure and Function Endpoints. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024. [PMID: 38415986 DOI: 10.1002/etc.5834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/29/2024]
Abstract
The use of novel high-throughput sequencing (HTS) technologies to examine the responses of natural multidomain microbial communities to scrubber effluent discharges to the marine environment is still limited. Thus, we applied metabarcoding sequencing targeting the planktonic unicellular eukaryotic and prokaryotic fraction (phytoplankton, bacterioplankton, and protozooplankton) in mesocosm experiments with natural microbial communities from a polluted and an unpolluted site. Furthermore, metagenomic analysis revealed changes in the taxonomic and functional dominance of multidomain marine microbial communities after scrubber effluent additions. The results indicated a clear shift in the microbial communities after such additions, which favored bacterial taxa with known oil and polycyclic aromatic hydrocarbons (PAHs) biodegradation capacities. These bacteria exhibited high connectedness with planktonic unicellular eukaryotes employing variable trophic strategies, suggesting that environmentally relevant bacteria can influence eukaryotic community structure. Furthermore, Clusters of Orthologous Genes associated with pathways of PAHs and monocyclic hydrocarbon degradation increased in numbers at treatments with high scrubber effluent additions acutely. These genes are known to express enzymes acting at various substrates including PAHs. These indications, in combination with the abrupt decrease in the most abundant PAHs in the scrubber effluent below the limit of detection-much faster than their known half-lives-could point toward a bacterioplankton-initiated rapid ultimate biodegradation of the most abundant toxic contaminants of the scrubber effluent. The implementation of HTS could be a valuable tool to develop multilevel biodiversity indicators of the scrubber effluent impacts on the marine environment, which could lead to improved impact assessment. Environ Toxicol Chem 2024;00:1-18. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
- Savvas Genitsaris
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Section of Ecology and Taxonomy, School of Biology, National and Kapodistrian University of Athens, Zografou Campus, Athens, Greece
| | - Natassa Stefanidou
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitris Hatzinikolaou
- Department of Botany, School of Biology, National and Kapodistrian University of Athens, Zografou Campus, Athens, Greece
| | - Polyxeni Kourkoutmani
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Evangelia Michaloudi
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitra Voutsa
- Environmental Pollution Control Laboratory, Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Meritxell Gros
- Catalan Institute for Water Research (ICRA), Girona, Spain
- University of Girona (UdG), Girona, Spain
| | - Elisa García-Gómez
- Catalan Institute for Water Research (ICRA), Girona, Spain
- University of Girona (UdG), Girona, Spain
| | - Mira Petrović
- Catalan Institute for Water Research (ICRA), Girona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Leonidas Ntziachristos
- Department of Mechanical Engineering, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Maria Moustaka-Gouni
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Liang C, Ye Q, Huang Y, Zhang Z, Wang C, Wang Y, Wang H. Distribution of the new functional marker gene (pahE) of aerobic polycyclic aromatic hydrocarbon (PAHs) degrading bacteria in different ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 865:161233. [PMID: 36586685 DOI: 10.1016/j.scitotenv.2022.161233] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/18/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Understanding the degradation potentials in PAHs-contaminated sites is significant for formulating effective bioremediation strategies. pahE encoding PAHs hydratase-aldolase has been proven as a better new functional marker gene of aerobic PAHs-degrading bacteria to assess the biodegradation potential of indigenous PAHs-degrading bacterial population. However, the distribution of pahE and its relationship with environmental factors remain unknown. The present study observed spatial variations in the diversity and abundance of pahE across oilfield soils, mangrove sediments, and urban roadside soils. nahE from Pseudomonas, bphE from Hyphomonas oceanitis, nagE from Comamonas testosterone, and novel pahE genes were widely present in these PAHs-polluted ecosystems. The abundance of pahE in PAHs-contaminated sites was in the range of 105-106 copies·g-1 (dry weight). Redundancy analysis and Pearson's correlation analysis implied that the distribution of pahE in the PAHs-contaminated environment was mainly shaped by environmental factors such as PAHs pollution level, nutrient level, salinity, and water content. This work was the first to explore the distribution of the new functional marker gene (pahE) and its links with environmental parameters, which provided new insights into the ecophysiology and distribution of indigenous aerobic PAHs-degrading bacteria in contaminated sites.
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Affiliation(s)
- Chengyue Liang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Quanhui Ye
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yong Huang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Zuotao Zhang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Chongyang Wang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yun Wang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hui Wang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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Wang J, Guo X, Li Y, Song G, Zhao L. Understanding the Variation of Bacteria in Response to Summertime Oxygen Depletion in Water Column of Bohai Sea. Front Microbiol 2022; 13:890973. [PMID: 35756048 PMCID: PMC9221365 DOI: 10.3389/fmicb.2022.890973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/05/2022] [Indexed: 11/14/2022] Open
Abstract
Aiming to reveal the variation in bacteria community under oxygen depletion formed every summer in water column of central Bohai Sea, a time-scenario sampling from June to August in 2018 at a 20-day interval along one inshore-offshore transect was settled. Water samples were collected at the surface, middle, and bottom layer and then analyzed by high-throughput sequencing targeting both 16S rRNA and nosZ genes. Compared to the surface and middle water, oxygen depletion occurred at bottom layer in August. In top two layers, Cyanobacteria dominated the bacterial community, whereas heterotrophic bacteria became dominant in bottom water of Bohai Sea. Based on the time scenario, distinct community separation was observed before (June and July) and after (August) oxygen depletion (p = 0.003). Vertically, strict stratification of nosZ gene was stably formed along 3 sampling layers. As a response to oxygen depletion, the diversity indices of both total bacteria (16S rRNA) and nosZ gene-encoded denitrification bacteria all increased, which indicated the intense potential of nitrogen lose when oxygen depleted. Dissolved oxygen (DO) was the key impacting factor on the community composition of total bacteria in June, whereas nutrients together with DO play the important roles in August for both total and denitrifying bacteria. The biotic impact was revealed further by strong correlations which showed between Cyanobacteria and heterotrophic bacteria in June from co-occurrence network analysis, which became weak in August when DO was depleted. This study discovered the variation in bacteria community in oxygen-depleted water with further effort to understand the potential role of denitrifying bacteria under oxygen depletion in Bohai Sea for the first time, which provided insights into the microbial response to the world-wide expanding oxygen depletion and their contributions in the ocean nitrogen cycling.
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Affiliation(s)
- Jing Wang
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China
| | - Xiaoxiao Guo
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China
| | - Yanying Li
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China
| | - Guisheng Song
- School of Marine Science and Technology, Tianjin University, Tianjin, China
| | - Liang Zhao
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China
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Taxonomic and functional trait-based approaches suggest that aerobic and anaerobic soil microorganisms allow the natural attenuation of oil from natural seeps. Sci Rep 2022; 12:7245. [PMID: 35508504 PMCID: PMC9068923 DOI: 10.1038/s41598-022-10850-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/31/2022] [Indexed: 12/02/2022] Open
Abstract
Natural attenuation, involving microbial adaptation, helps mitigating the effect of oil contamination of surface soils. We hypothesized that in soils under fluctuating conditions and receiving oil from seeps, aerobic and anaerobic bacteria as well as fungi could coexist to efficiently degrade hydrocarbons and prevent the spread of pollution. Microbial community diversity was studied in soil longitudinal and depth gradients contaminated with petroleum seeps for at least a century. Hydrocarbon contamination was high just next to the petroleum seeps but this level drastically lowered from 2 m distance and beyond. Fungal abundance and alpha-diversity indices were constant along the gradients. Bacterial abundance was constant but alpha-diversity indices were lower next to the oil seeps. Hydrocarbon contamination was the main driver of microbial community assemblage. 281 bacterial OTUs were identified as indicator taxa, tolerant to hydrocarbon, potentially involved in hydrocarbon-degradation or benefiting from the degradation by-products. These taxa belonging to lineages of aerobic and anaerobic bacteria, have specific functional traits indicating the development of a complex community adapted to the biodegradation of petroleum hydrocarbons and to fluctuating conditions. Fungi are less impacted by oil contamination but few taxa should contribute to the metabolic complementary within the microbial consortia forming an efficient barrier against petroleum dissemination.
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Zhou S, Peng S, Li Z, Zhang D, Zhu Y, Li X, Hong M, Li W, Lu P. Characterization of microbial communities and functions in shale gas wastewaters and sludge: Implications for pretreatment. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127649. [PMID: 34740504 DOI: 10.1016/j.jhazmat.2021.127649] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
As hydraulic fracturing (HF) practices keep expanding in China, a comparative understanding of biological characteristics of flowback and produced waters (FPW) and sludge in impoundments for FPW reserve will help propose appropriate treatment strategies. Therefore, in this study, the microbial communities and functions in impoundments that collected wastewaters from dozens of wells were characterized. The results showed that microbial richness and diversity were significantly increased in sludge compared with those in FPW. The vast majority of microorganisms found in FPW and sludge are organic degraders, providing the possibility of using these indigenous microorganisms to biodegrade organic compounds. Our laboratory findings first show that wastewater pretreatment using these microorganisms was effective, and organic compounds in FPW from different shale formations were removed by 35-68% within 72 h in a wide temperature range (8 - 30 ℃). Meanwhile, highly toxic compounds such as phthalate esters (PAEs), polycyclic aromatic hydrocarbons (PAHs), and petroleum hydrocarbons were effectively eliminated in reactors. The main microorganisms, key functional genes, and putative pathways for alkanes, PAHs, and PAEs degradation were also identified.
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Affiliation(s)
- Shangbo Zhou
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Shuchan Peng
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; College of Environment and Ecology, Chongqing University, Chongqing 400044, China; School of Civil Engineering and Architecture, Chongqing University of Science & Technology, Chongqing 401331, China
| | - Zhiqiang Li
- College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Daijun Zhang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Yantao Zhu
- College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Xingquan Li
- College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Mingyu Hong
- College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Weichang Li
- College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Peili Lu
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; College of Environment and Ecology, Chongqing University, Chongqing 400044, China.
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Moshi AA, Kyara EC, Mabula PL, Uroki EC, Kajeguka DC, Mkumbaye SI. Proportions of Pathogenic Bacteria Isolated from Door Locks and Working Benches in Clinical Laboratory: A Laboratory Based Study. East Afr Health Res J 2022; 6:106-112. [PMID: 37928867 PMCID: PMC10624217 DOI: 10.24248/eahrj.v6i1.685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/02/2022] [Indexed: 11/07/2023] Open
Abstract
Background Numerous studies have revealed the association of the door handle and contamination of pathogenic bacteria. Door handles of clinical and research laboratories have higher chances of contamination with pathogenic bacteria during closing and opening with contaminated gloves on, or sometimes after visiting the toilets without the use of disinfectant materials. There is limited epidemiological data regarding bacteria cross contamination of door locks of the Clinical laboratory at Kilimanjaro Christian Medical Centre. This study aimed at providing the proportions of bacteria contaminating medical laboratory doors. Methods A cross section laboratory-based study was conducted and it involved collection of swab samples from doors and working benches in the clinical laboratory. Results Prevalence of Staphylococcus aureus, Escherichia coli, Coagulase Negative Staphylococcus, Bacillus spp., Pseudomonas aeroginosa and coliforms were (26%, 22%, 18%, 8%, 4% and 4% respectively. Conclusion This study has reported high proportion of pathogenic bacteria. The results entails that, internal and external environments are responsible for laboratory door contamination.
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Affiliation(s)
- Abias Anthon Moshi
- Kilimanjaro Christian Medical University College, Department of Microbiology and Immunology, Moshi-Kilimanjaro, Tanzania
- Kilimanjaro Christian Medical Centre, Department of Clinical Laboratory, Moshi-Kilimanjaro, Tanzania
| | - Ester Colnel Kyara
- Kilimanjaro Christian Medical Centre, Department of Clinical Laboratory, Moshi-Kilimanjaro, Tanzania
| | - Patrick Lucas Mabula
- Kilimanjaro Christian Medical Centre, Department of Clinical Laboratory, Moshi-Kilimanjaro, Tanzania
| | - Emmanuel Charles Uroki
- Kilimanjaro Christian Medical Centre, Department of Clinical Laboratory, Moshi-Kilimanjaro, Tanzania
| | - Debora Charles Kajeguka
- Kilimanjaro Christian Medical University College, Department of Microbiology and Immunology, Moshi-Kilimanjaro, Tanzania
| | - Sixbert Isdory Mkumbaye
- Kilimanjaro Christian Medical University College, Department of Microbiology and Immunology, Moshi-Kilimanjaro, Tanzania
- Kilimanjaro Christian Medical Centre, Department of Clinical Laboratory, Moshi-Kilimanjaro, Tanzania
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Wang B, Teng Y, Yao H, Christie P. Detection of functional microorganisms in benzene [a] pyrene-contaminated soils using DNA-SIP technology. JOURNAL OF HAZARDOUS MATERIALS 2021; 407:124788. [PMID: 33321373 DOI: 10.1016/j.jhazmat.2020.124788] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
DNA-SIP technology was used to detect active BaP-degraders involved in the biodegradation of benzo [a] pyrene (BaP) in two soils separately and in mixture. The lowest BaP removal was observed in red soil, and Ramlibacter (OTU830) belonging to the γ-Proteobacteria was labeled as BaP degrader with 13C-BaP. The highest diversity of degrading microorganisms occurred in the paddy soil with OTUs belonging to Nocardioids, Micromonospora, Saccharothrix, Lysobacter and Methylium present and a BaP removal efficiency of 29.5% after 14 d. BaP degraders in the mixed microbiome of the soil mixture were Burkholderia and Phenylobacterium, together with Nocardioides and Micromonospora as in the paddy soil. These results indicated that the active BaP-degraders in the mixed microbiome were identical to the active BaP-degraders in paddy soil (OTU356 and OTU328), but also unique in the mixed microbiome, such as OTU393 and OTU392. The functional genes of PAH-ring hydroxylating dioxygenases (PAH-RHDα) were expressed and were positively related to the removal of BaP, and the active BaP degrading bacteria included both Gram-positive and Gram-negative bacteria. Saccharothrix, Phylobacterium, Micromonospora and Nocardioids are here reported as BaP degraders for the first time using DNA-SIP.
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Affiliation(s)
- Beibei Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Resources and Environmental Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Huaiying Yao
- Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, Ningbo 315800, China
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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Microbial Succession under Freeze-Thaw Events and Its Potential for Hydrocarbon Degradation in Nutrient-Amended Antarctic Soil. Microorganisms 2021; 9:microorganisms9030609. [PMID: 33809442 PMCID: PMC8000410 DOI: 10.3390/microorganisms9030609] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 12/24/2022] Open
Abstract
The polar regions have relatively low richness and diversity of plants and animals, and the basis of the entire ecological chain is supported by microbial diversity. In these regions, understanding the microbial response against environmental factors and anthropogenic disturbances is essential to understand patterns better, prevent isolated events, and apply biotechnology strategies. The Antarctic continent has been increasingly affected by anthropogenic contamination, and its constant temperature fluctuations limit the application of clean recovery strategies, such as bioremediation. We evaluated the bacterial response in oil-contaminated soil through a nutrient-amended microcosm experiment using two temperature regimes: (i) 4 °C and (ii) a freeze–thaw cycle (FTC) alternating between −20 and 4 °C. Bacterial taxa, such as Myxococcales, Chitinophagaceae, and Acidimicrobiales, were strongly related to the FTC. Rhodococcus was positively related to contaminated soils and further stimulated under FTC conditions. Additionally, the nutrient-amended treatment under the FTC regime enhanced bacterial groups with known biodegradation potential and was efficient in removing hydrocarbons of diesel oil. The experimental design, rates of bacterial succession, and level of hydrocarbon transformation can be considered as a baseline for further studies aimed at improving bioremediation strategies in environments affected by FTC regimes.
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Phulpoto IA, Hu B, Wang Y, Ndayisenga F, Li J, Yu Z. Effect of natural microbiome and culturable biosurfactants-producing bacterial consortia of freshwater lake on petroleum-hydrocarbon degradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 751:141720. [PMID: 32882554 DOI: 10.1016/j.scitotenv.2020.141720] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 06/11/2023]
Abstract
Freshwater lake ecosystem is a reservior of valuable microbial diversity. It needs to be explored for addressing key environmental issues like petroleum-hydrocarbon contamination. In this work, the microbial communities (pre and post enriched with petroleum-hydrocarbons) from different layers of freshwater lake, i.e. surface water, sediments and deepwater, were explored through metagenomic and culture-dependent approaches. A total of 41 bacterial phyla were retrieved from pre-enriched samples, which were significantly reduced in enriched samples where Proteobacteria were dominant (87% to 100%) followed by Bacteroidetes (7.37%) and Verrucomicrobia (3.06%). The most dominant hydrocarbon-degrading genera were extensively verified as Pseudomonas (48.65%), Acinetobacter (45.38%), Stenotrophomonas (3.16%) and Brevundimonas (2.07%) in surface water (S1WCC); Acinetobacter (62.46%), Aeromonas (10.7%), Sphingobacterium (5.20%) and Pseudomonas (4.23%) in sediment (S2MCC); and Acinetobacter (46.57%), Pseudomonas (13.10%), Comamonas (12.93%), Flavobacterium (12.18%) and Enterobacter (9.62%) in deep water (S4WCC). Additionally, the maximum biodegradation of petroleum-hydrocarbons (i.e. used engine oil or UEO) was achieved by microbiome of S2MCC (67.60 ± 0.08%) followed by S4WCC (59.70 ± 0.12%), whereas only 36.80 ± 0.10% degradation was achieved by S1WCC microbiome. On the other hand, UEO degradation by cultivable biosurfactant-producing single cultures such as Pseudomonas sp. S2WE, Pseudomonas sp. S2WG, Pseudomonas sp. S2MS, Ochrobactrum sp. S1MM and Bacillus nealsonii S2MT showed 31.10 ± 0.08% to 40.50 ± 0.11% biodegradation. Comparatively, the biodegradation efficiency was found higher (i.e. 42.20 ± 0.12% to 56.10 ± 0.12%) in each consortia comprising of two, three, four, and five bacterial cultures. Conclusively, the isolated culturable biosurfactants-producing bacterial consortium of freshwater lake demonstrated >80% contribution in the total petroleum-hydrocarbons degradation by the natural microbiome of the ecosystem.
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Affiliation(s)
- Irfan Ali Phulpoto
- College of Resources and Environment, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, PR China
| | - Bowen Hu
- College of Resources and Environment, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, PR China
| | - Yanfen Wang
- Yanshan Earth Critical Zone and Surface Fluxes Research Station, Chinese Academy of Sciences, No. 380 Huaibei Town, Huairou District, Beijing 101408, PR China
| | - Fabrice Ndayisenga
- College of Resources and Environment, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, PR China
| | - Jinmei Li
- College of Resources and Environment, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, PR China
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, PR China.
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11
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Xu L, Sun C, Fang C, Oren A, Xu XW. Genomic-based taxonomic classification of the family Erythrobacteraceae. Int J Syst Evol Microbiol 2020; 70:4470-4495. [PMID: 32726199 PMCID: PMC7660246 DOI: 10.1099/ijsem.0.004293] [Citation(s) in RCA: 290] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 06/01/2020] [Indexed: 12/22/2022] Open
Abstract
The family Erythrobacteraceae, belonging to the order Sphingomonadales, class Alphaproteobacteria, is globally distributed in various environments. Currently, this family consist of seven genera: Altererythrobacter, Croceibacterium, Croceicoccus, Erythrobacter, Erythromicrobium, Porphyrobacter and Qipengyuania. As more species are identified, the taxonomic status of the family Erythrobacteraceae should be revised at the genomic level because of its polyphyletic nature evident from 16S rRNA gene sequence analysis. Phylogenomic reconstruction based on 288 single-copy orthologous clusters led to the identification of three separate clades. Pairwise comparisons of average nucleotide identity, average amino acid identity (AAI), percentage of conserved protein and evolutionary distance indicated that AAI and evolutionary distance had the highest correlation. Thresholds for genera boundaries were proposed as 70 % and 0.4 for AAI and evolutionary distance, respectively. Based on the phylo-genomic and genomic similarity analysis, the three clades were classified into 16 genera, including 11 novel ones, for which the names Alteraurantiacibacter, Altericroceibacterium, Alteriqipengyuania, Alteripontixanthobacter, Aurantiacibacter, Paraurantiacibacter, Parerythrobacter, Parapontixanthobacter, Pelagerythrobacter, Tsuneonella and Pontixanthobacter are proposed. We reclassified all species of Erythromicrobium and Porphyrobacter as species of Erythrobacter. This study is the first genomic-based study of the family Erythrobacteraceae, and will contribute to further insights into the evolution of this family.
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Affiliation(s)
- Lin Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Cong Sun
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Chen Fang
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- College of Oceanography, Hohai University, Nanjing 210000, PR China
| | - Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, PR China
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12
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Nascimento JR, Easson CG, Jurelevicius DDA, Lopez JV, Bidone ED, Sabadini-Santos E. Microbial community shift under exposure of dredged sediments from a eutrophic bay. ENVIRONMENTAL MONITORING AND ASSESSMENT 2020; 192:539. [PMID: 32705349 DOI: 10.1007/s10661-020-08507-8] [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: 01/06/2020] [Accepted: 07/19/2020] [Indexed: 06/11/2023]
Abstract
Microbial communities occur in almost every habitat. To evaluate the homeostasis disruption of in situ microbiomes, dredged sediments from Guanabara Bay-Brazil (GB) were mixed with sediments from outside of the bay (D) in three different proportions (25%, 50%, and 75%) which we called GBD25, GBD50, and GBD75. Grain size, TOC, and metals-as indicators of complex contamination-dehydrogenase (DHA) and esterase enzymes (EST)-as indicators of microbial community availability-were determined. Microbial community composition was addressed by amplifying the 16S rRNA gene for DGGE analysis and sequencing using MiSeq platform (Illumina).We applied the quality ratio index (QR) to the GB, D, and every GBD mixture to integrate geochemical parameters with our microbiome data. QR indicated high environmental risk for GB and every GBD mixture, and low risk for D. The community shifted from aerobic to anaerobic profile, consistent with the characteristics of GB. Sample D was dominated by JTB255 marine benthic group, related to low impacted areas. Milano-WF1B-44 was the most representative of GB, often found in anaerobic and sulfur enriched environments. In GBD, the denitrifying sulfur-oxidizing bacteria, Sulfurovum, was the most representative, typically found in suboxic or anoxic niches. The canonical correspondence analysis was able to explain 60% of the community composition variation and exhibit the decrease of environmental quality as the contamination increases. Physiological and taxonomic shifts of the microbial assemblage in sediments were inferred by QR, which was suitable to determine sediment risk. The study produced sufficient information to improve the dredging plan and management.
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Affiliation(s)
- Juliana R Nascimento
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ, 24020-150, Brazil.
| | - Cole G Easson
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL, 33004, USA
- Biology Department, Middle Tennessee State University, Murfreesboro, TN, USA
| | - Diogo de A Jurelevicius
- Instituto de Microbiologia Professor Paulo de Góes, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21944-570, Brazil
| | - Jose V Lopez
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL, 33004, USA
| | - Edison D Bidone
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ, 24020-150, Brazil
| | - Elisamara Sabadini-Santos
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ, 24020-150, Brazil
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13
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Viggor S, Jõesaar M, Soares-Castro P, Ilmjärv T, Santos PM, Kapley A, Kivisaar M. Microbial Metabolic Potential of Phenol Degradation in Wastewater Treatment Plant of Crude Oil Refinery: Analysis of Metagenomes and Characterization of Isolates. Microorganisms 2020; 8:E652. [PMID: 32365784 PMCID: PMC7285258 DOI: 10.3390/microorganisms8050652] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/24/2020] [Accepted: 04/28/2020] [Indexed: 01/30/2023] Open
Abstract
The drilling, processing and transportation of oil are the main sources of pollution in water and soil. The current work analyzes the microbial diversity and aromatic compounds degradation potential in the metagenomes of communities in the wastewater treatment plant (WWTP) of a crude oil refinery. By focusing on the degradation of phenol, we observed the involvement of diverse indigenous microbial communities at different steps of the WWTP. The anaerobic bacterial and archaeal genera were replaced by aerobic and facultative anaerobic bacteria through the biological treatment processes. The phyla Proteobacteria, Bacteroidetes and Planctomycetes were dominating at different stages of the treatment. Most of the established protein sequences of the phenol degradation key enzymes belonged to bacteria from the class Alphaproteobacteria. From 35 isolated strains, 14 were able to grow on aromatic compounds, whereas several phenolic compound-degrading strains also degraded aliphatic hydrocarbons. Two strains, Acinetobacter venetianus ICP1 and Pseudomonas oleovorans ICTN13, were able to degrade various aromatic and aliphatic pollutants and were further characterized by whole genome sequencing and cultivation experiments in the presence of phenol to ascertain their metabolic capacity in phenol degradation. When grown alone, the intermediates of catechol degradation, the meta or ortho pathways, accumulated into the growth environment of these strains. In the mixed cultures of the strains ICP1 and ICTN13, phenol was degraded via cooperation, in which the strain ICP1 was responsible for the adherence of cells and ICTN13 diminished the accumulation of toxic intermediates.
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Affiliation(s)
- Signe Viggor
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010 Tartu, Estonia; (M.J.); (T.I.); (M.K.)
| | - Merike Jõesaar
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010 Tartu, Estonia; (M.J.); (T.I.); (M.K.)
| | - Pedro Soares-Castro
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (P.S.-C.); (P.M.S.)
| | - Tanel Ilmjärv
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010 Tartu, Estonia; (M.J.); (T.I.); (M.K.)
| | - Pedro M. Santos
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (P.S.-C.); (P.M.S.)
| | - Atya Kapley
- Director’s Research Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur 440 020, India;
| | - Maia Kivisaar
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010 Tartu, Estonia; (M.J.); (T.I.); (M.K.)
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Domingues PM, Oliveira V, Serafim LS, Gomes NCM, Cunha Â. Biosurfactant Production in Sub-Oxic Conditions Detected in Hydrocarbon-Degrading Isolates from Marine and Estuarine Sediments. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17051746. [PMID: 32156011 PMCID: PMC7084516 DOI: 10.3390/ijerph17051746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 11/16/2022]
Abstract
Hydrocarbon bioremediation in anoxic sediment layers is still challenging not only because it involves metabolic pathways with lower energy yields but also because the production of biosurfactants that contribute to the dispersion of the pollutant is limited by oxygen availability. This work aims at screening populations of culturable hydrocarbonoclastic and biosurfactant (BSF) producing bacteria from deep sub-seafloor sediments (mud volcanos from Gulf of Cadiz) and estuarine sub-surface sediments (Ria de Aveiro) for strains with potential to operate in sub-oxic conditions. Isolates were retrieved from anaerobic selective cultures in which crude oil was provided as sole carbon source and different supplements were provided as electron acceptors. Twelve representative isolates were obtained from selective cultures with deep-sea and estuary sediments, six from each. These were identified by sequencing of 16S rRNA gene fragments belonging to Pseudomonas, Bacillus, Ochrobactrum, Brevundimonas, Psychrobacter, Staphylococcus, Marinobacter and Curtobacterium genera. BSF production by the isolates was tested by atomized oil assay, surface tension measurement and determination of the emulsification index. All isolates were able to produce BSFs under aerobic and anaerobic conditions, except for isolate DS27 which only produced BSF under aerobic conditions. These isolates presented potential to be applied in bioremediation or microbial enhanced oil recovery strategies under conditions of oxygen limitation. For the first time, members of Ochrobactrum, Brevundimonas, Psychrobacter, Staphylococcus, Marinobacter and Curtobacterium genera are described as anaerobic producers of BSFs.
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Affiliation(s)
- Patrícia M. Domingues
- Department of Chemistry and CICECO, University of Aveiro, 3810-193 Aveiro, Portugal
- Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Vanessa Oliveira
- Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro, Portugal
| | | | - Newton C. M. Gomes
- Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Ângela Cunha
- Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro, Portugal
- Correspondence: ; Tel.: +351-234-370-784
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15
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Zhu L, Xu H, Xiao W, Lu J, Lu D, Chen X, Zheng X, Jeppesen E, Zhang W, Wang L. Ecotoxicological effects of sulfonamide on and its removal by the submerged plant Vallisneria natans (Lour.) Hara. WATER RESEARCH 2020; 170:115354. [PMID: 31811991 DOI: 10.1016/j.watres.2019.115354] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 06/10/2023]
Abstract
The extensive application of sulfonamides (SAs) raises concern regarding its negative environmental effects. In aquatic environments, macrophytes may not only be affected by various pollutants, they may also help to reduce the concentrations in the surrounding environment. We studied both the ecotoxicological effects of sulfonamide (SN) on and its removal by Vallisneria natans (Lour.) Hara, an important submerged macrophyte in Chinese lakes and rivers. The toxic effect and oxidative stress caused by SN resulted in a reduction of total chlorophyll (chl.a and b) and autofluorescence of chloroplast. Meanwhile, the levels of reactive oxygen species (ROS, including O2- and H2O2) and peroxidase (POD) increased with increasing SN concentration and duration of exposure. After 20 days' exposure, a reduction in the relative growth rate (RGR) and leaf length of V. natans was found under SN stress, but SN had only a weak effect on root length. Although high SN concentrations had toxic effects on the growth of V. natans, the plant was overall resistant to the SN doses that we used. We studied the effect of V. natans on sulfonamide removal in an additional 13-day exposure experiment with focus on the dynamics of dissolved oxygen (DO), the oxidation-reduction potential (ORP) and microbial communities in the water column, as well as in the periphyton on V. natans surfaces. The results show that presence of V. natans significantly improved the SN removal efficiency likely by increasing DO, ORP and bacterial diversity in the water column. The presence of V. natans led to higher relative abundances of Saccharimonadales and Rhizoniales. Lefse analysis showed that Saccharimonadales, Micrococcales, Sphingobacteriales, Bacteroidales, Obscuribacterales, Flavobacteriales, Pseudomonadaceae and Myxococcales, which are considered to be SN-resistant bacteria, increased significantly in the V + S+ (V. natans and SN) treatment compared with the V + S- (V. natans and no SN) treatment and V-S+ (no V. natans and SN) treatment. As far as we know, ours is the first study of the ecotoxicological effects of sulfonamide and its removal by submerged vascular plants (here V. natans). Thus, our results add to the understanding of the antibiotic removal mechanism of macrophytes in freshwater systems and help to clarify the linkages between antibiotics and macrophyte-microbe systems; thereby providing new insight into ecological-based removal of antibiotics in aquatic systems.
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Affiliation(s)
- Liming Zhu
- Centre for Research on Environmental Ecology and Fish Nutrient of the Ministry of Agriculture, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources of the Ministry of Education, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, PR China
| | - Houtao Xu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, PR China
| | - Wensheng Xiao
- Centre for Research on Environmental Ecology and Fish Nutrient of the Ministry of Agriculture, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources of the Ministry of Education, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, PR China
| | - Jianke Lu
- Centre for Research on Environmental Ecology and Fish Nutrient of the Ministry of Agriculture, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources of the Ministry of Education, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, PR China
| | - Di Lu
- Centre for Research on Environmental Ecology and Fish Nutrient of the Ministry of Agriculture, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources of the Ministry of Education, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, PR China
| | - Xiaoyu Chen
- Centre for Research on Environmental Ecology and Fish Nutrient of the Ministry of Agriculture, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources of the Ministry of Education, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, PR China
| | - Xiaoyan Zheng
- Shanghai Aquatic Environmental Engineering Co., Ltd, Shanghai, 201306, PR China
| | - Erik Jeppesen
- Department of Bioscience, Aarhus University, Silkeborg, 8600, Denmark; Sino-Danish Centre for Education and Research (SDC), University of Chinese Academy of Sciences, Beijing, 100049, PR China; Limnology Laboratory and EKOSAM, Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Wei Zhang
- Centre for Research on Environmental Ecology and Fish Nutrient of the Ministry of Agriculture, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources of the Ministry of Education, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, PR China.
| | - Liqing Wang
- Centre for Research on Environmental Ecology and Fish Nutrient of the Ministry of Agriculture, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources of the Ministry of Education, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, PR China.
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16
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Dai Y, Liu R, Zhou Y, Li N, Hou L, Ma Q, Gao B. Fire Phoenix facilitates phytoremediation of PAH-Cd co-contaminated soil through promotion of beneficial rhizosphere bacterial communities. ENVIRONMENT INTERNATIONAL 2020; 136:105421. [PMID: 31884414 DOI: 10.1016/j.envint.2019.105421] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/10/2019] [Accepted: 12/13/2019] [Indexed: 05/13/2023]
Abstract
Pot experiments were conducted in a growth chamber to evaluate the phytoremediation efficiency and rhizosphere regulation mechanism of Fire Phoenix (a mixture of Festuca L.) in polycyclic aromatic hydrocarbon-cadmium (PAH-Cd) co-contaminated soils. Plant biomass, removal rates of PAHs and Cd, soil enzyme activity, and soil bacterial community were determined. After 150 days of planting, the removal rates of the total 4 PAHs and Cd reached 64.57% and 40.93% in co-contaminated soils with low-PAH (104.79-144.87 mg·kg-1), and 68.29% and 25.40% in co-contaminated soils with high-PAH (169.17-197.44 mg·kg-1), respectively. The polyphenol oxidase (PPO) activity decreased in soils having Fire Phoenix, while the dehydrogenase (DHO) activity increased as the changes of DHO activity had a strong positive correlation with the removal rates of PAHs and Cd in the low-PAH soils (r = 0.862 (P < 0.006) and 0.913 (P < 0.002), respectively). Meanwhile, successional changes in the bacterial communities were detected using high-throughput 454 Gs-FLX pyrosequencing of the 16S rRNA, and these changes were especially apparent for the co-contaminated soils with the low PAH concentration. The Fire Phoenix could promote the growth of Mycobacterium, Dokdonella, Gordonia and Kaistobacter, which played important roles in PAHs degradation or Cd dissipation. These results indicated that Fire Phoenix could effectively motivate the soil enzyme and bacterial community and enhance the potential for phytoremediation of PAH-Cd co-contaminated soils.
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Affiliation(s)
- Yuanyuan Dai
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, Liaoning, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Liu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, Liaoning, China.
| | - Yuemei Zhou
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, Liaoning, China
| | - Na Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, Liaoning, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liqun Hou
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, Liaoning, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Ma
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, Liaoning, China
| | - Bin Gao
- Department of Agricultural and Biological Engineering, University of Florida, Gainesville, FL 32611, USA
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17
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Shin B, Bociu I, Kolton M, Huettel M, Kostka JE. Succession of microbial populations and nitrogen-fixation associated with the biodegradation of sediment-oil-agglomerates buried in a Florida sandy beach. Sci Rep 2019; 9:19401. [PMID: 31852991 PMCID: PMC6920467 DOI: 10.1038/s41598-019-55625-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 12/02/2019] [Indexed: 01/06/2023] Open
Abstract
The Deepwater Horizon (DWH) oil spill contaminated coastlines from Louisiana to Florida, burying oil up to 70 cm depth in sandy beaches, posing a potential threat to environmental and human health. The dry and nutrient-poor beach sand presents a taxing environment for microbial growth, raising the question how the biodegradation of the buried oil would proceed. Here we report the results of an in-situ experiment that (i) characterized the dominant microbial communities contained in sediment oil agglomerates (SOAs) of DWH oil buried in a North Florida sandy beach, (ii) elucidated the long-term succession of the microbial populations that developed in the SOAs, and (iii) revealed the coupling of SOA degradation to nitrogen fixation. Orders of magnitude higher bacterial abundances in SOAs compared to surrounding sands distinguished SOAs as hotspots of microbial growth. Blooms of bacterial taxa with a demonstrated potential for hydrocarbon degradation (Gammaproteobacteria, Alphaproteobacteria, Actinobacteria) developed in the SOAs, initiating a succession of microbial populations that mirrored the evolution of the petroleum hydrocarbons. Growth of nitrogen-fixing prokaryotes or diazotrophs (Rhizobiales and Frankiales), reflected in increased abundances of nitrogenase genes (nifH), catalyzed biodegradation of the nitrogen-poor petroleum hydrocarbons, emphasizing nitrogen fixation as a central mechanism facilitating the recovery of sandy beaches after oil contamination.
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Affiliation(s)
- Boryoung Shin
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ioana Bociu
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL, USA
| | - Max Kolton
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Markus Huettel
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL, USA
| | - Joel E Kostka
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA. .,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
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Molina‐Menor E, Tanner K, Vidal‐Verdú À, Peretó J, Porcar M. Microbial communities of the Mediterranean rocky shore: ecology and biotechnological potential of the sea-land transition. Microb Biotechnol 2019; 12:1359-1370. [PMID: 31562755 PMCID: PMC6801134 DOI: 10.1111/1751-7915.13475] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 12/29/2022] Open
Abstract
Microbial communities from harsh environments hold great promise as sources of biotechnologically relevant strains and compounds. In the present work, we have characterized the microorganisms from the supralittoral and splash zone in three different rocky locations of the Western Mediterranean coast, a tough environment characterized by high levels of irradiation and large temperature and salinity fluctuations. We have retrieved a complete view of the ecology and functional aspects of these communities and assessed the biotechnological potential of the cultivable microorganisms. All three locations displayed very similar taxonomic profiles, with the genus Rubrobacter and the families Xenococcaceae, Flammeovirgaceae, Phyllobacteriaceae, Rhodobacteraceae and Trueperaceae being the most abundant taxa; and Ascomycota and halotolerant archaea as members of the eukaryotic and archaeal community respectively. In parallel, the culture-dependent approach yielded a 100-isolates collection, out of which 12 displayed high antioxidant activities, as evidenced by two in vitro (hydrogen peroxide and DPPH) and confirmed in vivo with Caenorhabditis elegans assays, in which two isolates, CR22 and CR24, resulted in extended survival rates of the nematodes. This work is the first complete characterization of the Mediterranean splash-zone coastal microbiome, and our results indicate that this microbial niche is home of an extremophilic community that holds biotechnological potential.
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Affiliation(s)
- Esther Molina‐Menor
- Institute for Integrative Systems Biology ISysBioUniversitat de València‐CSICPaterna46980Spain
| | - Kristie Tanner
- Institute for Integrative Systems Biology ISysBioUniversitat de València‐CSICPaterna46980Spain
- Darwin Bioprospecting Excellence S.L. Parc Científic Universitat de ValènciaPaterna46980Spain
| | - Àngela Vidal‐Verdú
- Institute for Integrative Systems Biology ISysBioUniversitat de València‐CSICPaterna46980Spain
| | - Juli Peretó
- Institute for Integrative Systems Biology ISysBioUniversitat de València‐CSICPaterna46980Spain
- Darwin Bioprospecting Excellence S.L. Parc Científic Universitat de ValènciaPaterna46980Spain
- Departament de Bioquímica i Biologia MolecularUniversitat de ValènciaBurjassot46100Spain
| | - Manuel Porcar
- Institute for Integrative Systems Biology ISysBioUniversitat de València‐CSICPaterna46980Spain
- Darwin Bioprospecting Excellence S.L. Parc Científic Universitat de ValènciaPaterna46980Spain
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19
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Thomas F, Corre E, Cébron A. Stable isotope probing and metagenomics highlight the effect of plants on uncultured phenanthrene-degrading bacterial consortium in polluted soil. THE ISME JOURNAL 2019; 13:1814-1830. [PMID: 30872807 PMCID: PMC6775975 DOI: 10.1038/s41396-019-0394-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 02/08/2019] [Accepted: 02/28/2019] [Indexed: 11/09/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil pollutants. The discovery that plants can stimulate microbial degradation of PAHs has promoted research on rhizoremediation strategies. We combined DNA-SIP with metagenomics to assess the influence of plants on the identity and metabolic functions of active PAH-degrading bacteria in contaminated soil, using phenanthrene (PHE) as a model hydrocarbon. 13C-PHE dissipation was 2.5-fold lower in ryegrass-planted conditions than in bare soil. Metabarcoding of 16S rDNA revealed significantly enriched OTUs in 13C-SIP incubations compared to 12C-controls, namely 130 OTUs from bare soil and 73 OTUs from planted soil. Active PHE-degraders were taxonomically diverse (Proteobacteria, Actinobacteria and Firmicutes), with Sphingomonas and Sphingobium dominating in bare and planted soil, respectively. Plant root exudates favored the development of PHE-degraders having specific functional traits at the genome level. Indeed, metagenomes of 13C-enriched DNA fractions contained more genes involved in aromatic compound metabolism in bare soil, whereas carbohydrate catabolism genes were more abundant in planted soil. Functional gene annotation allowed reconstruction of complete pathways with several routes for PHE catabolism. Sphingomonadales were the major taxa performing the first steps of PHE degradation in both conditions, suggesting their critical role to initiate in situ PAH remediation. Active PHE-degraders act in a consortium, whereby complete PHE mineralization is achieved through the combined activity of taxonomically diverse co-occurring bacteria performing successive metabolic steps. Our study reveals hitherto underestimated functional interactions for full microbial detoxification in contaminated soils.
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Affiliation(s)
- François Thomas
- Université de Lorraine, CNRS, LIEC, 54500, Nancy, France
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680, Roscoff, France
| | - Erwan Corre
- CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, 29680, Roscoff, France
| | - Aurélie Cébron
- Université de Lorraine, CNRS, LIEC, 54500, Nancy, France.
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Potts LD, Perez Calderon LJ, Gontikaki E, Keith L, Gubry-Rangin C, Anderson JA, Witte U. Effect of spatial origin and hydrocarbon composition on bacterial consortia community structure and hydrocarbon biodegradation rates. FEMS Microbiol Ecol 2019; 94:5047303. [PMID: 29982504 PMCID: PMC6166136 DOI: 10.1093/femsec/fiy127] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/26/2018] [Indexed: 12/30/2022] Open
Abstract
Oil reserves in deep-sea sediments are currently subject to intense exploration, with associated risks of oil spills. Previous research suggests that microbial communities from deep-sea sediment (>1000m) can degrade hydrocarbons (HCs), but have a lower degradation ability than shallow (<200m) communities, probably due to in situ temperature. This study aimed to assess the effect of marine origin on microbial HC degradation potential while separating the influence of temperature, and to characterise associated HC-degrading bacterial communities. Microbial communities from 135 and 1000 m deep sediments were selectively enriched on crude oil at in situ temperatures and both consortia were subsequently incubated for 42 days at 20°C with two HC mixtures: diesel fuel or model oil. Significant HC biodegradation occurred rapidly in the presence of both consortia, especially of low molecular weight HCs and was concomitant with microbial community changes. Further, oil degradation was higher with the shallow consortium than with the deep one. Dominant HC-degrading bacteria differed based on both spatial origin of the consortia and supplemented HC types. This study provides evidence for influence of sediment spatial origin and HC composition on the selection and activity of marine HC-degrading bacterial communities and is relevant for future bioremediationdevelopments.
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Affiliation(s)
- Lloyd D Potts
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UL, United Kingdom.,Materials and Chemical Engineering, School of Engineering, University of Aberdeen, Fraser Noble Building, Elphinstone Road, Aberdeen, AB24 3UE, United Kingdom
| | - Luis J Perez Calderon
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UL, United Kingdom.,Materials and Chemical Engineering, School of Engineering, University of Aberdeen, Fraser Noble Building, Elphinstone Road, Aberdeen, AB24 3UE, United Kingdom
| | - Evangelia Gontikaki
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UL, United Kingdom
| | - Lehanne Keith
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UL, United Kingdom
| | - Cécile Gubry-Rangin
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UL, United Kingdom
| | - James A Anderson
- Materials and Chemical Engineering, School of Engineering, University of Aberdeen, Fraser Noble Building, Elphinstone Road, Aberdeen, AB24 3UE, United Kingdom
| | - Ursula Witte
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UL, United Kingdom
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21
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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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22
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Potts LD, Perez Calderon LJ, Gubry-Rangin C, Witte U, Anderson JA. Characterisation of microbial communities of drill cuttings piles from offshore oil and gas installations. MARINE POLLUTION BULLETIN 2019; 142:169-177. [PMID: 31232291 DOI: 10.1016/j.marpolbul.2019.03.014] [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: 11/13/2018] [Revised: 03/03/2019] [Accepted: 03/08/2019] [Indexed: 06/09/2023]
Abstract
Drill cuttings (DC) are produced during hydrocarbon drilling operations and are composed of subsurface rock coated with hydrocarbons and drilling fluids. Historic disposal of DC at sea has resulted in the formation of large piles on the seabed that may be left in situ following infrastructure decommissioning. This study provides a first insight into the microbial abundance, diversity and community structure of two DC piles from North Sea oil and gas installations. The abundance of both bacteria and archaea was lower in DC than in surrounding natural sediments. Microbial diversity and richness within DC were low but increased with distance from the piles. Microbial community structure was significantly different in DC piles compared to nearby natural sediments. DC bacterial communities were dominated by Halomonas, Dietzia and Dethiobacter. The presence of such organisms suggests a potential function of hydrocarbon degradation ability and may play an active role in DC pile remediation.
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Affiliation(s)
- Lloyd D Potts
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom; Chemical and Materials Engineering, School of Engineering, University of Aberdeen, Aberdeen, United Kingdom.
| | - Luis J Perez Calderon
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom; Chemical and Materials Engineering, School of Engineering, University of Aberdeen, Aberdeen, United Kingdom
| | - Cecile Gubry-Rangin
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Ursula Witte
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - James A Anderson
- Chemical and Materials Engineering, School of Engineering, University of Aberdeen, Aberdeen, United Kingdom
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23
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Zeng J, Zhu Q, Li Y, Dai Y, Wu Y, Sun Y, Miu L, Chen H, Lin X. Isolation of diverse pyrene-degrading bacteria via introducing readily utilized phenanthrene. CHEMOSPHERE 2019; 222:534-540. [PMID: 30721812 DOI: 10.1016/j.chemosphere.2019.01.189] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 01/17/2019] [Accepted: 01/31/2019] [Indexed: 06/09/2023]
Abstract
Bacteria able to degrade pyrene play a critical role in the biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons (PAHs). However, the traditional isolation procedure only obtains strains related to the genus Mycobacterium. The aim of the present study was to develop a modified method to isolate taxonomically distinct pyrene-degrading strains. The results indicated that replacing pyrene with phenanthrene in the isolation step improved the isolation efficiency. Using the modified method, six PAH degraders belonging to the genera Bosea, Arthrobacter, Paenibacillus, Bacillus, and Rhodococcus were obtained. They were capable of effectively utilizing pyrene (∼100%) as their sole carbon source, and could co-metabolize the degradation of benzo [a]pyrene (26.9-71.5%). In contrast, a small amount of pyrene (5.6%) and benzo [a]pyrene (8.6%) were degraded by a phenanthrene-degrading Sphingobium sp. NS7 under the same conditions. The difference in PAHs degradation between agar plate culture and liquid culture may lead to the low isolation efficiency in the traditional procedure. Hereditary stability analysis showed that PAH degradation capability of the Bosea, Paenibacillus, and Rhodococcus strains were easily lost without PAH pressure, which may partly explain why those strains were difficult to obtain using the traditional method.
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Affiliation(s)
- Jun Zeng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, PR China
| | - Qinghe Zhu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, PR China
| | - Yanjie Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, PR China
| | - Yeliang Dai
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, PR China
| | - Yucheng Wu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, PR China
| | - Yuhan Sun
- High School Affiliated To Nanjing Normal University, Chahaer Road, 37, Nanjing, 210003, PR China
| | - Luyi Miu
- High School Affiliated To Nanjing Normal University, Chahaer Road, 37, Nanjing, 210003, PR China
| | - Hong Chen
- Soil and Environment Analysis Center, Institute of Soil Science, Chinese Academy of Science, PR China
| | - Xiangui Lin
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing, 210008, PR China.
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24
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Pichel A, Moreno R, Figueroa M, Campos JL, Mendez R, Mosquera-Corral A, Val del Rio A. How to cope with NOB activity and pig manure inhibition in a partial nitritation-anammox process? Sep Purif Technol 2019. [DOI: 10.1016/j.seppur.2018.11.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Spini G, Spina F, Poli A, Blieux AL, Regnier T, Gramellini C, Varese GC, Puglisi E. Molecular and Microbiological Insights on the Enrichment Procedures for the Isolation of Petroleum Degrading Bacteria and Fungi. Front Microbiol 2018; 9:2543. [PMID: 30425689 PMCID: PMC6218658 DOI: 10.3389/fmicb.2018.02543] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/05/2018] [Indexed: 12/15/2022] Open
Abstract
Autochthonous bioaugmentation, by exploiting the indigenous microorganisms of the contaminated environment to be treated, can represent a successful bioremediation strategy. In this perspective, we have assessed by molecular methods the evolution of bacterial and fungal communities during the selective enrichment on different pollutants of a soil strongly polluted by mixtures of aliphatic and polycyclic hydrocarbons. Three consecutive enrichments were carried out on soil samples from different soil depths (0-1, 1-2, 2-3 m), and analyzed at each step by means of high-throughput sequencing of bacterial and fungal amplicons biomarkers. At the end of the enrichments, bacterial and fungal contaminants degrading strains were isolated and identified in order to (i) compare the composition of enriched communities by culture-dependent and culture-independent molecular methods and to (ii) obtain a collection of hydrocarbon degrading microorganisms potentially exploitable for soil bioremediation. Molecular results highlighted that for both bacteria and fungi the pollutant had a partial shaping effect on the enriched communities, with paraffin creating distinct enriched bacterial community from oil, and polycyclic aromatic hydrocarbons generally overlapping; interestingly neither the soil depth or the enrichment step had significant effects on the composition of the final enriched communities. Molecular analyses well-agreed with culture-dependent analyses in terms of most abundant microbial genera. A total of 95 bacterial and 94 fungal strains were isolated after selective enrichment procedure on different pollutants. On the whole, isolated bacteria where manly ascribed to Pseudomonas genus followed by Sphingobacterium, Bacillus, Stenothrophomonas, Achromobacter, and Serratia. As for fungi, Fusarium was the most abundant genus followed by Trichoderma and Aspergillus. The species comprising more isolates, such as Pseudomonas putida, Achromobacter xylosoxidans and Ochromobactrum anthropi for bacteria, Fusarium oxysporum and Fusarium solani for fungi, were also the dominant OTUs assessed in Illumina.
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Affiliation(s)
- Giulia Spini
- Department for Sustainable Food Processes, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Federica Spina
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis, University of Turin, Turin, Italy
| | - Anna Poli
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis, University of Turin, Turin, Italy
| | | | | | | | - Giovanna C. Varese
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis, University of Turin, Turin, Italy
| | - Edoardo Puglisi
- Department for Sustainable Food Processes, Università Cattolica del Sacro Cuore, Piacenza, Italy
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26
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Mulet M, Sánchez D, Rodríguez AC, Nogales B, Bosch R, Busquets A, Gomila M, Lalucat J, García-Valdés E. Pseudomonas gallaeciensis sp. nov., isolated from crude-oil-contaminated intertidal sand samples after the Prestige oil spill. Syst Appl Microbiol 2018; 41:340-347. [DOI: 10.1016/j.syapm.2018.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 03/26/2018] [Accepted: 03/30/2018] [Indexed: 10/17/2022]
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27
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Homologous Recombination in Core Genomes Facilitates Marine Bacterial Adaptation. Appl Environ Microbiol 2018; 84:AEM.02545-17. [PMID: 29572211 DOI: 10.1128/aem.02545-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/20/2018] [Indexed: 01/01/2023] Open
Abstract
Acquisition of ecologically relevant genes is common among ocean bacteria, but whether it has a major impact on genome evolution in marine environments remains unknown. Here, we analyzed the core genomes of 16 phylogenetically diverse and ecologically relevant bacterioplankton lineages, each consisting of up to five genomes varying at the strain level. Statistical approaches identified from each lineage up to ∼50 loci showing anomalously high divergence at synonymous sites, which is best explained by recombination with distantly related organisms. The enriched gene categories in these outlier loci match well with the characteristics previously identified as the key phenotypes of these lineages. Examples are antibiotic synthesis and detoxification in Phaeobacter inhibens, exopolysaccharide production in Alteromonas macleodii, hydrocarbon degradation in Marinobacter hydrocarbonoclasticus, and cold adaptation in Pseudoalteromonas haloplanktis Intriguingly, the outlier loci feature polysaccharide catabolism in Cellulophaga baltica but not in Cellulophaga lytica, consistent with their primary habitat preferences in macroalgae and beach sands, respectively. Likewise, analysis of Prochlorococcus showed that photosynthesis-related genes listed in the outlier loci are found only in the high-light-adapted ecotype and not in the low-light adapted ecotype. These observations strongly suggest that recombination with distant relatives is a key mechanism driving the ecological diversification among marine bacterial lineages.IMPORTANCE Acquisition of new metabolic genes has been known as an important mechanism driving bacterial evolution and adaptation in the ocean, but acquisition of novel alleles of existing genes and its potential ecological role have not been examined. Guided by population genetic theories, our genomic analysis showed that divergent allele acquisition is prevalent in phylogenetically diverse marine bacterial lineages and that the affected loci often encode metabolic functions that underlie the known ecological roles of the lineages under study.
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28
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Doyle SM, Whitaker EA, De Pascuale V, Wade TL, Knap AH, Santschi PH, Quigg A, Sylvan JB. Rapid Formation of Microbe-Oil Aggregates and Changes in Community Composition in Coastal Surface Water Following Exposure to Oil and the Dispersant Corexit. Front Microbiol 2018; 9:689. [PMID: 29696005 PMCID: PMC5904270 DOI: 10.3389/fmicb.2018.00689] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 03/23/2018] [Indexed: 12/15/2022] Open
Abstract
During the Deepwater Horizon (DWH) oil spill, massive quantities of oil were deposited on the seafloor via a large-scale marine oil-snow sedimentation and flocculent accumulation (MOSSFA) event. The role of chemical dispersants (e.g., Corexit) applied during the DWH oil spill clean-up in helping or hindering the formation of this MOSSFA event are not well-understood. Here, we present the first experiment related to the DWH oil spill to specifically investigate the relationship between microbial community structure, oil and Corexit®, and marine oil-snow in coastal surface waters. We observed the formation of micron-scale aggregates of microbial cells around droplets of oil and dispersant and found that their rate of formation was directly related to the concentration of oil within the water column. These micro-aggregates are potentially important precursors to the formation of larger marine oil-snow particles. Therefore, our observation that Corexit® significantly enhanced their formation suggests dispersant application may play a role in the development of MOSSFA events. We also observed that microbial communities in marine surface waters respond to oil and oil plus Corexit® differently and much more rapidly than previously measured, with major shifts in community composition occurring within only a few hours of experiment initiation. In the oil-amended treatments without Corexit®, this manifested as an increase in community diversity due to the outgrowth of several putative aliphatic- and aromatic-hydrocarbon degrading genera, including phytoplankton-associated taxa. In contrast, microbial community diversity was reduced in mesocosms containing chemically dispersed oil. Importantly, different consortia of hydrocarbon degrading bacteria responded to oil and chemically dispersed oil, indicating that functional redundancy in the pre-spill community likely results in hydrocarbon consumption in both undispersed and dispersed oils, but by different bacterial taxa. Taken together, these data improve our understanding of how dispersants influence the degradation and transport of oil in marine surface waters following an oil spill and provide valuable insight into the early response of complex microbial communities to oil exposure.
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Affiliation(s)
- Shawn M Doyle
- Department of Oceanography, Texas A&M University, College Station, TX, United States
| | - Emily A Whitaker
- Department of Oceanography, Texas A&M University, College Station, TX, United States
| | - Veronica De Pascuale
- Department of Oceanography, Texas A&M University, College Station, TX, United States
| | - Terry L Wade
- Department of Oceanography, Texas A&M University, College Station, TX, United States.,Geochemical and Environmental Research Group, Texas A&M University, College Station, TX, United States
| | - Anthony H Knap
- Department of Oceanography, Texas A&M University, College Station, TX, United States.,Geochemical and Environmental Research Group, Texas A&M University, College Station, TX, United States
| | - Peter H Santschi
- Department of Oceanography, Texas A&M University, College Station, TX, United States.,Department of Marine Science, Texas A&M University at Galveston, Galveston, TX, United States
| | - Antonietta Quigg
- Department of Oceanography, Texas A&M University, College Station, TX, United States.,Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, United States
| | - Jason B Sylvan
- Department of Oceanography, Texas A&M University, College Station, TX, United States
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29
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Val Del Rio A, Pichel A, Fernandez-Gonzalez N, Pedrouso A, Fra-Vázquez A, Morales N, Mendez R, Campos JL, Mosquera-Corral A. Performance and microbial features of the partial nitritation-anammox process treating fish canning wastewater with variable salt concentrations. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 208:112-121. [PMID: 29253740 DOI: 10.1016/j.jenvman.2017.12.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 10/31/2017] [Accepted: 12/04/2017] [Indexed: 06/07/2023]
Abstract
The partial nitritation-anammox (PN-AMX) process applied to wastewaters with high NaCl concentration was studied until now using simulated media, without considering the effect of organic matter concentration and the shift in microbial populations. This research work presents results on the application of this process to the treatment of saline industrial wastewater. Obtained results indicated that the PN-AMX process has the capability to recover its initial activity after a sudden/acute salt inhibition event (up to 16 g NaCl/L). With a progressive salt concentration increase for 150 days, the PN-AMX process was able to remove the 80% of the nitrogen at 7-9 g NaCl/L. The microbiological data indicated that NaCl and ammonia concentrations and temperature are important factors shaping PN-AMX communities. Thus, the NOB abundance (Nitrospira) decreases with the increase of the salt concentration, while heterotrophic denitrifiers are able to outcompete anammox after a peak of organic matter in the feeding.
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Affiliation(s)
- Angeles Val Del Rio
- Department of Chemical Engineering, School of Engineering, Universidade de Santiago de Compostela, E- 15705 Santiago de Compostela, Spain.
| | - Andres Pichel
- Department of Chemical Engineering, School of Engineering, Universidade de Santiago de Compostela, E- 15705 Santiago de Compostela, Spain.
| | - Nuria Fernandez-Gonzalez
- Department of Chemical Engineering, School of Engineering, Universidade de Santiago de Compostela, E- 15705 Santiago de Compostela, Spain.
| | - Alba Pedrouso
- Department of Chemical Engineering, School of Engineering, Universidade de Santiago de Compostela, E- 15705 Santiago de Compostela, Spain.
| | - Andrea Fra-Vázquez
- Department of Chemical Engineering, School of Engineering, Universidade de Santiago de Compostela, E- 15705 Santiago de Compostela, Spain.
| | - Nicolas Morales
- Aqualia, Guillarei WWTP, Camino de la Veiga s/n, E-36720 Tui, Spain.
| | - Ramon Mendez
- Department of Chemical Engineering, School of Engineering, Universidade de Santiago de Compostela, E- 15705 Santiago de Compostela, Spain.
| | - Jose Luis Campos
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Avda Padre Hurtado 750, Viña del Mar, E- 2503500, Chile.
| | - Anuska Mosquera-Corral
- Department of Chemical Engineering, School of Engineering, Universidade de Santiago de Compostela, E- 15705 Santiago de Compostela, Spain.
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30
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Kim J, Lee AH, Chang W. Enhanced bioremediation of nutrient-amended, petroleum hydrocarbon-contaminated soils over a cold-climate winter: The rate and extent of hydrocarbon biodegradation and microbial response in a pilot-scale biopile subjected to natural seasonal freeze-thaw temperatures. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 612:903-913. [PMID: 28886542 DOI: 10.1016/j.scitotenv.2017.08.227] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 08/20/2017] [Accepted: 08/21/2017] [Indexed: 06/07/2023]
Abstract
A pilot-scale biopile field experiment for nutrient-amended petroleum-contaminated fine-grained soils was performed over the winter at a cold-climate site. The rate and extent of hydrocarbon biodegradation and microbial responses were determined and corresponded to the on-site soil phase changes (from unfrozen to partially frozen, deeply frozen, and thawed) associated with natural seasonal freeze-thaw conditions. Treated and untreated biopiles were constructed (~3500kg each) on an open outdoor surface at a remediation facility in Saskatoon, Canada. The treated biopile received N-P-K-based nutrient and humate amendments before seasonal freezing. Real-time field monitoring indicated significant unfrozen water content in the treated and untreated biopiles throughout the freezing period, from the middle of November to early March. Unfrozen water was slightly more available in the treated biopile due to the aqueous nutrient supply. Soil CO2 production and O2 consumption in the treated biopile were generally greater than in the untreated biopile. Total removal percentages for F2 (>C10-C16), F3 (>C16-C34), and total petroleum hydrocarbons (TPH) in the treated biopile were 57, 58, and 58%, respectively, of which 26, 39, and 33% were removed during seasonal freezing and early thawing between November to early March. F3 degradation largely occurred during freezing while F2 hydrocarbons were primarily removed during thawing. Biomarker-based hydrocarbon analyses confirmed enhanced biodegradation in the treated biopile during freezing. The soil treatment increased the first-order rate constants for F2, F3, and TPH degradation by a factor of 2 to 7 compared to the untreated biopile. Shifts in bacterial community appeared in both biopiles as the biopile soils seasonally froze and thawed. Increased alkB1 gene copy numbers in the treated biopile, especially in the partially thawed phase during early thawing, suggest extended hydrocarbon biodegradation to the seasonal freeze-thaw season, due to the nutrients supplied prior to seasonal freezing.
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Affiliation(s)
- Jihun Kim
- Department of Civil, Geological, and Environmental Engineering, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Aslan Hwanhwi Lee
- Department of Civil, Geological, and Environmental Engineering, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Wonjae Chang
- Department of Civil, Geological, and Environmental Engineering, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
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31
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Su S, Dong H, Chai L, Zhang X, Banat IM, Wang Z, Hou D, Zhang F, She Y. Dynamics of a microbial community during an effective boost MEOR trial using high-throughput sequencing. RSC Adv 2018; 8:690-697. [PMID: 35538991 PMCID: PMC9076845 DOI: 10.1039/c7ra12245d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 12/11/2017] [Indexed: 11/21/2022] Open
Abstract
Using 454 pyrosequencing of 16S rRNA gene amplicons, microbial communities in samples of injection water and production water during a serial microbial enhanced oil recovery (MEOR) field trial in a water flooded high pour point oil reservoir were determined. There was a close microbial community compositional relationship between the injection water and the successful first round MEOR processed oil reservoir which was indicated by the result of 43 shared dominant operational taxonomic units detected in both the injection water and the production water. Alterations of microbial community after the injection of boost nutrients showed that microbes giving positive responses were mainly those belonging to the genera of Comamonas, Brevundimonas, Azospirillum, Achromobacter, Pseudomonas, and Hyphomonas, which were detected both in the injection water and in the production water and usually detected in oil reservoir environments or associated with hydrocarbon degradation. Additionally, microbes only dominant in the production waters were significantly inhibited with a sharp decline in their relative abundance. Based on these findings, a suggestion of re-optimization of the boost nutrients, targetting the microbes co-existing in the injection water and the oil reservoir and having survival ability in both surface and subsurface environments, rather than simple repeats for the subsequent in situ MEOR applications was proposed.
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Affiliation(s)
- Sanbao Su
- School of Petroleum Engineering, Yangtze University Wuhan Hubei 430010 China
| | - Hao Dong
- College of Chemistry and Environmental Engineering, Yangtze University Jingzhou Hubei 434023 China
| | - Lujun Chai
- The Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism, Ministry of Education, School of Energy Resources, China University of Geosciences (Beijing) Beijing 100083 China
| | - Xiaotao Zhang
- The Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism, Ministry of Education, School of Energy Resources, China University of Geosciences (Beijing) Beijing 100083 China
| | - Ibrahim M Banat
- Faculty of Life and Health Sciences, University of Ulster Coleraine BT52 1SA UK
| | - Zhengliang Wang
- College of Chemistry and Environmental Engineering, Yangtze University Jingzhou Hubei 434023 China
| | - Dujie Hou
- The Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism, Ministry of Education, School of Energy Resources, China University of Geosciences (Beijing) Beijing 100083 China
| | - Fan Zhang
- The Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism, Ministry of Education, School of Energy Resources, China University of Geosciences (Beijing) Beijing 100083 China
| | - Yuehui She
- College of Chemistry and Environmental Engineering, Yangtze University Jingzhou Hubei 434023 China
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Espínola F, Dionisi HM, Borglin S, Brislawn CJ, Jansson JK, Mac Cormack WP, Carroll J, Sjöling S, Lozada M. Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes. MICROBIAL ECOLOGY 2018; 75:123-139. [PMID: 28702706 DOI: 10.1007/s00248-017-1028-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 06/27/2017] [Indexed: 06/07/2023]
Abstract
In this work, we analyzed the community structure and metabolic potential of sediment microbial communities in high-latitude coastal environments subjected to low to moderate levels of chronic pollution. Subtidal sediments from four low-energy inlets located in polar and subpolar regions from both Hemispheres were analyzed using large-scale 16S rRNA gene and metagenomic sequencing. Communities showed high diversity (Shannon's index 6.8 to 10.2), with distinct phylogenetic structures (<40% shared taxa at the Phylum level among regions) but similar metabolic potential in terms of sequences assigned to KOs. Environmental factors (mainly salinity, temperature, and in less extent organic pollution) were drivers of both phylogenetic and functional traits. Bacterial taxa correlating with hydrocarbon pollution included families of anaerobic or facultative anaerobic lifestyle, such as Desulfuromonadaceae, Geobacteraceae, and Rhodocyclaceae. In accordance, biomarker genes for anaerobic hydrocarbon degradation (bamA, ebdA, bcrA, and bssA) were prevalent, only outnumbered by alkB, and their sequences were taxonomically binned to the same bacterial groups. BssA-assigned metagenomic sequences showed an extremely wide diversity distributed all along the phylogeny known for this gene, including bssA sensu stricto, nmsA, assA, and other clusters from poorly or not yet described variants. This work increases our understanding of microbial community patterns in cold coastal sediments, and highlights the relevance of anaerobic hydrocarbon degradation processes in subtidal environments.
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Affiliation(s)
- Fernando Espínola
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Centro Nacional Patagónico, Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Hebe M Dionisi
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Centro Nacional Patagónico, Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Sharon Borglin
- Energy Geosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Walter P Mac Cormack
- Instituto Nanobiotec, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
- Instituto Antártico Argentino, Buenos Aires, Argentina
| | - JoLynn Carroll
- Akvaplan-niva, Fram-High North Research Centre for Climate and the Environment, and ARCEx-Research Centre for Arctic Petroleum Exploration, Department of Geosciences, UiT The Arctic University of Norway, N-9037, Tromsø, Norway
| | - Sara Sjöling
- School of Natural Sciences and Environmental Studies, Södertörn University, Huddinge, Sweden
| | - Mariana Lozada
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Centro Nacional Patagónico, Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina.
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33
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Wright J, Kirchner V, Bernard W, Ulrich N, McLimans C, Campa MF, Hazen T, Macbeth T, Marabello D, McDermott J, Mackelprang R, Roth K, Lamendella R. Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation. Front Microbiol 2017; 8:2300. [PMID: 29213257 PMCID: PMC5702783 DOI: 10.3389/fmicb.2017.02300] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 11/07/2017] [Indexed: 01/05/2023] Open
Abstract
The uncontrolled release of the industrial solvent methylene chloride, also known as dichloromethane (DCM), has resulted in widespread groundwater contamination in the United States. Here we investigate the role of groundwater bacterial communities in the natural attenuation of DCM at an undisclosed manufacturing site in New Jersey. This study investigates the bacterial community structure of groundwater samples differentially contaminated with DCM to better understand the biodegradation potential of these autochthonous bacterial communities. Bacterial community analysis was completed using high-throughput sequencing of the 16S rRNA gene of groundwater samples (n = 26) with DCM contamination ranging from 0.89 to 9,800,000 μg/L. Significant DCM concentration-driven shifts in overall bacterial community structure were identified between samples, including an increase in the abundance of Firmicutes within the most contaminated samples. Across all samples, a total of 6,134 unique operational taxonomic units (OTUs) were identified, with 16 taxa having strong correlations with increased DCM concentration. Putative DCM degraders such as Pseudomonas, Dehalobacterium and Desulfovibrio were present within groundwater across all levels of DCM contamination. Interestingly, each of these taxa dominated specific DCM contamination ranges respectively. Potential DCM degrading lineages yet to be cited specifically as a DCM degrading organisms, such as the Desulfosporosinus, thrived within the most heavily contaminated groundwater samples. Co-occurrence network analysis revealed aerobic and anaerobic bacterial taxa with DCM-degrading potential were present at the study site. Our 16S rRNA gene survey serves as the first in situ bacterial community assessment of contaminated groundwater harboring DCM concentrations ranging over seven orders of magnitude. Diversity analyses revealed known as well as potentially novel DCM degrading taxa within defined DCM concentration ranges, indicating niche-specific responses of these autochthonous populations. Altogether, our findings suggest that monitored natural attenuation is an appropriate remediation strategy for DCM contamination, and that high-throughput sequencing technologies are a robust method for assessing the potential role of biodegrading bacterial assemblages in the apparent reduction of DCM concentrations in environmental scenarios.
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Affiliation(s)
- Justin Wright
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States.,Wright Labs, LLC, Huntingdon, PA, United States
| | - Veronica Kirchner
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States
| | - William Bernard
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States
| | - Nikea Ulrich
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States
| | - Christopher McLimans
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States
| | - Maria F Campa
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States.,Biosciences Division, Oak Ridge National Laboratory (DOE), Oak Ridge, TN, United States.,Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, United States
| | - Terry Hazen
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States.,Biosciences Division, Oak Ridge National Laboratory (DOE), Oak Ridge, TN, United States.,Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, United States.,Department of Microbiology, University of Tennessee, Knoxville, TN, United States.,Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, United States.,Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, United States
| | | | | | | | - Rachel Mackelprang
- Department of Biology, California State University Northridge, Northridge, PA, United States
| | - Kimberly Roth
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States
| | - Regina Lamendella
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States.,Wright Labs, LLC, Huntingdon, PA, United States
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34
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Zhang K, Sun Y, Cui Z, Yu D, Zheng L, Liu P, Lv Z. Periodically spilled-oil input as a trigger to stimulate the development of hydrocarbon-degrading consortia in a beach ecosystem. Sci Rep 2017; 7:12446. [PMID: 28963537 PMCID: PMC5622073 DOI: 10.1038/s41598-017-12820-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/15/2017] [Indexed: 11/09/2022] Open
Abstract
In this study, time-series samples were taken from a gravel beach to ascertain whether a periodic oil input induced by tidal action at the early stage of an oil spill can be a trigger to stimulate the development of hydrocarbon-degrading bacteria under natural in situ attenuation. High-throughput sequencing shows that the microbial community in beach sediments is characterized by the enrichment of hydrocarbon-degrading bacteria, including Alcanivorax, Dietzia, and Marinobacter. Accompanying the periodic floating-oil input, dynamic successions of microbial communities and corresponding fluctuations in functional genes (alkB and RDH) are clearly indicated in a time sequence, which keeps pace with the ongoing biodegradation of the spilled oil. The microbial succession that accompanies tidal action could benefit from the enhanced exchange of oxygen and nutrients; however, regular inputs of floating oil can be a trigger to stimulate an in situ "seed bank" of hydrocarbon-degrading bacteria. This leads to the continued blooming of hydrocarbon-degrading consortia in beach ecosystems. The results provide new insights into the beach microbial community structure and function in response to oil spills.
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Affiliation(s)
- Kai Zhang
- Environmental and Biogeochemical Institute (eBig), School of Earth Science, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Yongge Sun
- Environmental and Biogeochemical Institute (eBig), School of Earth Science, Zhejiang University, Hangzhou, Zhejiang, 310027, China.
| | - Zhisong Cui
- The First Institute of Oceanography, SOA, Qingdao, Shandong, 266061, China
| | - Di Yu
- Environmental and Biogeochemical Institute (eBig), School of Earth Science, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Li Zheng
- The First Institute of Oceanography, SOA, Qingdao, Shandong, 266061, China
| | - Peng Liu
- Environmental and Biogeochemical Institute (eBig), School of Earth Science, Zhejiang University, Hangzhou, Zhejiang, 310027, China.,Wuxi Research Institute of Petroleum Geology, SINOPEC, Wuxi, Jiangsu, 214126, China.,State Key Laboratory of Shale Oil and Gas Enrichment Mechanisms and Effective Development, Wuxi, Jiangsu, 214126, China
| | - Zhenmei Lv
- School of Life Science, Zhejiang University, Hangzhou, Zhejiang, 310058, China
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35
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Čučak DI, Spasojević JM, Babić OB, Maletić SP, Simeunović JB, Rončević SD, Dalmacija BD, Tamaš I, Radnović DV. A chemical and microbiological characterization and toxicity assessment of the Pančevo industrial complex wastewater canal sediments, Serbia. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:8458-8468. [PMID: 28188553 DOI: 10.1007/s11356-017-8513-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 01/26/2017] [Indexed: 06/06/2023]
Abstract
The wastewater canal Vojlovica of the Pančevo industrial area, Serbia, is the main collector of the effluents from the local industrial complex. The canal is directly connected to the Europe's second largest river, the Danube. Here, we present a chemical and microbiological analysis of the sediment in order to determine the fate of pollutants over the years, as well as its current condition. Dry matter, clay and organic matter content, a Kjeldahl ammonia, phosphorus, metals, and polychlorinated biphenyls as well as polycyclic aromatic hydrocarbons concentrations were measured. Microbiological analysis included heterotrophic and oil-degrading bacterial counts, isolation of the phenanthrene-degrading bacteria, and identification of cyanobacteria. Generally, in comparison to the results from previous studies, concentrations of the measured pollutants have been in a decline. Specifically, the metal and polycyclic aromatic hydrocarbon concentrations were reduced whereas microbial counts and toxicity tests did not indicate significant pollution. The obtained results are probably a consequence of an improved wastewater treatment and microbial degradation of pollutants.
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Affiliation(s)
- Dragana I Čučak
- Department of Chemistry, Biochemistry and Environmental Protection, University of Novi Sad Faculty of Sciences, Trg Dositeja Obradovića 3, Novi Sad, 21000, Serbia.
| | - Jelena M Spasojević
- Department of Chemistry, Biochemistry and Environmental Protection, University of Novi Sad Faculty of Sciences, Trg Dositeja Obradovića 3, Novi Sad, 21000, Serbia
| | - Olivera B Babić
- Department of Biology and Ecology, University of Novi Sad Faculty of Sciences, Trg Dositeja Obradovića 2, Novi Sad, 21000, Serbia
| | - Snežana P Maletić
- Department of Chemistry, Biochemistry and Environmental Protection, University of Novi Sad Faculty of Sciences, Trg Dositeja Obradovića 3, Novi Sad, 21000, Serbia
| | - Jelica B Simeunović
- Department of Biology and Ecology, University of Novi Sad Faculty of Sciences, Trg Dositeja Obradovića 2, Novi Sad, 21000, Serbia
| | - Srđan D Rončević
- Department of Chemistry, Biochemistry and Environmental Protection, University of Novi Sad Faculty of Sciences, Trg Dositeja Obradovića 3, Novi Sad, 21000, Serbia
| | - Božo D Dalmacija
- Department of Chemistry, Biochemistry and Environmental Protection, University of Novi Sad Faculty of Sciences, Trg Dositeja Obradovića 3, Novi Sad, 21000, Serbia
| | - Ivica Tamaš
- Department of Biology and Ecology, University of Novi Sad Faculty of Sciences, Trg Dositeja Obradovića 2, Novi Sad, 21000, Serbia
| | - Dragan V Radnović
- Department of Biology and Ecology, University of Novi Sad Faculty of Sciences, Trg Dositeja Obradovića 2, Novi Sad, 21000, Serbia
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36
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Zhu F, Storey S, Ashaari MM, Clipson N, Doyle E. Benzo(a)pyrene degradation and microbial community responses in composted soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:5404-5414. [PMID: 28025788 DOI: 10.1007/s11356-016-8251-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 12/12/2016] [Indexed: 06/06/2023]
Abstract
Benzo(a)pyrene degradation was compared in soil that was either composted, incubated at a constant temperature of 22 °C, or incubated under a temperature regime typical of a composting process. After 84 days, significantly more (61%) benzo(a)pyrene was removed from composted soil compared to soils incubated at a constant temperature (29%) or at composting temperatures (46%). Molecular fingerprinting approaches indicated that in composted soils, bacterial community changes were driven by both temperature and organic amendment, while fungal community changes were primarily driven by temperature. Next-generation sequencing data revealed that the bacterial community in composted soil was dominated by Actinobacteria (order Actinomycetales), Firmicutes (class Bacilli), and Proteobacteria (classes Gammaproteobacteria and Alphaproteobacteria), regardless of whether benzo(a)pyrene was present or not. The relative abundance of unclassified Actinomycetales (Actinobacteria) was significantly higher in composted soil when degradation was occurring, indicating a potential role for these organisms in benzo(a)pyrene metabolism. This study provides baseline data for employing straw-based composting strategies for the removal of high molecular weight PAHs from soil and contributes to the knowledge of how microbial communities respond to incubation conditions and pollutant degradation.
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Affiliation(s)
- Fengxiao Zhu
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Sean Storey
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Mardiana Mohd Ashaari
- Department of Biotechnology, Kulliyah of Science, International Islamic University Malaysia, Kuantan, Malaysia
| | - Nicholas Clipson
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Evelyn Doyle
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland.
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37
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Sarkar J, Kazy SK, Gupta A, Dutta A, Mohapatra B, Roy A, Bera P, Mitra A, Sar P. Biostimulation of Indigenous Microbial Community for Bioremediation of Petroleum Refinery Sludge. Front Microbiol 2016; 7:1407. [PMID: 27708623 PMCID: PMC5030240 DOI: 10.3389/fmicb.2016.01407] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 08/25/2016] [Indexed: 11/18/2022] Open
Abstract
Nutrient deficiency severely impairs the catabolic activity of indigenous microorganisms in hydrocarbon rich environments (HREs) and limits the rate of intrinsic bioremediation. The present study aimed to characterize the microbial community in refinery waste and evaluate the scope for biostimulation based in situ bioremediation. Samples recovered from the wastewater lagoon of Guwahati refinery revealed a hydrocarbon enriched [high total petroleum hydrocarbon (TPH)], oxygen-, moisture-limited, reducing environment. Intrinsic biodegradation ability of the indigenous microorganisms was enhanced significantly (>80% reduction in TPH by 90 days) with nitrate amendment. Preferred utilization of both higher- (>C30) and middle- chain (C20-30) length hydrocarbons were evident from GC-MS analysis. Denaturing gradient gel electrophoresis and community level physiological profiling analyses indicated distinct shift in community’s composition and metabolic abilities following nitrogen (N) amendment. High throughput deep sequencing of 16S rRNA gene showed that the native community was mainly composed of hydrocarbon degrading, syntrophic, methanogenic, nitrate/iron/sulfur reducing facultative anaerobic bacteria and archaebacteria, affiliated to γ- and δ-Proteobacteria and Euryarchaeota respectively. Genes for aerobic and anaerobic alkane metabolism (alkB and bssA), methanogenesis (mcrA), denitrification (nirS and narG) and N2 fixation (nifH) were detected. Concomitant to hydrocarbon degradation, lowering of dissolve O2 and increase in oxidation-reduction potential (ORP) marked with an enrichment of N2 fixing, nitrate reducing aerobic/facultative anaerobic members [e.g., Azovibrio, Pseudoxanthomonas and Comamonadaceae members] was evident in N amended microcosm. This study highlighted that indigenous community of refinery sludge was intrinsically diverse, yet appreciable rate of in situ bioremediation could be achieved by supplying adequate N sources.
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Affiliation(s)
- Jayeeta Sarkar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
| | - Sufia K Kazy
- Department of Biotechnology, National Institute of Technology Durgapur, India
| | - Abhishek Gupta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
| | - Avishek Dutta
- School of Bioscience, Indian Institute of Technology Kharagpur, India
| | - Balaram Mohapatra
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
| | - Ajoy Roy
- Department of Biotechnology, National Institute of Technology Durgapur, India
| | - Paramita Bera
- Department of Agricultural and Food Engineering, Indian Institute of Technology Kharagpur, India
| | - Adinpunya Mitra
- Department of Agricultural and Food Engineering, Indian Institute of Technology Kharagpur, India
| | - Pinaki Sar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
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38
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Li P, Cai Q, Lin W, Chen B, Zhang B. Offshore oil spill response practices and emerging challenges. MARINE POLLUTION BULLETIN 2016; 110:6-27. [PMID: 27393213 DOI: 10.1016/j.marpolbul.2016.06.020] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 06/02/2016] [Accepted: 06/03/2016] [Indexed: 06/06/2023]
Abstract
Offshore oil spills are of tremendous concern due to their potential impact on economic and ecological systems. A number of major oil spills triggered worldwide consciousness of oil spill preparedness and response. Challenges remain in diverse aspects such as oil spill monitoring, analysis, assessment, contingency planning, response, cleanup, and decision support. This article provides a comprehensive review of the current situations and impacts of offshore oil spills, as well as the policies and technologies in offshore oil spill response and countermeasures. Correspondingly, new strategies and a decision support framework are recommended for improving the capacities and effectiveness of oil spill response and countermeasures. In addition, the emerging challenges in cold and harsh environments are reviewed with recommendations due to increasing risk of oil spills in the northern regions from the expansion of the Arctic Passage.
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Affiliation(s)
- Pu Li
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL, Canada, A1B 3X5
| | - Qinhong Cai
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL, Canada, A1B 3X5
| | - Weiyun Lin
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL, Canada, A1B 3X5
| | - Bing Chen
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL, Canada, A1B 3X5.
| | - Baiyu Zhang
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL, Canada, A1B 3X5.
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39
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Ghosal D, Ghosh S, Dutta TK, Ahn Y. Current State of Knowledge in Microbial Degradation of Polycyclic Aromatic Hydrocarbons (PAHs): A Review. Front Microbiol 2016; 7:1369. [PMID: 27630626 PMCID: PMC5006600 DOI: 10.3389/fmicb.2016.01369] [Citation(s) in RCA: 249] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 08/18/2016] [Indexed: 12/22/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) include a group of organic priority pollutants of critical environmental and public health concern due to their toxic, genotoxic, mutagenic and/or carcinogenic properties and their ubiquitous occurrence as well as recalcitrance. The increased awareness of their various adverse effects on ecosystem and human health has led to a dramatic increase in research aimed toward removing PAHs from the environment. PAHs may undergo adsorption, volatilization, photolysis, and chemical oxidation, although transformation by microorganisms is the major neutralization process of PAH-contaminated sites in an ecologically accepted manner. Microbial degradation of PAHs depends on various environmental conditions, such as nutrients, number and kind of the microorganisms, nature as well as chemical property of the PAH being degraded. A wide variety of bacterial, fungal and algal species have the potential to degrade/transform PAHs, among which bacteria and fungi mediated degradation has been studied most extensively. In last few decades microbial community analysis, biochemical pathway for PAHs degradation, gene organization, enzyme system, genetic regulation for PAH degradation have been explored in great detail. Although, xenobiotic-degrading microorganisms have incredible potential to restore contaminated environments inexpensively yet effectively, but new advancements are required to make such microbes effective and more powerful in removing those compounds, which were once thought to be recalcitrant. Recent analytical chemistry and genetic engineering tools might help to improve the efficiency of degradation of PAHs by microorganisms, and minimize uncertainties of successful bioremediation. However, appropriate implementation of the potential of naturally occurring microorganisms for field bioremediation could be considerably enhanced by optimizing certain factors such as bioavailability, adsorption and mass transfer of PAHs. The main purpose of this review is to provide an overview of current knowledge of bacteria, halophilic archaea, fungi and algae mediated degradation/transformation of PAHs. In addition, factors affecting PAHs degradation in the environment, recent advancement in genetic, genomic, proteomic and metabolomic techniques are also highlighted with an aim to facilitate the development of a new insight into the bioremediation of PAH in the environment.
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Affiliation(s)
- Debajyoti Ghosal
- Environmental Engineering Laboratory, Department of Civil Engineering, Yeungnam UniversityGyeongsan, South Korea
| | - Shreya Ghosh
- Disasters Prevention Research Institute, Yeungnam UniversityGyeongsan, South Korea
| | - Tapan K. Dutta
- Department of Microbiology, Bose InstituteKolkata, India
| | - Youngho Ahn
- Environmental Engineering Laboratory, Department of Civil Engineering, Yeungnam UniversityGyeongsan, South Korea
- Disasters Prevention Research Institute, Yeungnam UniversityGyeongsan, South Korea
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40
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Wang X, Zhao X, Li H, Jia J, Liu Y, Ejenavi O, Ding A, Sun Y, Zhang D. Separating and characterizing functional alkane degraders from crude-oil-contaminated sites via magnetic nanoparticle-mediated isolation. Res Microbiol 2016; 167:731-744. [PMID: 27475037 DOI: 10.1016/j.resmic.2016.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 07/06/2016] [Accepted: 07/08/2016] [Indexed: 11/18/2022]
Abstract
Uncultivable microorganisms account for over 99% of all species on the planet, but their functions are yet not well characterized. Though many cultivable degraders for n-alkanes have been intensively investigated, the roles of functional n-alkane degraders remain hidden in the natural environment. This study introduces the novel magnetic nanoparticle-mediated isolation (MMI) technology in Nigerian soils and successfully separates functional microbes belonging to the families Oxalobacteraceae and Moraxellaceae, which are dominant and responsible for alkane metabolism in situ. The alkR-type n-alkane monooxygenase genes, instead of alkA- or alkP-type, were the key functional genes involved in the n-alkane degradation process. Further physiological investigation via a BIOLOG PM plate revealed some carbon (Tween 20, Tween 40 and Tween 80) and nitrogen (tyramine, l-glutamine and d-aspartic acid) sources promoting microbial respiration and n-alkane degradation. With further addition of promoter carbon or nitrogen sources, the separated functional alkane degraders significantly improved n-alkane biodegradation rates. This suggests that MMI is a promising technology for separating functional microbes from complex microbiota, with deeper insight into their ecological functions and influencing factors. The technique also broadens the application of the BIOLOG PM plate for physiological research on functional yet uncultivable microorganisms.
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Affiliation(s)
- Xinzi Wang
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK
| | - Xiaohui Zhao
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK; College of Water Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Hanbing Li
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK
| | - Jianli Jia
- School of Chemical and Environmental Engineering, China University of Mining & Technology (Beijing), Beijing 100083, PR China
| | - Yueqiao Liu
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK; College of Water Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Odafe Ejenavi
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK
| | - Aizhong Ding
- College of Water Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Yujiao Sun
- College of Water Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Dayi Zhang
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK.
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41
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Tarn J, Peoples LM, Hardy K, Cameron J, Bartlett DH. Identification of Free-Living and Particle-Associated Microbial Communities Present in Hadal Regions of the Mariana Trench. Front Microbiol 2016; 7:665. [PMID: 27242695 PMCID: PMC4860528 DOI: 10.3389/fmicb.2016.00665] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/21/2016] [Indexed: 02/01/2023] Open
Abstract
Relatively few studies have described the microbial populations present in ultra-deep hadal environments, largely as a result of difficulties associated with sampling. Here we report Illumina-tag V6 16S rRNA sequence-based analyses of the free-living and particle-associated microbial communities recovered from locations within two of the deepest hadal sites on Earth, the Challenger Deep (10,918 meters below surface-mbs) and the Sirena Deep (10,667 mbs) within the Mariana Trench, as well as one control site (Ulithi Atoll, 761 mbs). Seawater samples were collected using an autonomous lander positioned ~1 m above the seafloor. The bacterial populations within the Mariana Trench bottom water samples were dissimilar to other deep-sea microbial communities, though with overlap with those of diffuse flow hydrothermal vents and deep-subsurface locations. Distinct particle-associated and free-living bacterial communities were found to exist. The hadal bacterial populations were also markedly different from one another, indicating the likelihood of different chemical conditions at the two sites. In contrast to the bacteria, the hadal archaeal communities were more similar to other less deep datasets and to each other due to an abundance of cosmopolitan deep-sea taxa. The hadal communities were enriched in 34 bacterial and 4 archaeal operational taxonomic units (OTUs) including members of the Gammaproteobacteria, Epsilonproteobacteria, Marinimicrobia, Cyanobacteria, Deltaproteobacteria, Gemmatimonadetes, Atribacteria, Spirochaetes, and Euryarchaeota. Sequences matching cultivated piezophiles were notably enriched in the Challenger Deep, especially within the particle-associated fraction, and were found in higher abundances than in other hadal studies, where they were either far less prevalent or missing. Our results indicate the importance of heterotrophy, sulfur-cycling, and methane and hydrogen utilization within the bottom waters of the deeper regions of the Mariana Trench, and highlight novel community features of these extreme habitats.
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Affiliation(s)
- Jonathan Tarn
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Logan M Peoples
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kevin Hardy
- Global Ocean Dynamics, Global Ocean Design San Diego, CA, USA
| | | | - Douglas H Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
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42
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Yang CW, Hsiao WC, Chang BV. Biodegradation of sulfonamide antibiotics in sludge. CHEMOSPHERE 2016; 150:559-565. [PMID: 26921914 DOI: 10.1016/j.chemosphere.2016.02.064] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 02/15/2016] [Accepted: 02/15/2016] [Indexed: 06/05/2023]
Abstract
Sulfonamide antibiotics are widely used in human and veterinary medicine. This study assessed the degradation of three sulfonamides (100 mg kg(-1) each of sulfamethoxazole, sulfadimethoxine and sulfamethazine) and changes in the microbial communities of sewage sludge. Sulfamethoxazole degradation was enhanced by spent mushroom compost (SMC), SMC extract, and extract-containing microcapsules in the sludge. The degradation of sulfonamides in sludge and SMC mixtures occurred in the order of sulfamethoxazole > sulfadimethoxine > sulfamethazine. Bioreactor experiments revealed that the sulfonamides removal rates in sludge with SMC were greater than those in sludge alone. The sulfonamides removal rates were enhanced by the addition of SMC for six time additions. The sulfonamides concentrations were 200 and 500 mg kg(-1) for the first to third additions and the fourth to sixth additions, respectively. With the high correlations between TOC and the proportions of sulfonamides remaining in sludge, sulfonamides may be mineralized to a greater extent with SMC in sludge than in sludge alone. Four bacterial genera were identified from the different settings and stages of the bioreactor experiments. Acinetobacter and Pseudomonas were major bacterial communities that were responsible for sulfonamide degradation in sludge.
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Affiliation(s)
- Chu-Wen Yang
- Department of Microbiology, Soochow University, Taipei, Taiwan
| | - Wan-Chun Hsiao
- Department of Microbiology, Soochow University, Taipei, Taiwan
| | - Bea-Ven Chang
- Department of Microbiology, Soochow University, Taipei, Taiwan.
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43
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Aires T, Serrão EA, Engelen AH. Host and Environmental Specificity in Bacterial Communities Associated to Two Highly Invasive Marine Species (Genus Asparagopsis). Front Microbiol 2016; 7:559. [PMID: 27148239 PMCID: PMC4839258 DOI: 10.3389/fmicb.2016.00559] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 04/04/2016] [Indexed: 11/29/2022] Open
Abstract
As habitats change due to global and local pressures, population resilience, and adaptive processes depend not only on their gene pools but also on their associated bacteria communities. The hologenome can play a determinant role in adaptive evolution of higher organisms that rely on their bacterial associates for vital processes. In this study, we focus on the associated bacteria of the two most invasive seaweeds in southwest Iberia (coastal mainland) and nearby offshore Atlantic islands, Asparagopsis taxiformis and Asparagopsis armata. Bacterial communities were characterized using 16S rRNA barcoding through 454 next generation sequencing and exploratory shotgun metagenomics to provide functional insights and a backbone for future functional studies. The bacterial community composition was clearly different between the two species A. taxiformis and A. armata and between continental and island habitats. The latter was mainly due to higher abundances of Acidimicrobiales, Sphingomonadales, Xanthomonadales, Myxococcales, and Alteromonadales on the continent. Metabolic assignments for these groups contained a higher number of reads in functions related to oxidative stress and resistance to toxic compounds, more precisely heavy metals. These results are in agreement with their usual association with hydrocarbon degradation and heavy-metals detoxification. In contrast, A. taxiformis from islands contained more bacteria related to oligotrophic environments which might putatively play a role in mineralization of dissolved organic matter. The higher number of functional assignments found in the metagenomes of A. taxiformis collected from Cape Verde Islands suggest a higher contribution of bacteria to compensate nutrient limitation in oligotrophic environments. Our results show that Asparagopsis-associated bacterial communities have host-specificity and are modulated by environmental conditions. Whether this environmental effect reflects the host's selective requirements or the locally available bacteria remains to be addressed. However, the known functional capacities of these bacterial communities indicate their potential for eco-physiological functions that could be valuable for the host fitness.
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Affiliation(s)
- Tânia Aires
- Centro de Ciências do Mar-CIMAR, Universidade do Algarve Faro, Portugal
| | - Ester A Serrão
- Centro de Ciências do Mar-CIMAR, Universidade do Algarve Faro, Portugal
| | - Aschwin H Engelen
- Centro de Ciências do Mar-CIMAR, Universidade do Algarve Faro, Portugal
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44
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Oil removal and effects of spilled oil on active microbial communities in close to salt-saturation brines. Extremophiles 2016; 20:235-50. [DOI: 10.1007/s00792-016-0818-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 02/14/2016] [Indexed: 11/25/2022]
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45
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Martínez-Pascual E, Grotenhuis T, Solanas AM, Viñas M. Coupling chemical oxidation and biostimulation: Effects on the natural attenuation capacity and resilience of the native microbial community in alkylbenzene-polluted soil. JOURNAL OF HAZARDOUS MATERIALS 2015; 300:135-143. [PMID: 26177489 DOI: 10.1016/j.jhazmat.2015.06.061] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 06/17/2015] [Accepted: 06/24/2015] [Indexed: 06/04/2023]
Abstract
Coupling chemical oxidation with bioremediation could be a cost-effective system to cope with soil and groundwater pollution. However, the effects of chemical oxidation on autochthonous microbial communities are scarcely known. A detailed analysis that considers both the efficiency of the two technologies and the response of the microbial communities was performed on a linear alkylbenzene-polluted soil and groundwater samples. The impacts of a modified Fenton's reaction (MFR) at various dosages and of permanganate on the microbiota over 4 weeks were assessed. The permanganate and MFR negatively affected microbial abundance and activity. However, the resilience of certain microbial populations was observed, with a final increase in potential hydrocarbon-degrading populations as determined by both the alkB gene abundance and the predominance of well-known hydrocarbon-degrading phylotypes such as Rhodococcus, Ochrobactrum, Acinetobacter and Cupriavidus genera as determined by 16S rRNA-based DGGE fingerprinting. The assessment of the chemical oxidant impact on autochthonous microbiota should be considered for the optimization of coupled field remediation technologies.
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Affiliation(s)
| | - Tim Grotenhuis
- Department of Environmental Technology, Wageningen University, Wageningen, The Netherlands
| | - Anna M Solanas
- Department of Microbiology, University of Barcelona, Diagonal 645, E-08028 Barcelona, Spain
| | - Marc Viñas
- GIRO Joint Research Unit IRTA-UPC, IRTA, Torre Marimon, E-08140 Caldes de Montbui, Spain.
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46
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Caruso G, La Ferla R, Azzaro M, Zoppini A, Marino G, Petochi T, Corinaldesi C, Leonardi M, Zaccone R, Fonda Umani S, Caroppo C, Monticelli L, Azzaro F, Decembrini F, Maimone G, Cavallo RA, Stabili L, Hristova Todorova N, K. Karamfilov V, Rastelli E, Cappello S, Acquaviva MI, Narracci M, De Angelis R, Del Negro P, Latini M, Danovaro R. Microbial assemblages for environmental quality assessment: Knowledge, gaps and usefulness in the European Marine Strategy Framework Directive. Crit Rev Microbiol 2015; 42:883-904. [DOI: 10.3109/1040841x.2015.1087380] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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47
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Militon C, Jézéquel R, Gilbert F, Corsellis Y, Sylvi L, Cravo-Laureau C, Duran R, Cuny P. Dynamics of bacterial assemblages and removal of polycyclic aromatic hydrocarbons in oil-contaminated coastal marine sediments subjected to contrasted oxygen regimes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15260-15272. [PMID: 25997808 DOI: 10.1007/s11356-015-4510-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/07/2015] [Indexed: 06/04/2023]
Abstract
To study the impact of oxygen regimes on the removal of polycylic aromatic hydrocarbons (PAHs) in oil-spill-affected coastal marine sediments, we used a thin-layer incubation method to ensure that the incubated sediment was fully oxic, anoxic, or was influenced by oxic-anoxic switches without sediment stirring. Hydrocarbon content and microbial assemblages were followed during 60 days to determine PAH degradation kinetics and microbial community dynamics according to the oxygenation regimes. The highest PAH removal, with 69 % reduction, was obtained at the end of the experiment under oxic conditions, whereas weaker removals were obtained under oscillating and anoxic conditions (18 and 12 %, respectively). Bacterial community structure during the experiment was determined using a dual 16S rRNA genes/16S rRNA transcripts approach, allowing the characterization of metabolically active bacteria responsible for the functioning of the bacterial community in the contaminated sediment. The shift of the metabolically active bacterial communities showed that the selection of first responders belonged to Pseudomonas spp. and Labrenzia sp. and included an unidentified Deltaproteobacteria-irrespective of the oxygen regime-followed by the selection of late responders adapted to the oxygen regime. A novel unaffiliated phylotype (B38) was highly active during the last stage of the experiment, at which time, the low-molecular-weight (LMW) PAH biodegradation rates were significant for permanent oxic- and oxygen-oscillating conditions, suggesting that this novel phylotype plays an active role during the restoration phase of the studied ecosystem.
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Affiliation(s)
- Cécile Militon
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, 13288, Marseille, France.
- Campus de Luminy, case 901, 163 avenue de Luminy, 13288, Marseille Cedex 09, France.
| | - Ronan Jézéquel
- Centre de Documentation, de Recherche et d'Expérimentations sur les pollutions accidentelles des Eaux, 715 rue Alain Colas, CS 41836, 29218, Brest, France
| | - Franck Gilbert
- Université de Toulouse; INP, UPS; EcoLab (Laboratoire écologie fonctionnelle et environnement), 118 Route de Narbonne, 31062, Toulouse, France
- CNRS; EcoLab, 31062, Toulouse, France
| | - Yannick Corsellis
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, 13288, Marseille, France
| | - Léa Sylvi
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, 13288, Marseille, France
| | - Cristiana Cravo-Laureau
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Robert Duran
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Philippe Cuny
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, 13288, Marseille, France
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48
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Acosta-González A, Martirani-von Abercron SM, Rosselló-Móra R, Wittich RM, Marqués S. The effect of oil spills on the bacterial diversity and catabolic function in coastal sediments: a case study on the Prestige oil spill. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15200-14. [PMID: 25869434 DOI: 10.1007/s11356-015-4458-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/27/2015] [Indexed: 05/20/2023]
Abstract
The accident of the Prestige oil tanker in 2002 contaminated approximately 900 km of the coastline along the northern Spanish shore, as well as parts of Portugal and France coast, with a mixture of heavy crude oil consisting of polycyclic aromatic hydrocarbons, alkanes, asphaltenes and resins. The capacity of the autochthonous bacterial communities to respond to the oil spill was assessed indirectly by determining the hydrocarbon profiles of weathered oil samples collected along the shore, as well as through isotope ratios of seawater-dissolved CO2, and directly by analyses of denaturing gradient gel electrophoresis fingerprints and 16S rRNA gene libraries. Overall, the results evidenced biodegradation of crude oil components mediated by natural bacterial communities, with a bias towards lighter and less substituted compounds. The changes observed in the Proteobacteria, the most abundant phylum in marine sediments, were related to the metabolic profiles of the sediment. The presence of crude oil in the supratidal and intertidal zones increased the abundance of Alpha- and Gammaproteobacteria, dominated by the groups Sphingomonadaceae, Rhodobacteraceae and Chromatiales, whilst Gamma- and Deltaproteobacteria were more relevant in subtidal zones. The phylum Actinobacteria, and particularly the genus Rhodococcus, was a key player in the microbial response to the spill, especially in the degradation of the alkane fraction. The addition of inorganic fertilizers enhanced total biodegradation rates, suggesting that, in these environments, nutrients were insufficient to support significant growth after the huge increase in carbon sources, as evidenced in other spills. The presence of bacterial communities able to respond to a massive oil input in this area was consistent with the important history of pollution of the region by crude oil.
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Affiliation(s)
- Alejandro Acosta-González
- Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Profesor Albareda 1, 18008, Granada, Spain
- Facultad de Ingeniería, Universidad de La Sabana, Autopista Norte km 7, Chía, Cundinamarca, Colombia
| | - Sophie-Marie Martirani-von Abercron
- Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Profesor Albareda 1, 18008, Granada, Spain
| | - Ramon Rosselló-Móra
- Institut Mediterrani d'Estudis Avançats, IMEDEA, CSIC-UIB, C/. Miquel Marqués 21, 07190, Esporles, Illes Balears, Spain
| | - Regina-Michaela Wittich
- Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Profesor Albareda 1, 18008, Granada, Spain
| | - Silvia Marqués
- Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Profesor Albareda 1, 18008, Granada, Spain.
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49
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Al-Jawasim M, Yu K, Park JW. Synergistic effect of crude oil plus dispersant on bacterial community in a louisiana salt marsh sediment. FEMS Microbiol Lett 2015; 362:fnv144. [DOI: 10.1093/femsle/fnv144] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2015] [Indexed: 11/13/2022] Open
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50
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Bacterial PAH degradation in marine and terrestrial habitats. Curr Opin Biotechnol 2015; 33:95-102. [DOI: 10.1016/j.copbio.2015.01.006] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 12/15/2014] [Accepted: 01/14/2015] [Indexed: 11/22/2022]
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