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Yang L, Han P, Wang Q, Lin H, Wang D, Mao J, Qi W, Bai Y, Qu J. Disinfectant-induced ammonia oxidation disruption in microbial N-cycling process in aquatic ecosystem after the COVID-19 outbreak. WATER RESEARCH 2024; 258:121761. [PMID: 38749183 DOI: 10.1016/j.watres.2024.121761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/19/2024] [Accepted: 05/08/2024] [Indexed: 06/16/2024]
Abstract
Anthropogenic activities significantly impact the elemental cycles in aquatic ecosystems, with the N-cycling playing a critical role in potential nutrient turnover and substance cycling. We hypothesized that measures to prevent COVID-19 transmission profoundly altered the nitrogen cycle in riverine ecosystems. To investigate this, we re-analyzed metagenomic data and identified 60 N-cycling genes and 21 host metagenomes from four urban reaches (one upstream city, Wuhan, and two downstream cities) along the Yangtze River. Our analyses revealed a marked decrease in the abundance of bacterial ammonia monooxygenase genes, as well as in the host, ammonia-oxidizing autotrophic Nitrosomonas, followed by a substantial recovery post-pandemic. We posited that discharge of sodium hypochlorite (NaOCl) disinfectant may be a primary factor in the reduction of N-cycling process. To test this hypothesis, we exposed pure cultures of Nitrosomonas europaea to NaOCl to explore the microbial stress response. Results indicated that NaOCl exposure rapidly compromised the cell structure and inhibited ammonia oxidation of N. europaea, likely due to oxidative stress damage and reduced expression of nitrogen metabolism-related ammonia monooxygenase. Using the functional tagging technique, we determined that NaOCl directly destroyed the ammonia monooxygenase protein and DNA structure. This study highlights the negative impacts of chlorine disinfectants on the function of aquatic ecosystems and elucidates potential mechanisms of action.
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Affiliation(s)
- Lutong Yang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Science, Beijing, 100049, China
| | - Ping Han
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Qiaojuan Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Science, Beijing, 100049, China
| | - Hui Lin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Science, Beijing, 100049, China
| | - Donglin Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Jie Mao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Weixiao Qi
- Center for Water and Ecology, Tsinghua University, Beijing, 100084, China
| | - Yaohui Bai
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Jiuhui Qu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
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Villela H, Modolon F, Schultz J, Delgadillo-Ordoñez N, Carvalho S, Soriano AU, Peixoto RS. Genome analysis of a coral-associated bacterial consortium highlights complementary hydrocarbon degradation ability and other beneficial mechanisms for the host. Sci Rep 2023; 13:12273. [PMID: 37507453 PMCID: PMC10382565 DOI: 10.1038/s41598-023-38512-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
Here we report the oil degradation genetic potential of six oil-degrading bacteria (ODB), previously used as a bioremediation consortium, isolated from the hydrocoral Millepora alcicornis and seawater. The strains were identified as Halomonas sp. (LC_1), Cobetia sp. (LC_6), Pseudoalteromonas shioyasakiensis (LC_2), Halopseudomonas aestusnigri (LC_3), Shewanella algae (LC_4), and Brucella intermedia (LC_5). The taxonomic identification differed from that of the original paper when we used whole genome gene markers instead of just 16S rRNA gene. Genes responsible for the degradation of aromatic hydrocarbons and n-alkanes were found in all genomes, although different (and complementary) steps of the metabolic pathways were unique to each strain. Genes for naphthalene and toluene degradation were found in various strains. We annotated quinate degradation genes in LC_6, while LC_3 and LC_5 presented genes for biosurfactant and rhamnolipid biosynthesis. We also annotated genes related to beneficial mechanisms for corals, such as genes involved in nitrogen and DMSP metabolism, cobalamin biosynthesis and antimicrobial compounds production. Our findings reinforce the importance of using bacterial consortia for bioremediation approaches instead of single strains, due to their complementary genomic arsenals. We also propose a genome-based framework to select complementary ODB that can provide additional benefits to coral health.
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Affiliation(s)
- Helena Villela
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Flúvio Modolon
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Júnia Schultz
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Computational Biology Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Nathalia Delgadillo-Ordoñez
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Marine Science and Bioscience Programs, Biological, Environmental and Engineering Sciences Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | | | - Raquel Silva Peixoto
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
- Computational Biology Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
- Marine Science and Bioscience Programs, Biological, Environmental and Engineering Sciences Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
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3
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Elyamine AM, Wang H, Oummu-Kulthum MAH, Raissa S, Nahdhoit AR, Meng S, Tao P, Hu Z. Mangroves leaves phyllosphere bacteria community and its ability to survive under pyrene stress during the acclimation process. MARINE ENVIRONMENTAL RESEARCH 2023; 187:105920. [PMID: 36931048 DOI: 10.1016/j.marenvres.2023.105920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Plants in general and mangroves in particular can harbor hyper-diverse microorganisms in their different compartments including the phyllosphere area. This study used the leaves of three mangrove species; black mangrove (Avicenia germinans), red mangrove (Rhizophora mangle) and mangrove apple (Sonneratia alba) in order to evaluate the phyllosphere epiphytic bacterial community on their leaves surface and assess the ability of some epiphytic bacteria to tolerate and survive under pyrene stress. Through the 16S rRNA genes sequencing, 380203, 405203 and 344863 OTUs were identified respectively in the leaves of mangroves apple, black and red mangroves. The identified OTUs was positively correlated with leaves-wax (p < 0.05, r2 = 0.904), nitrogen (r2 = 0.72), phosphorus content (r2 = 0.62) and the water factor (r2 = 0.93). It was however highly and negatively correlated with the canopy cover (r2 = 0.93). The pyrene degradation rate in the mineral salt medium (MSM) containing pyrene as external stress was different in each mangrove species and varied depending on various factors. Therefore, through the succession culture in MSM, several bacteria strain belonging to Rhizobiales and Enterobacteres were found to be abundant in red mangroves. Bacteria belonging to Bacilliales and Sphingobacteriales were more abundant in mangroves apples and bacteria from Xanthomonadales and Sphingomonadales were more presents in back mangroves. The important finding was to reveal that the black mangrove at the non-submerged substrate, recorded the highest number of OTU, coinciding with its highest leaf's nitrogen and phosphorus content and most importantly, its highest rate of pyrene degradation. The general result of this study join previous research results and get place in the mangrove agenda, as part of a better understanding insight into the role of plant identity in driving the phyllosphere epiphytic microbial community structures in mangrove ecosystems.
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Affiliation(s)
- Ali Mohamed Elyamine
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou City, Guangdong, 515063, China; Department of Life Science, Faculty of Science and Technology, University of Comoros, Moroni, 269, Comoros
| | - Han Wang
- Huanhuai University, Zhumadian, 46000, China
| | | | - Sailine Raissa
- Department of Life Science, Faculty of Science and Technology, University of Comoros, Moroni, 269, Comoros
| | - Ahamada Rachid Nahdhoit
- Institute of Graduate Studies, Fundamental and Industrial Microbiology, Istanbul University, 34134, Vezneciler Faith, Istanbul, Turkey
| | - Shanshan Meng
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou City, Guangdong, 515063, China
| | - Peng Tao
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou City, Guangdong, 515063, China
| | - Zhong Hu
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou City, Guangdong, 515063, China.
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Anju VT, Busi S, Mohan MS, Salim SA, Ar S, Imchen M, Kumavath R, Dyavaiah M, Prasad R. Surveillance and mitigation of soil pollution through metagenomic approaches. Biotechnol Genet Eng Rev 2023:1-34. [PMID: 36881114 DOI: 10.1080/02648725.2023.2186330] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 02/23/2023] [Indexed: 03/08/2023]
Abstract
Soil pollution is one of the serious global threats causing risk to environment and humans. The major cause of accumulation of pollutants in soil are anthropogenic activities and some natural processes. There are several types of soil pollutants which deteriorate the quality of human life and animal health. They are recalcitrant hydrocarbon compounds, metals, antibiotics, persistent organic compounds, pesticides and different kinds of plastics. Due to the detrimental properties of pollutants present in soil on human life and ecosystem such as carcinogenic, genotoxic and mutagenic effects, alternate and effective methods to degrade the pollutants are recommended. Bioremediation is an effective and inexpensive method of biological degradation of pollutants using plants, microorganisms and fungi. With the advent of new detection methods, the identification and degradation of soil pollutants in different ecosystems were made easy. Metagenomic approaches are a boon for the identification of unculturable microorganisms and to explore the vast bioremediation potential for different pollutants. Metagenomics is a power tool to study the microbial load in polluted or contaminated land and its role in bioremediation. In addition, the negative ecosystem and health effect of pathogens, antibiotic and metal resistant genes found in the polluted area can be studied. Also, the identification of novel compounds/genes/proteins involved in the biotechnology and sustainable agriculture practices can be performed with the integration of metagenomics.
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Affiliation(s)
- V T Anju
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Siddhardha Busi
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Mahima S Mohan
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Simi Asma Salim
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Sabna Ar
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Madangchanok Imchen
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Ranjith Kumavath
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, India
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kerala, India
| | - Madhu Dyavaiah
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Ram Prasad
- Department of Botany, School of Life Sciences, Mahatma Gandhi Central University, Bihar, India
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Habibi N, Uddin S, Al-Sarawi H, Aldhameer A, Shajan A, Zakir F, Abdul Razzack N, Alam F. Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and Resistome. Microorganisms 2023; 11:microorganisms11020531. [PMID: 36838497 PMCID: PMC9960530 DOI: 10.3390/microorganisms11020531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/03/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Coastal sediments in the proximity of wastewater and emergency outfalls are often sinks of pharmaceutical compounds and other organic and inorganic contaminants that are likely to affect the microbial community. The metabolites of these contaminants affect microbial diversity and their metabolic processes, resulting in undesirable effects on ecosystem functioning, thus necessitating the need to understand their composition and functions. In the present investigation, we studied the metagenomes of 12 coastal surface sediments through whole genome shot-gun sequencing. Taxonomic binning of the genes predicted about 86% as bacteria, 1% as archaea, >0.001% as viruses and Eukaryota, and 12% as other communities. The dominant bacterial, archaeal, and fungal genera were Woeseia, Nitrosopumilus, and Rhizophagus, respectively. The most prevalent viral families were Myoviridae and Siphoviridae, and the T4 virus was the most dominant bacteriophage. The unigenes further aligned to 26 clusters of orthologous genes (COGs) and five carbohydrate-active enzymes (CAZy) classes. Glycoside hydrolases (GH) and glycoside transferase (GT) were the highest-recorded CAzymes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) level 3 functions were subjugated by purine metabolism > ABC transporters > oxidative phosphorylation > two-component system > pyrimidine metabolism > pyruvate metabolism > quorum sensing > carbon fixation pathways > ribosomes > and glyoxalate and dicarboxylate metabolism. Sequences allying with plasmids, integrons, insertion sequences and antibiotic-resistance genes were also observed. Both the taxonomies and functional abundances exhibited variation in relative abundances, with limited spatial variability (ANOVA p > 0.05; ANOSIM-0.05, p > 0.05). This study underlines the dominant microbial communities and functional genes in the marine sediments of Kuwait as a baseline for future biomonitoring programs.
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Affiliation(s)
- Nazima Habibi
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
- Correspondence:
| | - Saif Uddin
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
| | - Hanan Al-Sarawi
- Environment Public Authority, Fourth Ring Road, Shuwaikh Industrial 70050, Kuwait
| | - Ahmed Aldhameer
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
| | - Anisha Shajan
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
| | - Farhana Zakir
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
| | - Nasreem Abdul Razzack
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
| | - Faiz Alam
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
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6
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Zhang Z, Sun J, Gong X, Wang C, Wang H. Novel synergistic metabolic processes for phenanthrene biodegradation by a nitrate-reducing phenanthrene-degrading culture and an anammox culture. WATER RESEARCH 2023; 230:119593. [PMID: 36642028 DOI: 10.1016/j.watres.2023.119593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/24/2022] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
The synergistic metabolism by anammox cultures and nitrate-reducers for anaerobic PAH biodegradation is largely unknown, including whether anammox culture and which kind of anammox bacterium can perform nitrogen metabolism in the anaerobic PAH biodegradation processes, the inhibitory effect of PAH on anammox activity and nitrite on PAH-degrading nitrate-reducers activity, and the synergistic metabolic processes. Herein, an anammox culture that can eliminate nitrite accumulation and decrease inorganic carbon emission during anaerobic phenanthrene (a model of PAH in this study) biodegradation, the synergistic mechanism for phenanthrene biodegradation by a nitrate-reducer and such anammox culture, and the inhibition effect of phenanthrene on such anammox culture and nitrite on a phenanthrene-degrading nitrate-reducer were newly discussed. The results showed that nitrite largely accumulated during anaerobic phenanthrene biodegradation (nitrate accumulation is a common phenomenon for the biodegradation of refractory matter, including PAHs, by nitrate-reducers) by a nitrate-reducer, PheN2, which mineralizes phenanthrene to inorganic carbon, and nitrite was verified as an inhibiting factor for further biodegradation. Anaerobic phenanthrene biodegradation rates and nitrite concentrations (0-7 mM) appeared to have a negative linear correlation. The anammox culture that mainly contained Candidatus Kuenenia was newly found to efficiently reduce nitrite accumulation and inorganic carbon emissions and significantly promote biodegradation efficiency by ∼1.94-fold. Our results showed that phenanthrene absorbed in and on anammox cells had a more direct relationship with the inhibitory effect on anammox activity than phenanthrene in the environment, and 15.2 mg/gVSS phenanthrene absorbed in and on the cells (4 mM concentration in the culture) showed nearly complete inhibition of anammox culture in this study. In addition, few (less than 2% abundance) anammox bacteria were found to be enough for the removal of nitrite produced from anaerobic phenanthrene biodegradation. In an ideal world, co-pollutants of ammonia, nitrate, phenanthrene, and nitrite could be converted to nitrogen gas and biomass by the synergistic metabolism of anammox cultures and nitrate reducers. Our study reveals a new synergistic process that may exist in our environments for PAH elimination by an anammox culture and a nitrate-reducer, which provides a new strategy for the bioremediation of PAH-polluted anoxic zones.
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Affiliation(s)
- Zuotao Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiao Sun
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xiaoqiang Gong
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Chongyang Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hui Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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7
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Oyetibo GO, Adebusoye SA, Ilori MO, Amund OO. Heavy metals assessment of ecosystem polluted with wastewaters and taxonomic profiling of multi-resistant bacteria with potential for petroleum hydrocarbon catabolism in nitrogen-limiting medium. World J Microbiol Biotechnol 2023; 39:84. [PMID: 36693977 DOI: 10.1007/s11274-023-03524-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 01/11/2023] [Indexed: 01/26/2023]
Abstract
The coexistence of heavy metals (HMs) and petroleum hydrocarbons (PHs) exacerbates ecotoxicity and impair the drivers of eco-functionalities that stimulate essential nutrients for the productivity of the impacted environment. Profiling the bacteria that stem the ecological impact via HMs sequestration and PHs catabolism with nitrogen fixation is imperative to bioremediation of the polluted sites. The sediment of site that was consistently contaminated with industrial wastewaters was analysed for ecological toxicants and the bacterial strains that combined HMs resistance with PHs catabolism in a nitrogen-limiting system were isolated from the sediment and characterized. The geochemistry of the samples revealed the co-occurrence of the above-benchmark concentrations of HMs with the derivatives of hydrocarbons. Notwithstanding, nickel and mercury (with 5% each of the total metal concentrations in the polluted site) exhibited probable effect concentrations on the biota and thus hazardous to the ecosystem. Approx. 31% of the bacterial community, comprising unclassified Planococcaceae, unclassified Bradyrhizobiaceae, Rhodococcus, and Bacillus species, resisted 160 µmol Hg2+ in the nitrogen-limiting system within 24 h post-inoculation. The bacterial strains adopt volatilization, and sometimes in combination with adsorption/bioaccumulation strategies to sequester Hg2+ toxicity while utilizing PHs as sources of carbon and energy. Efficient metabolism of petroleum biomarkers (> 87%) and Hg2+ sequestration (≥ 75% of 40 µmol Hg2+) displayed by the selected bacterial strains portend the potential applicability of the bacilli for biotechnological restoration of the polluted site.
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Affiliation(s)
- Ganiyu O Oyetibo
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, 101017, Lagos State, Nigeria. .,Institute of Maritime Studies, University of Lagos, Akoka, Yaba, 101017, Lagos State, Nigeria.
| | - Sunday A Adebusoye
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, 101017, Lagos State, Nigeria
| | - Matthew O Ilori
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, 101017, Lagos State, Nigeria.,Institute of Maritime Studies, University of Lagos, Akoka, Yaba, 101017, Lagos State, Nigeria
| | - Olukayode O Amund
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, 101017, Lagos State, Nigeria.,Office of the Vice Chancellor, Elizade University, Ilara-Mokin, Ondo State, Nigeria
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Marimuthu J, Rangamaran VR, Subramanian SHS, Balachandran KRS, Thenmozhi Kulasekaran N, Vasudevan D, Lee JK, Ramalingam K, Gopal D. Deep-sea sediment metagenome from Bay of Bengal reveals distinct microbial diversity and functional significance. Genomics 2022; 114:110524. [PMID: 36423774 DOI: 10.1016/j.ygeno.2022.110524] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 11/06/2022] [Accepted: 11/20/2022] [Indexed: 11/23/2022]
Abstract
Bay of Bengal (BoB) has immense significance with respect to ecological diversity and natural resources. Studies on microbial profiling and their functional significance at sediment level of BoB remain poorly represented. Herein, we describe the microbial diversity and metabolic potentials of BOB deep-sea sediment samples by subjecting the metagenomes to Nanopore sequencing. Taxonomic diversity ascertained at various levels revealed that bacteria belonging to phylum Proteobacteria predominantly represented in sediment samples NIOT_S7 and NIOT_S9. A comparative study with 16S datasets from similar ecological sites revealed depth as a crucial factor in determining taxonomic diversity. KEGG annotation indicated that bacterial communities possess sequence reads corresponding to carbon dioxide fixation, sulfur, nitrogen metabolism, but at varying levels. Additionally, gene sequences related to bioremediation of dyes, plastics, hydrocarbon, antibiotic resistance, secondary metabolite synthesis and metal resistance from both the samples as studied indicate BoB to represent a highly diverse environmental niche for further exploration.
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Affiliation(s)
- Jeya Marimuthu
- Marine Biotechnology Division, National Institute of Ocean Technology, Chennai 600100, India.
| | | | | | | | | | - Dinakaran Vasudevan
- KMCH Research Foundation, Coimbatore Medical Center and Hospital, Coimbatore 641014, India
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul 143 701, Republic of Korea
| | - Kirubagaran Ramalingam
- Marine Biotechnology Division, National Institute of Ocean Technology, Chennai 600100, India
| | - Dharani Gopal
- Marine Biotechnology Division, National Institute of Ocean Technology, Chennai 600100, India.
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9
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Khandelwal A, Sugavanam R, Ramakrishnan B, Dutta A, Varghese E, Banerjee T, Nain L, Singh SB, Singh N. Bio-polysaccharide composites mediated degradation of polyaromatic hydrocarbons in a sandy soil using free and immobilized consortium of Kocuria rosea and Aspergillus sydowii. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:80005-80020. [PMID: 35220535 DOI: 10.1007/s11356-022-19252-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/12/2022] [Indexed: 06/14/2023]
Abstract
Based on our previous study in minimal medium, Kocuria rosea and Aspergillus sydowii were identified as the best microbes for degradation of mixture of polyaromatic hydrocarbons (PAHs). The present study reports PAH degradation potential of these microbes in free and immobilized form. PAHs were extracted using QuEChERS-mediated process followed by quantification by high performance liquid chromatography. The microbial consortium of Kocuria rosea + Aspergillus sydowii was formulated in three bio-formulations, namely (i) bentonite-alginate composite beads; (ii) water dispersible granule composite using guar gum-nanobentonite; and (iii) composites of carboxymethyl cellulose-bentonite and were applied in PAH fortified (100 µg g-1) sandy loam soil. Results suggested that degradation data fitted well to first order kinetics as in most of the cases, the values of correlation coefficient (r) were > 0.95. The half-life (t1/2) values for PAHs in the uninoculated control soil were: naphthalene (10.43 d), fluorene (22.43 d), phenanthrene (24.64 d), anthracene (38.47 d), and pyrene (34.34 d). Inoculation of soil with free culture microbial consortium (without or with nutrient) and bio-formulation of degrading cultures enhanced degradation of all PAHs and half-life values were significantly reduced for each PAH: naphthalene (1.76-2.00 d), fluorene (2.52-6.65 d), phenanthrene (4.61-6.37 d), anthracene (9.01-12.22 d), and pyrene (10.98-15.55 d). Among different bio-formulations, guar gum-nanobentonite-based composite exhibited better efficacy for degradation of naphthalene, fluorene, phenanthrene, anthracene, and pyrene. The addition of microbial consortium in PAH fortified soil increased 16S rRNA gene copies of Alphaproteobacteria and Bacteroidetes, compared to the uninoculated, PAH-fortified control. The microbial functional gene assays showed that the gene copies of amoA, nirK, nirS, and anammox increased, suggesting nitrogen regulation in the PAH-fortified soil.
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Affiliation(s)
- Ashish Khandelwal
- Division of Agricultural Chemicals, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India
- Division of Environment Science, ICAR- Indian Agricultural Research Institute, New Delhi, 110 012, India
| | - Ramya Sugavanam
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India
| | | | - Anirban Dutta
- Division of Agricultural Chemicals, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India
| | - Eldho Varghese
- Fishery Resources Assessment Division, ICAR-Central Marine Fisheries Research Institute, Kochi, 682 018, Kerala, India
| | - Tirthankar Banerjee
- Division of Agricultural Chemicals, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India
| | - Lata Nain
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India
| | - Shashi Bala Singh
- Division of Agricultural Chemicals, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India
| | - Neera Singh
- Division of Agricultural Chemicals, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India.
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10
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Palit K, Rath S, Chatterjee S, Das S. Microbial diversity and ecological interactions of microorganisms in the mangrove ecosystem: Threats, vulnerability, and adaptations. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:32467-32512. [PMID: 35182344 DOI: 10.1007/s11356-022-19048-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Mangroves are among the world's most productive ecosystems and a part of the "blue carbon" sink. They act as a connection between the terrestrial and marine ecosystems, providing habitat to countless organisms. Among these, microorganisms (e.g., bacteria, archaea, fungi, phytoplankton, and protozoa) play a crucial role in this ecosystem. Microbial cycling of major nutrients (carbon, nitrogen, phosphorus, and sulfur) helps maintain the high productivity of this ecosystem. However, mangrove ecosystems are being disturbed by the increasing concentration of greenhouse gases within the atmosphere. Both the anthropogenic and natural factors contribute to the upsurge of greenhouse gas concentration, resulting in global warming. Changing climate due to global warming and the increasing rate of human interferences such as pollution and deforestation are significant concerns for the mangrove ecosystem. Mangroves are susceptible to such environmental perturbations. Global warming, human interventions, and its consequences are destroying the ecosystem, and the dreadful impacts are experienced worldwide. Therefore, the conservation of mangrove ecosystems is necessary for protecting them from the changing environment-a step toward preserving the globe for better living. This review highlights the importance of mangroves and their microbial components on a global scale and the degree of vulnerability of the ecosystems toward anthropic and climate change factors. The future scenario of the mangrove ecosystem and the resilience of plants and microbes have also been discussed.
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Affiliation(s)
- Krishna Palit
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Sonalin Rath
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Shreosi Chatterjee
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India.
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Wang X, Teng Y, Ren W, Han Y, Wang X, Li X. Soil bacterial diversity and functionality are driven by plant species for enhancing polycyclic aromatic hydrocarbons dissipation in soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:149204. [PMID: 34346367 DOI: 10.1016/j.scitotenv.2021.149204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 07/13/2021] [Accepted: 07/18/2021] [Indexed: 05/27/2023]
Abstract
Plant-microorganisms symbiosis has been widely used in developing strategies for the rhizoremediation of polycyclic aromatic hydrocarbon (PAHs) contaminated agricultural soils. However, understanding the potential mechanisms for using complex plant-microbe interactions to enhance rhizoremediation in contaminated soils is still limited. In this study, rhizosphere microbiomes were established by cultivating four types of cover crops for 15 months in a PAHs-contaminated field. The results showed that the PAHs removal rates were significantly higher in rhizosphere soils (55.2-82.3%) than the bare soils (20.5%). Of the four cover crops, the rhizosphere soils associated with the alfalfa and clover had higher removal rates for high molecular weight (HMW) PAHs (78.5-87.1%) than the grasses (39.0-46.2%). High-throughput sequencing analysis showed that bacterial community structure between the planted and bare soils, and among four cover crops rhizosphere soils were significantly different. The rhizosphere soils associated with the alfalfa and clover had more abundant degradation-related taxa. Correlation network analysis showed that bacterial communities with high removal rates have stronger interactions. Metagenome analysis indicated that the relative abundance of the key functional genes involved in PAHs degradation and nutrient metabolisms were significantly higher in rhizosphere soils, especially for alfalfa and clover. Overall, this study provides new insights for us to understand the mechanisms by different plants enhancing PAHs dissipation from the viewpoint of microbiology.
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Affiliation(s)
- Xia Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Wenjie Ren
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yujuan Han
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiaomi Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiufen Li
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
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Semanti P, Robin RS, Purvaja R, Ramesh R. Fatty acid signatures of sediment microbial community in the chronically polluted mangrove ecosystem. MARINE POLLUTION BULLETIN 2021; 172:112885. [PMID: 34461371 DOI: 10.1016/j.marpolbul.2021.112885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 08/14/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Phospholipid fatty acid (PLFA) analysis was used to examine variation in the distribution of microbial communities in heavily polluted mangrove sediments of Thane creek, west coast of India. A total of 40 individual PLFAs representing 11 functional groups were identified in the sediment and were mainly dominated by saturated fatty acids (anaerobic prokaryotes) >50%. Significant dominance of PUFA, 16:3 ω6c (34.2%) indicators of micro-eukaryotes, in subsurface depth (p < 0.05) suggests input from the remnants of marine microalgae. Declined mean relative abundance of fungi (<6%) and actinomycetes (<1%) were detected in the sediment indicating their sensitivity to anthropic stressors. Homogenous profile of microbial diversity indicating active bioturbation. Cumulative metabolic stress evident from SAT/MUFA (>1), B/F (>1) and G+/G- (<1) ratio and prolonged hypoxia to be prevalent in the creek during the study. In conclusion, PLFA signatures can thus be used as potential biomarkers of environmental monitoring and proxy for interpreting ecosystem health.
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Affiliation(s)
- P Semanti
- National Centre for Sustainable Coastal Management, Ministry of Environment, Forest and Climate Change, Chennai 600 025, India
| | - R S Robin
- National Centre for Sustainable Coastal Management, Ministry of Environment, Forest and Climate Change, Chennai 600 025, India
| | - R Purvaja
- National Centre for Sustainable Coastal Management, Ministry of Environment, Forest and Climate Change, Chennai 600 025, India
| | - R Ramesh
- National Centre for Sustainable Coastal Management, Ministry of Environment, Forest and Climate Change, Chennai 600 025, India.
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Wang C, Gao H, Chen J, Wang P, Zhang J, Hu Y, Pan Y. Long-term effects of decabromodiphenyl ether on denitrification in eutrophic lake sediments: Different sensitivity of six-type denitrifying bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 774:145147. [PMID: 33609823 DOI: 10.1016/j.scitotenv.2021.145147] [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: 12/01/2020] [Revised: 01/07/2021] [Accepted: 01/09/2021] [Indexed: 05/28/2023]
Abstract
The widespread use of polybrominated diphenyl ethers inevitably results in their increased release into natural waters and subsequent deposition in sediments. However, their long-term effects on the bacteria participating in each step of denitrification in eutrophic lake sediments are still unknown. Here, we conducted a one-year microcosm experiment to determine the long-term effects of decabromodiphenyl ether (BDE-209), at low (2 mg kg-1 dry weight) and high (20 mg kg-1 dry weight) contamination levels, on six-type denitrifying bacteria and their activities in sediments collected from Taihu Lake, a typical eutrophic lake in China. At the end of the experiment, sediment denitrifying reductase activities were inhibited by BDE-209 at both levels, with the greatest inhibition seen for nitric oxide reductase activity. The higher nitrate concentration in the contaminated sediments was attributed to the inhibition of nitrate reductase activities. The abundances of six-type denitrifying genes (narG, napA, nirK, nirS, norB, and nosZ) significantly decreased under high BDE-209 treatment, and narG and napA genes were more sensitive to the toxicity of BDE-209. The results from pyrosequencing showed that BDE-209, at either treatment concentration, decreased the six-type denitrifying bacterial diversities and altered their community composition. This shift of six-type denitrifying bacterial communities might also be driven by the debrominated products concentrations of BDE-209 and variations in sediment inorganic nitrogen concentrations. In particular, some genera from phylum Proteobacteria such as Pseudomonas, Cupriavidus, and Azoarcus were decreased significantly because of BDE-209 and its debrominated products.
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Affiliation(s)
- Chao Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Han Gao
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China.
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Jingjing Zhang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Yu Hu
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Ying Pan
- School of Ecology, Sun Yat-sen University, Guangzhou 510275, PR China
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Gao Y, Du J, Bahar MM, Wang H, Subashchandrabose S, Duan L, Yang X, Megharaj M, Zhao Q, Zhang W, Liu Y, Wang J, Naidu R. Metagenomics analysis identifies nitrogen metabolic pathway in bioremediation of diesel contaminated soil. CHEMOSPHERE 2021; 271:129566. [PMID: 33460896 DOI: 10.1016/j.chemosphere.2021.129566] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 11/11/2020] [Accepted: 01/02/2021] [Indexed: 06/12/2023]
Abstract
Nitrogen amendment is known to effectively enhance the bioremediation of hydrocarbon-contaminated soil, but the nitrogen metabolism in this process is not well understood. To unravel the nitrogen metabolic pathway(s) of diesel contaminated soil, six types of nitrogen sources were added to the diesel contaminated soil. Changes in microbial community and soil enzyme genes were investigated by metagenomics analysis and chemical analysis through a 30-day incubation study. The results showed that ammonium based nitrogen sources significantly accelerated the degradation of total petroleum hydrocarbon (TPH) (79-81%) compared to the control treatment (38%) and other non-ammonium based nitrogen amendments (43-57%). Different types of nitrogen sources could dramatically change the microbial community structure and soil enzyme gene abundance. Proteobacteria and Actinobacteria were identified as the two dominant phyla in the remediation of diesel contaminated soil. Metagenomics analysis revealed that the preferred metabolic pathway of nitrogen was from ammonium to glutamate via glutamine, and the enzymes governing this transformation were glutamine synthetase and glutamate synthetase; while in nitrate based amendment, the conversion from nitrite to ammonium was restrained by the low abundance of nitrite reductase enzyme and therefore retarded the TPH degradation rate. It is concluded that during the process of nitrogen enhanced bioremediation, the most efficient nitrogen cycling direction was from ammonium to glutamine, then to glutamate, and finally joined with carbon metabolism after transforming to 2-oxoglutarate.
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Affiliation(s)
- Yongchao Gao
- Qilu University of Technology (Shandong Academy of Sciences), Ecology Institute, Shandong Provincial Key Laboratory of Applied Microbiology, 28789 East Jingshi Road, Jinan, 250103, China; Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, Callaghan, NSW, 2308, Australia.
| | - Jianhua Du
- Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Md Mezbaul Bahar
- Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Hui Wang
- School of Resources and Environment, University of Jinan, Jinan, 250022, China
| | - Suresh Subashchandrabose
- Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Luchun Duan
- Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Xiaodong Yang
- Department of Geography & Spatial Information Technology, Ningbo University, Ningbo, 315211, China
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Qingqing Zhao
- Qilu University of Technology (Shandong Academy of Sciences), Ecology Institute, Shandong Provincial Key Laboratory of Applied Microbiology, 28789 East Jingshi Road, Jinan, 250103, China
| | - Wen Zhang
- Qilu University of Technology (Shandong Academy of Sciences), Ecology Institute, Shandong Provincial Key Laboratory of Applied Microbiology, 28789 East Jingshi Road, Jinan, 250103, China
| | - Yanju Liu
- Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Jianing Wang
- Qilu University of Technology (Shandong Academy of Sciences), Ecology Institute, Shandong Provincial Key Laboratory of Applied Microbiology, 28789 East Jingshi Road, Jinan, 250103, China
| | - Ravi Naidu
- Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, Callaghan, NSW, 2308, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environment, Australia.
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Han X, Wang F, Zhang D, Feng T, Zhang L. Nitrate-assisted biodegradation of polycyclic aromatic hydrocarbons (PAHs) in the water-level-fluctuation zone of the three Gorges Reservoir, China: Insights from in situ microbial interaction analyses and a microcosmic experiment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115693. [PMID: 33002789 DOI: 10.1016/j.envpol.2020.115693] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 09/13/2020] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
Abstract
An increase in polycyclic aromatic hydrocarbon (PAH) pollution poses significant challenges to human and ecosystem health in the Three Gorges Reservoir (TGR) of the Yangtze River. Based on the combination of PAH analysis with qPCR and high-throughput sequencing of bacteria, 32 topsoil samples collected from 16 sites along the TGR were used to investigate the distribution and biodegradation pathways of PAHs in the water-level-fluctuation zone (WLFZ). The results indicated that the concentrations of PAHs were 43.8-228.2 and 30.8-206.3 ng/g soil (dry weight) under the high- and low-water-level (HWL and LWL) conditions, respectively. The PAH concentration in urban areas was higher than that in rural areas. Under both the HWL and LWL conditions, the abundance of the bamA gene, a biomarker of anaerobic PAH biodegradation, was significantly higher than that of the ring-hydroxylating-dioxygenase (RHD) gene, a biomarker of aerobic PAH biodegradation. The abundance of the bamA gene was significantly positively correlated with PAHs (R2 = 0.8), and the biodegradation percentage of PAHs incubated anaerobically was greater than that in the aerobically incubated microcosm experiments. These data implicated a key role of the anaerobic pathway in PAH biodegradation. Co-occurrence network analysis suggested that anaerobic Anaerolineaceae, Dechloromonas, Bacteroidetes_vadin HA17 and Geobacter were key participants in the biodegradation of PAHs. The diversity analysis of functional bacteria based on the bamA gene and microcosm experiments further demonstrated that nitrate was the primary electron acceptor for PAH biodegradation. These findings provide a new perspective on the mechanism of PAH biodegradation in the TGR and knowledge that can be used to develop strategies for environmental management.
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Affiliation(s)
- Xinkuan Han
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, China; Department of Environmental Science, Chongqing University, Chongqing, 400044, China
| | - Fengwen Wang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, China; Department of Environmental Science, Chongqing University, Chongqing, 400044, China
| | - Daijun Zhang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, China; Department of Environmental Science, Chongqing University, Chongqing, 400044, China.
| | - Ting Feng
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, China; Department of Environmental Science, Chongqing University, Chongqing, 400044, China
| | - Lilan Zhang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, China; Department of Environmental Science, Chongqing University, Chongqing, 400044, China
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16
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Chemical Profiling Provides Insights into the Metabolic Machinery of Hydrocarbon-Degrading Deep-Sea Microbes. mSystems 2020; 5:5/6/e00824-20. [PMID: 33172970 PMCID: PMC7657597 DOI: 10.1128/msystems.00824-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine microbes are known to degrade hydrocarbons; however, microbes inhabiting deep-sea sediments remain largely unexplored. Previous studies into the classical pathways of marine microbial metabolism reveal diverse chemistries; however, metabolic profiling of marine microbes cultured with hydrocarbons is limited. In this study, taxonomic (amplicon sequencing) profiles of two environmental deep-sea sediments (>1,200 m deep) were obtained, along with taxonomic and metabolomic (mass spectrometry-based metabolomics) profiles of microbes harbored in deep-sea sediments cultured with hydrocarbons as the sole energy source. Samples were collected from the Gulf of México (GM) and cultured for 28 days using simple (toluene, benzene, hexadecane, and naphthalene) and complex (petroleum API 40) hydrocarbon mixtures as the sole energy sources. The sediment samples harbored diverse microbial communities predominantly classified into Woeseiaceae and Kiloniellaceae families, whereas Pseudomonadaceae and Enterobacteriaceae families prevailed after sediments were cultured with hydrocarbons. Chemical profiling of microbial metabolomes revealed diverse chemical groups belonging primarily to the lipids and lipid-like molecules superclass, as well as the organoheterocyclic compound superclass (ClassyFire annotation). Metabolomic data and prediction of functional profiles indicated an increase in aromatic and alkane degradation in samples cultured with hydrocarbons. Previously unreported metabolites, identified as intermediates in the degradation of hydrocarbons, were annotated as hydroxylated polyunsaturated fatty acids and carboxylated benzene derivatives. In summary, this study used mass spectrometry-based metabolomics coupled to chemoinformatics to demonstrate how microbes from deep-sea sediments could be cultured in the presence of hydrocarbons. This study also highlights how this experimental approach can be used to increase the understanding of hydrocarbon degradation by deep-sea sediment microbes.IMPORTANCE High-throughput technologies and emerging informatics tools have significantly advanced knowledge of hydrocarbon metabolism by marine microbes. However, research into microbes inhabiting deep-sea sediments (>1,000 m) is limited compared to those found in shallow waters. In this study, a nontargeted and nonclassical approach was used to examine the diversity of bacterial taxa and the metabolic profiles of hydrocarbon-degrading deep-sea microbes. In conclusion, this study used metabolomics and chemoinformatics to demonstrate that microbes from deep-sea sediment origin thrive in the presence of toxic and difficult-to-metabolize hydrocarbons. Notably, this study provides evidence of previously unreported metabolites and the global chemical repertoire associated with the metabolism of hydrocarbons by deep-sea microbes.
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Zhao R, Summers ZM, Christman GD, Yoshimura KM, Biddle JF. Metagenomic views of microbial dynamics influenced by hydrocarbon seepage in sediments of the Gulf of Mexico. Sci Rep 2020; 10:5772. [PMID: 32238866 PMCID: PMC7113308 DOI: 10.1038/s41598-020-62840-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 03/16/2020] [Indexed: 12/12/2022] Open
Abstract
Microbial cells in the seabed are thought to persist by slow population turnover rates and extremely low energy requirements. External stimulations such as seafloor hydrocarbon seeps have been demonstrated to significantly boost microbial growth; however, the microbial community response has not been fully understood. Here we report a comparative metagenomic study of microbial response to natural hydrocarbon seeps in the Gulf of Mexico. Subsurface sediments (10-15 cm below seafloor) were collected from five natural seep sites and two reference sites. The resulting metagenome sequencing datasets were analyzed with both gene-based and genome-based approaches. 16S rRNA gene-based analyses suggest that the seep samples are distinct from the references by both 16S rRNA fractional content and phylogeny, with the former dominated by ANME-1 archaea (~50% of total) and Desulfobacterales, and the latter dominated by the Deltaproteobacteria, Planctomycetes, and Chloroflexi phyla. Sulfate-reducing bacteria (SRB) are present in both types of samples, with higher relative abundances in seep samples than the references. Genes for nitrogen fixation were predominantly found in the seep sites, whereas the reference sites showed a dominant signal for anaerobic ammonium oxidation (anammox). We recovered 49 metagenome-assembled genomes and assessed the microbial functional potentials in both types of samples. By this genome-based analysis, the seep samples were dominated by ANME-1 archaea and SRB, with the capacity for methane oxidation coupled to sulfate reduction, which is consistent with the 16S rRNA-gene based characterization. Although ANME-1 archaea and SRB are present in low relative abundances, genome bins from the reference sites are dominated by uncultured members of NC10 and anammox Scalindua, suggesting a prevalence of nitrogen transformations for energy in non-seep pelagic sediments. This study suggests that hydrocarbon seeps can greatly change the microbial community structure by stimulating nitrogen fixation, inherently shifting the nitrogen metabolism compared to those of the reference sediments.
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Affiliation(s)
- Rui Zhao
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States
| | - Zarath M Summers
- Corporate Strategic Research, ExxonMobil Research and Engineering, Annandale, NJ, United States
| | - Glenn D Christman
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States
| | - Kristin M Yoshimura
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States
| | - Jennifer F Biddle
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States.
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18
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Gaget V, Hobson P, Keulen A, Newton K, Monis P, Humpage AR, Weyrich LS, Brookes JD. Toolbox for the sampling and monitoring of benthic cyanobacteria. WATER RESEARCH 2020; 169:115222. [PMID: 31675609 DOI: 10.1016/j.watres.2019.115222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 10/10/2019] [Accepted: 10/21/2019] [Indexed: 06/10/2023]
Abstract
Benthic cyanobacteria are a nuisance because they produce highly potent toxins and taste and odour compounds. Despite this, benthic cyanobacteria remain far less studied than their planktonic counterparts. For example, little is known about their growth or the seasonality of their secondary metabolite production. Moreover, sampling and monitoring techniques commonly used for the survey of planktonic species are not necessarily applicable to benthic forms. This study aimed to develop and validate a new sampling device for the routine monitoring of benthic mats. Molecular monitoring techniques were established and validated on environmental samples collected in a South Australian reservoir (SA-L2). A total of eight qPCR assays were applied to samples in order to track seasonal variations in cyanobacteria concentrations and associated secondary metabolite production. Next Generation Sequencing was utilised to conduct a microbial community composition analysis and to select the most appropriate substrate material for the sampling of benthic cyanobacteria. The concentration of the secondary metabolites geosmin and 2-methyl-isoborneol were quantified using High-Performance Liquid Chromatography, and concentrations of key nutrients (N, P) were quantified in water samples. The sampling device designed proved efficient and easy to use in the field. The qPCR assay designed for the amplification of the cyanobacterial MIB synthase had a high efficiency with a minimum limit of quantification of 4 cell-equivalents per reaction and identified a potential source of MIB in SA-L2 Reservoir. The peak season for benthic growth and secondary metabolite production was observed in spring. Proportionally, 35% of the variability in water geosmin concentrations can be explained by benthic actinobacterial and cyanobacterial activity, showing that freshwater benthic mats represent a significant source of taste and odour compounds.
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Affiliation(s)
- Virginie Gaget
- Water Research Centre, Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of Adelaide, South Australia, 5005, Australia.
| | - Peter Hobson
- Australian Water Quality Centre, South Australia Water Corporation, Adelaide, South Australia, 5000, Australia
| | - Angela Keulen
- Water Research Centre, Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of Adelaide, South Australia, 5005, Australia
| | - Kelly Newton
- Australian Water Quality Centre, South Australia Water Corporation, Adelaide, South Australia, 5000, Australia
| | - Paul Monis
- Water Research Centre, Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of Adelaide, South Australia, 5005, Australia; Australian Water Quality Centre, South Australia Water Corporation, Adelaide, South Australia, 5000, Australia
| | - Andrew R Humpage
- Australian Water Quality Centre, South Australia Water Corporation, Adelaide, South Australia, 5000, Australia
| | - Laura S Weyrich
- Australian Centre for Ancient DNA, Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of Adelaide, South Australia, 5005, Australia
| | - Justin D Brookes
- Water Research Centre, Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of Adelaide, South Australia, 5005, Australia
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Falk N, Reid T, Skoyles A, Grgicak-Mannion A, Drouillard K, Weisener CG. Microbial metatranscriptomic investigations across contaminant gradients of the Detroit River. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 690:121-131. [PMID: 31284186 DOI: 10.1016/j.scitotenv.2019.06.451] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 06/09/2023]
Abstract
Microbial community function in freshwater sediments is influenced by the presence and persistence of anthropogenic pollutants, yet simultaneously imposes significant control on their transformation. Thus, microbes provide valuable ecosystem services in terms of biodegradation and bioindicators of compromised habitats. From a remediation perspective it is valuable to leverage the suite of microbial genes at the transcriptional level that are active in either natural versus stressed environments to provide insight into the cycling and fate of contaminants. Metatranscriptomic analysis of total bacterial and archaeal messenger RNA (mRNA) is a useful tool in this facet and was applied to sediments sampled from the Detroit River; a binational Area of Concern (AOC) in the Great Lakes. Previously established sediment surveys and modelling delineated the river into contaminant gradients based on concentrations of polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and metals. Differential expression analysis through DESeq2 revealed that microbial transcripts associated with nitrate reduction, methanogenesis, and beta-oxidation were significant in legacy polluted sediments and linked with energetic pathways key in the generation of cellular currencies (acetyl-CoA, succinyl-CoA). Gluconeogenesis and polyester synthesis also showed high abundance in contaminated regions, along with increased expression of stress response genes and transposons, despite decreases in community α-diversity. Aromatic cleavage genes were detected, but in low abundance across the contaminant gradient. These results suggest that microbial communities within the Detroit River exploit unique anabolic and catabolic pathways to derive and store energy from legacy organic contaminants while simultaneously recruiting stress-response and gene transfer mechanisms to cope with xenobiotic pressures. By coupling well-resolved chemical datasets with metatranscriptomics, this study adds to the spatial understanding of in-situ microbial activities in pristine and perturbed freshwater sediments.
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Affiliation(s)
- N Falk
- Great Lakes Institute for Environmental Research, University of Windsor, 2990 Riverside Dr W, Windsor, ON N9C 1A2, Canada.
| | - T Reid
- Great Lakes Institute for Environmental Research, University of Windsor, 2990 Riverside Dr W, Windsor, ON N9C 1A2, Canada
| | - A Skoyles
- Great Lakes Institute for Environmental Research, University of Windsor, 2990 Riverside Dr W, Windsor, ON N9C 1A2, Canada
| | - A Grgicak-Mannion
- Great Lakes Institute for Environmental Research, University of Windsor, 2990 Riverside Dr W, Windsor, ON N9C 1A2, Canada
| | - K Drouillard
- Great Lakes Institute for Environmental Research, University of Windsor, 2990 Riverside Dr W, Windsor, ON N9C 1A2, Canada
| | - C G Weisener
- Great Lakes Institute for Environmental Research, University of Windsor, 2990 Riverside Dr W, Windsor, ON N9C 1A2, Canada
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20
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Zhang S, Hu Z, Wang H. Metagenomic analysis exhibited the co-metabolism of polycyclic aromatic hydrocarbons by bacterial community from estuarine sediment. ENVIRONMENT INTERNATIONAL 2019; 129:308-319. [PMID: 31150973 DOI: 10.1016/j.envint.2019.05.028] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/15/2019] [Accepted: 05/08/2019] [Indexed: 06/09/2023]
Abstract
The bacterial community from estuarine sediment undertakes the bioremediation and energy transformation of anthropogenic pollutants especially polycyclic aromatic hydrocarbons (PAHs). However, information and studies on bacterial synergism and related metabolic profiles under the stress of PAHs are limited. In this study, sediments from estuarine were collected and co-incubated with a classical PAH, pyrene. The results showed that Alpha- and Gammaproteobacteria became abundant at the late domesticating phase with the dominant genus of ZD0117, the uncultivated bacteria affiliated into Gammaproteobacteria. Functional gene analysis based on metagenomic sequencing showed that quantitatively changes of genes directly related to the degradation of aromatic hydrocarbon coordinated with genes involved into various metabolic pathways such as acylglycerol degradation, nitrogen fixation, sulfate transport system, Arnon-Buchanan cycle, and Calvin cycle (P < 0.01 and |ρ| > 0.8). Fifty-six metagenome-assembled genomes (MAGs) were reconstructed, which were primarily composed by Alpha- and Gammaproteobacteria. Bacteria belonging to the phylum Proteobacteria were found to be abundant in MAGs and contained genes encoding for dehydrogenase, which are key enzymes for pyrene degradation. In addition, genomes of uncultivated bacteria were successfully reconstructed and were proven to carry genes of synergistically metabolizing pyrene. Based on analysis of typical MAGs, the metabolic pathways involved in syntrophic associations of a pyrene-degrading consortium were reconstructed. The results in this study could make us fully understand the metabolic patterns of pyrene-degrading consortium from the estuarine sediment and widen the scope of functional bacteria.
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Affiliation(s)
- Shuangfei Zhang
- Biology Department, College of Science, Shantou University, Shantou 515063, China
| | - Zhong Hu
- Biology Department, College of Science, Shantou University, Shantou 515063, China
| | - Hui Wang
- Biology Department, College of Science, Shantou University, Shantou 515063, China.
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21
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Chen J, McIlroy SE, Archana A, Baker DM, Panagiotou G. A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments. MICROBIOME 2019; 7:104. [PMID: 31307536 PMCID: PMC6632204 DOI: 10.1186/s40168-019-0714-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 06/17/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND Coastal marine environments are one of the most productive ecosystems on Earth. However, anthropogenic impacts exert significant pressure on coastal marine biodiversity, contributing to functional shifts in microbial communities and human health risk factors. However, relatively little is known about the impact of eutrophication-human-derived nutrient pollution-on the marine microbial biosphere. RESULTS Here, we tested the hypothesis that benthic microbial diversity and function varies along a pollution gradient, with a focus on human pathogens and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG annotation revealed that zinc, lead, total volatile solids, and ammonia nitrogen were correlated with microbial diversity and function. We propose several microbes, including Planctomycetes and sulfate-reducing microbes as candidates to reflect pollution concentration. Annotation of antibiotic resistance genes showed that the highest abundance of efflux pumps was found at the most polluted site, corroborating the relationship between pollution and human health risk factors. This result suggests that sediments at polluted sites harbor microbes with a higher capacity to reduce intracellular levels of antibiotics, heavy metals, or other environmental contaminants. CONCLUSIONS Our findings suggest a correlation between pollution and the marine sediment microbiome and provide insight into the role of high-turnover microbial communities as well as potential pathogenic organisms as real-time indicators of water quality, with implications for human health and demonstrate the inner functional shifts contributed by the microcommunities.
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Affiliation(s)
- Jiarui Chen
- Systems Biology & Bioinformatics Group, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, China
| | - Shelby E McIlroy
- Swire Institute of Marine Science, The University of Hong Kong, Hong Kong SAR, China
| | - Anand Archana
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Kadoorie Biological Sciences Building, Pok Fu Lam Road, Hong Kong SAR, China
| | - David M Baker
- Swire Institute of Marine Science, The University of Hong Kong, Hong Kong SAR, China.
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Kadoorie Biological Sciences Building, Pok Fu Lam Road, Hong Kong SAR, China.
| | - Gianni Panagiotou
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoll Institute, Beutenbergstrasse 11a, Jena, 07745, Germany.
- Department of Microbiology Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- Systems Biology & Bioinformatics Group, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, China.
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22
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Reid T, Droppo IG, Chaganti SR, Weisener CG. Microbial metabolic strategies for overcoming low-oxygen in naturalized freshwater reservoirs surrounding the Athabasca Oil Sands: A proxy for End-Pit Lakes? THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 665:113-124. [PMID: 30772540 DOI: 10.1016/j.scitotenv.2019.02.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 02/01/2019] [Accepted: 02/02/2019] [Indexed: 06/09/2023]
Abstract
The success and sustainability of aquatic ecosystems are driven by the complex, cooperative metabolism of microbes. Ecological engineering strategies often strive to harness this syntrophic synergy of microbial metabolism for the reclamation of contaminated environments worldwide. Currently, there is a significant knowledge gap in our understanding of how the natural microbial ecology overcomes thermodynamic limitations in recovering contaminated environments. Here, we used in-situ metatranscriptomics and associated metataxonomic analyses on sediments collected from naturalized freshwater man-made reservoirs within the Athabasca Oil Sands region of Alberta, Canada. These reservoirs are unique since they are untouched by industrial mining processes and serve as representative endpoints for model landscape reconstruction. Results indicate that a microbial syntrophic cooperation has been established represented by the oxygenic and anoxygenic phototrophs, sustained through the efficient use of novel cellular mechanistic adaptations tailored to these unique thermodynamic conditions. Specifically, chemotaxis transcripts (cheY & MCPs-methyl-accepting chemotaxis proteins) were highly expressed, suggesting a highly active microbial response to gradients in environmental stimuli, resulting indirectly from hydrocarbon compound alteration. A high expression of photosynthetic activity, likely sustaining nutrient delivery to the similarly highly expressed methanogenic community acting in syntrophy during the breakdown of organics. Overall the more diversified functionality within sub-oxic sample locations indicates an ability to maintain efficient metabolism under thermodynamic constraints. This is the first study to holistically identify and characterize these types of in-situ, metabolic processes and address their thermodynamic feasibility within a global context for large landscape reconstruction. These characterizations of regional, natural landscapes surrounding the oil sands mining operation are severely lacking, but truly provide invaluable insight into end-point goals and targets for reclamation procedures.
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Affiliation(s)
- Thomas Reid
- Great Lakes Institute for Environmental Research, 401 Sunset Ave, University of Windsor, Windsor, Ontario N9B 3P4, Canada.
| | - Ian G Droppo
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - Subba Rao Chaganti
- Great Lakes Institute for Environmental Research, 401 Sunset Ave, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Christopher G Weisener
- Great Lakes Institute for Environmental Research, 401 Sunset Ave, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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23
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Easson CG, Lopez JV. Depth-Dependent Environmental Drivers of Microbial Plankton Community Structure in the Northern Gulf of Mexico. Front Microbiol 2019; 9:3175. [PMID: 30662434 PMCID: PMC6328475 DOI: 10.3389/fmicb.2018.03175] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/07/2018] [Indexed: 02/01/2023] Open
Abstract
The Gulf of Mexico (GoM) is a dynamic marine ecosystem influenced by multiple natural and anthropogenic processes and inputs, such as the intrusion of warm oligotrophic water via the Loop Current, freshwater and nutrient input by the Mississippi River, and hydrocarbon inputs via natural seeps and industrial spills. Microbial plankton communities are important to pelagic food webs including in the GoM but understanding the drivers of the natural dynamics of these passively distributed microorganisms can be challenging in such a large and heterogeneous system. As part of the DEEPEND consortium, we applied high throughput 16S rRNA sequencing to investigate the spatial and temporal dynamics of pelagic microbial plankton related to several environmental conditions during two offshore cruises in 2015. Our results show dramatic community shifts across depths, especially between photic and aphotic zones. Though we only have two time points within a single year, observed temporal shifts in microbial plankton communities were restricted to the seasonally influenced epipelagic zone (0-200 m), and appear mainly driven by changes in temperature. Environmental selection in microbial plankton communities was depth-specific, with variables such as turbidity, salinity, and abundance of photosynthetic taxa strongly correlating with community structure in the epipelagic zone, while variables such as oxygen and specific nutrient concentrations were correlated with community structure at deeper depths.
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Affiliation(s)
- Cole G. Easson
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, United States
| | - Jose V. Lopez
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL, United States
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24
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Tatariw C, Flournoy N, Kleinhuizen AA, Tollette D, Overton EB, Sobecky PA, Mortazavi B. Salt marsh denitrification is impacted by oiling intensity six years after the Deepwater Horizon oil spill. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 243:1606-1614. [PMID: 30296756 DOI: 10.1016/j.envpol.2018.09.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/22/2018] [Accepted: 09/05/2018] [Indexed: 06/08/2023]
Abstract
Coastal salt marshes provide the valuable ecosystem service of removing anthropogenic nitrogen (N) via microbially-mediated denitrification. During the 2010 Deepwater Horizon (DWH) spill, oil exposure killed marsh plants in some regions and contributed to rapid compositional shifts in sediment microbial communities, which can impact ecosystem denitrification capacity. Within 3-5 years of the spill, plant biomass and microbial communities in some impacted marshes can recover to a new stable state. The objective of this study was to determine whether marsh recovery 6 years after the DWH oil spill results in subsequent recovery of denitrification capacity. We measured denitrification capacity (isotope pairing technique), microbial 16S rRNA gene composition, and denitrifier abundance (quantitative PCR) at sites subjected to light, moderate, and heavy oiling during the spill that were not targeted by any clean-up efforts. There were no differences in plant belowground biomass, sediment extractable NH4+, inorganic nitrogen flux, 16S rRNA composition, 16S rRNA diversity, or denitrifier functional gene (nirS, norB, and nosZ) abundances associated with oiling status, indicating that certain drivers of ecosystem denitrification capacity have recovered or achieved a new stable state six years after the spill. However, on average, denitrification capacities at the moderately and heavily oiled sites were less than 49% of that of the lightly oiled site (27.7 ± 14.7 and 37.2 ± 24.5 vs 71.8 ± 33.8 μmol N m-2 h-1, respectively). The presence of heavily weathered oiled residue (matched and non-matched for MC252) had no effect on process rates or microbial composition. The loss of function at the moderately and heavily oiled sites compared to the lightly oiled site despite the comparable microbial and environmental factors suggests that oiling intensity plays a role in the long-term recovery of marsh ecosystem services.
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Affiliation(s)
- Corianne Tatariw
- University of Alabama, Department of Biological Sciences, Tuscaloosa, AL, 35487, United States; Dauphin Island Sea Lab, 101 Bienville Blvd Dauphin Island, Dauphin Island, AL, 36528, United States.
| | - Nikaela Flournoy
- University of Alabama, Department of Biological Sciences, Tuscaloosa, AL, 35487, United States
| | - Alice A Kleinhuizen
- University of Alabama, Department of Biological Sciences, Tuscaloosa, AL, 35487, United States; Dauphin Island Sea Lab, 101 Bienville Blvd Dauphin Island, Dauphin Island, AL, 36528, United States
| | - Derek Tollette
- University of Alabama, Department of Biological Sciences, Tuscaloosa, AL, 35487, United States; Dauphin Island Sea Lab, 101 Bienville Blvd Dauphin Island, Dauphin Island, AL, 36528, United States
| | - Edward B Overton
- Department of Environmental Sciences, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Patricia A Sobecky
- University of Alabama, Department of Biological Sciences, Tuscaloosa, AL, 35487, United States
| | - Behzad Mortazavi
- University of Alabama, Department of Biological Sciences, Tuscaloosa, AL, 35487, United States; Dauphin Island Sea Lab, 101 Bienville Blvd Dauphin Island, Dauphin Island, AL, 36528, United States.
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25
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Calderoli PA, Espínola FJ, Dionisi HM, Gil MN, Jansson JK, Lozada M. Predominance and high diversity of genes associated to denitrification in metagenomes of subantarctic coastal sediments exposed to urban pollution. PLoS One 2018; 13:e0207606. [PMID: 30496195 PMCID: PMC6264515 DOI: 10.1371/journal.pone.0207606] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 11/02/2018] [Indexed: 11/20/2022] Open
Abstract
The aim of this work was to characterize the microbial nitrogen cycling potential in sediments from Ushuaia Bay, a subantarctic environment that has suffered a recent explosive demographic growth. Subtidal sediment samples were retrieved in triplicate from two urban points in the Bay, and analyzed through metagenomic shotgun sequencing. Sequences assigned to genes related to nitrification, nitrate reduction and denitrification were predominant in this environment with respect to metagenomes from other environments, including other marine sediments. The nosZ gene, responsible for nitrous oxide transformation into di-nitrogen, presented a high diversity. The majority of NosZ sequences were classified as Clade II (atypical) variants affiliated to different bacterial lineages such as Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, Verrucomicrobia, as well as to Archaea. The analysis of a fosmid metagenomic library from the same site showed that the genomic context of atypical variants was variable, and was accompanied by distinct regulatory elements, suggesting the evolution of differential ecophysiological roles. This work increases our understanding of the microbial ecology of nitrogen transformations in cold coastal environments and provides evidence of an enhanced denitrification potential in impacted sediment microbial communities. In addition, it highlights the role of yet overlooked populations in the mitigation of environmentally harmful forms of nitrogen.
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Affiliation(s)
- Priscila A Calderoli
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
| | - Fernando J Espínola
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
| | - Hebe M Dionisi
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
| | - Mónica N Gil
- Laboratorio de Oceanografía Química y Contaminación de Aguas, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina.,Laboratorio de Química General y Análisis de Elementos, CCT CONICET CENPAT, Puerto Madryn, Chubut Province, Argentina
| | - Janet K Jansson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Mariana Lozada
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
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26
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Urakawa H, Rajan S, Feeney ME, Sobecky PA, Mortazavi B. Ecological response of nitrification to oil spills and its impact on the nitrogen cycle. Environ Microbiol 2018; 21:18-33. [DOI: 10.1111/1462-2920.14391] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 08/11/2018] [Accepted: 08/17/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Hidetoshi Urakawa
- Department of Marine and Ecological Sciences Florida Gulf Coast University Fort Myers FL, 33965 USA
| | - Suja Rajan
- Department of Biological Sciences University of Alabama Tuscaloosa AL, 35487 USA
| | - Megan E. Feeney
- Department of Marine and Ecological Sciences Florida Gulf Coast University Fort Myers FL, 33965 USA
| | - Patricia A. Sobecky
- Department of Biological Sciences University of Alabama Tuscaloosa AL, 35487 USA
| | - Behzad Mortazavi
- Department of Biological Sciences University of Alabama Tuscaloosa AL, 35487 USA
- Dauphin Island Sea Lab Dauphin Island AL, 36528 USA
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27
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Birrer SC, Dafforn KA, Simpson SL, Kelaher BP, Potts J, Scanes P, Johnston EL. Interactive effects of multiple stressors revealed by sequencing total (DNA) and active (RNA) components of experimental sediment microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:1383-1394. [PMID: 29801231 DOI: 10.1016/j.scitotenv.2018.05.065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/04/2018] [Accepted: 05/05/2018] [Indexed: 06/08/2023]
Abstract
Coastal waterways are increasingly exposed to multiple stressors, e.g. contaminants that can be delivered via pulse or press exposures. Therefore, it is crucial that ecological impacts can be differentiated among stressors to manage ecosystem threats. We investigated microbial community development in sediments exposed to press and pulse stressors. Press exposures were created with in situ mesocosm sediments containing a range of 'metal' concentrations (sediment contaminated with multiple metal(loid)s) and organic enrichment (fertiliser), while the pulse exposure was simulated by a single dose of organic fertiliser. All treatments and exposure concentrations were crossed in a fully factorial field experiment. We used amplicon sequencing to compare the sensitivity of the 1) total (DNA) and active (RNA) component of 2) bacterial (16S rRNA) and eukaryotic (18S rRNA) communities to contaminant exposures. Overall microbial community change was greater when exposed to press than pulse stressors, with the bacterial community responding more strongly than the eukaryotes. The total bacterial community represents a more time-integrated measure of change and proved to be more sensitive to multiple stressors than the active community. Metals and organic enrichment treatments interacted such that the effect of metals was weaker when the sediment was organically enriched. Taxa-level analyses revealed that press enrichment resulted in potential functional changes, mainly involving nitrogen cycling. Furthermore, enrichment generally reduced the abundance of active eukaryotes in the sediment. As well as demonstrating interactive impacts of metals and organic enrichment, this study highlights the sensitivity of next-generation sequencing for ecosystem biomonitoring of interacting stressors and identifies opportunities for more targeted application.
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Affiliation(s)
- Simone C Birrer
- Applied Marine and Estuarine Ecology Lab, School of BEES, University of New South Wales, Sydney 2052, NSW, Australia; The Sydney Institute of Marine Science, Mosman 2088, NSW, Australia.
| | - Katherine A Dafforn
- The Sydney Institute of Marine Science, Mosman 2088, NSW, Australia; Department of Environmental Sciences, Macquarie University, North Ryde NSW 2109, Australia
| | | | - Brendan P Kelaher
- National Marine Science Centre and Centre for Coastal Biogeochemistry Research, Southern Cross University, Coffs Harbour 2450, NSW, Australia
| | - Jaimie Potts
- NSW Office of Environment and Heritage, Lidcombe 2141, NSW, Australia
| | - Peter Scanes
- NSW Office of Environment and Heritage, Lidcombe 2141, NSW, Australia
| | - Emma L Johnston
- Applied Marine and Estuarine Ecology Lab, School of BEES, University of New South Wales, Sydney 2052, NSW, Australia; The Sydney Institute of Marine Science, Mosman 2088, NSW, Australia
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28
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Reid T, Chaganti SR, Droppo IG, Weisener CG. Novel insights into freshwater hydrocarbon-rich sediments using metatranscriptomics: Opening the black box. WATER RESEARCH 2018; 136:1-11. [PMID: 29486256 DOI: 10.1016/j.watres.2018.02.039] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 01/25/2018] [Accepted: 02/16/2018] [Indexed: 06/08/2023]
Abstract
Baseline biogeochemical surveys of natural environments is an often overlooked field of environmental studies. Too often research begins once contamination has occurred, with a knowledge gap as to how the affected area behaved prior to outside (often anthropogenic) influences. These baseline characterizations can provide insight into proposed bioremediation strategies crucial in cleaning up chemical spill sites or heavily mined regions. Hence, this study was conducted to survey the in-situ microbial activity within freshwater hydrocarbon-rich environments cutting through the McMurray formation - the geologic strata constituting the oil sands. We are the first to report in-situ functional variations among these freshwater microbial ecosystems using metatranscriptomics, providing insight into the in-situ gene expression within these naturally hydrocarbon-rich sites. Key genes involved in energy metabolism (nitrogen, sulfur and methane) and hydrocarbon degradation, including transcripts relating to the observed expression of methane oxidation are reported. This information provides better linkages between hydrocarbon impacted environments, closing knowledge gaps for optimizing not only oil sands mine reclamation but also enhancing microbial reclamation strategies in various freshwater environments. These finding can also be applied to existing contaminated environments, in need of efficient reclamation efforts.
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Affiliation(s)
- Thomas Reid
- University of Windsor - Great Lakes Institute for Environmental Research, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada.
| | - Subba Rao Chaganti
- University of Windsor - Great Lakes Institute for Environmental Research, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada
| | - Ian G Droppo
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - Christopher G Weisener
- University of Windsor - Great Lakes Institute for Environmental Research, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada
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29
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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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30
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Sampaio DS, Almeida JRB, de Jesus HE, Rosado AS, Seldin L, Jurelevicius D. Distribution of Anaerobic Hydrocarbon-Degrading Bacteria in Soils from King George Island, Maritime Antarctica. MICROBIAL ECOLOGY 2017; 74:810-820. [PMID: 28484799 DOI: 10.1007/s00248-017-0973-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/24/2017] [Indexed: 06/07/2023]
Abstract
Anaerobic diesel fuel Arctic (DFA) degradation has already been demonstrated in Antarctic soils. However, studies comparing the distribution of anaerobic bacterial groups and of anaerobic hydrocarbon-degrading bacteria in Antarctic soils containing different concentrations of DFA are scarce. In this study, functional genes were used to study the diversity and distribution of anaerobic hydrocarbon-degrading bacteria (bamA, assA, and bssA) and of sulfate-reducing bacteria (SRB-apsR) in highly, intermediate, and non-DFA-contaminated soils collected during the summers of 2009, 2010, and 2011 from King George Island, Antarctica. Signatures of bamA genes were detected in all soils analyzed, whereas bssA and assA were found in only 4 of 10 soils. The concentration of DFA was the main factor influencing the distribution of bamA-containing bacteria and of SRB in the analyzed soils, as shown by PCR-DGGE results. bamA sequences related to genes previously described in Desulfuromonas, Lautropia, Magnetospirillum, Sulfuritalea, Rhodovolum, Rhodomicrobium, Azoarcus, Geobacter, Ramlibacter, and Gemmatimonas genera were dominant in King George Island soils. Although DFA modulated the distribution of bamA-hosting bacteria, DFA concentration was not related to bamA abundance in the soils studied here. This result suggests that King George Island soils show functional redundancy for aromatic hydrocarbon degradation. The results obtained in this study support the hypothesis that specialized anaerobic hydrocarbon-degrading bacteria have been selected by hydrocarbon concentrations present in King George Island soils.
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Affiliation(s)
- Dayanna Souza Sampaio
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - Hugo E de Jesus
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Alexandre S Rosado
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Lucy Seldin
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Diogo Jurelevicius
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
- Laboratório de Genética Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes (IMPPG), Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde, Bloco I, Ilha do Fundão, Rio de Janeiro, 21941-590, Brazil.
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31
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Handley KM, Piceno YM, Hu P, Tom LM, Mason OU, Andersen GL, Jansson JK, Gilbert JA. Metabolic and spatio-taxonomic response of uncultivated seafloor bacteria following the Deepwater Horizon oil spill. ISME JOURNAL 2017; 11:2569-2583. [PMID: 28777379 DOI: 10.1038/ismej.2017.110] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 04/10/2017] [Accepted: 05/30/2017] [Indexed: 11/09/2022]
Abstract
The release of 700 million liters of oil into the Gulf of Mexico over a few months in 2010 produced dramatic changes in the microbial ecology of the water and sediment. Here, we reconstructed the genomes of 57 widespread uncultivated bacteria from post-spill deep-sea sediments, and recovered their gene expression pattern across the seafloor. These genomes comprised a common collection of bacteria that were enriched in heavily affected sediments around the wellhead. Although rare in distal sediments, some members were still detectable at sites up to 60 km away. Many of these genomes exhibited phylogenetic clustering indicative of common trait selection by the environment, and within half we identified 264 genes associated with hydrocarbon degradation. Alkane degradation ability was near ubiquitous among candidate hydrocarbon degraders, whereas just three harbored elaborate gene inventories for the degradation of alkanes and aromatic and polycyclic aromatic hydrocarbons (PAHs). Differential gene expression profiles revealed a spill-promoted microbial sulfur cycle alongside gene upregulation associated with PAH degradation. Gene expression associated with alkane degradation was widespread, although active alkane degrader identities changed along the pollution gradient. Analyses suggest that a broad metabolic capacity to respond to oil inputs exists across a large array of usually rare indigenous deep-sea bacteria.
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Affiliation(s)
- K M Handley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA.,Institute for Genomic and Systems Biology, Argonne National Laboratory, Lemont, IL, USA
| | - Y M Piceno
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - P Hu
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - L M Tom
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - O U Mason
- Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL, USA
| | - G L Andersen
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - J K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - J A Gilbert
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA.,Institute for Genomic and Systems Biology, Argonne National Laboratory, Lemont, IL, USA.,The Microbiome Center, Department of Surgery, The University of Chicago, Chicago, IL, USA
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32
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Reyes C, Schneider D, Lipka M, Thürmer A, Böttcher ME, Friedrich MW. Nitrogen Metabolism Genes from Temperate Marine Sediments. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:175-190. [PMID: 28283802 PMCID: PMC5405112 DOI: 10.1007/s10126-017-9741-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 02/05/2017] [Indexed: 05/26/2023]
Abstract
In this study, we analysed metagenomes along with biogeochemical profiles from Skagerrak (SK) and Bothnian Bay (BB) sediments, to trace the prevailing nitrogen pathways. NO3- was present in the top 5 cm below the sediment-water interface at both sites. NH4+ increased with depth below 5 cm where it overlapped with the NO3- zone. Steady-state modelling of NO3- and NH4+ porewater profiles indicates zones of net nitrogen species transformations. Bacterial protease and hydratase genes appeared to make up the bulk of total ammonification genes. Genes involved in ammonia oxidation (amo, hao), denitrification (nir, nor), dissimilatory NO3- reduction to NH4+ (nfr and otr) and in both of the latter two pathways (nar, nap) were also present. Results show ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are similarly abundant in both sediments. Also, denitrification genes appeared more abundant than DNRA genes. 16S rRNA gene analysis showed that the relative abundance of the nitrifying group Nitrosopumilales and other groups involved in nitrification and denitrification (Nitrobacter, Nitrosomonas, Nitrospira, Nitrosococcus and Nitrosomonas) appeared less abundant in SK sediments compared to BB sediments. Beggiatoa and Thiothrix 16S rRNA genes were also present, suggesting chemolithoautotrophic NO3- reduction to NO2- or NH4+ as a possible pathway. Our results show the metabolic potential for ammonification, nitrification, DNRA and denitrification activities in North Sea and Baltic Sea sediments.
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Affiliation(s)
- Carolina Reyes
- Microbial Ecophysiology, University of Bremen, Leobener Strasse, D-28359, Bremen, Germany.
- Department of Environmental Geosciences, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
| | - Dominik Schneider
- Department of Genomic and Applied Microbiology, University of Göttingen, Grisebachstrasse 8, D-37077, Göttingen, Germany
| | - Marko Lipka
- Geochemistry and Stable Isotope Biogeochemistry Group, Leibniz Institute for Baltic Sea Research (IOW), Seestrasse 15, D-18119, Warnemünde, Germany
| | - Andrea Thürmer
- Department of Genomic and Applied Microbiology, University of Göttingen, Grisebachstrasse 8, D-37077, Göttingen, Germany
| | - Michael E Böttcher
- Geochemistry and Stable Isotope Biogeochemistry Group, Leibniz Institute for Baltic Sea Research (IOW), Seestrasse 15, D-18119, Warnemünde, Germany
| | - Michael W Friedrich
- Microbial Ecophysiology, University of Bremen, Leobener Strasse, D-28359, Bremen, Germany
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Ribeiro H, Mucha AP, Azevedo I, Salgado P, Teixeira C, Almeida CMR, Joye SB, Magalhães C. Differential effects of crude oil on denitrification and anammox, and the impact on N2O production. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 216:391-399. [PMID: 27395442 DOI: 10.1016/j.envpol.2016.05.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 06/06/2023]
Abstract
Denitrification and anammox are key processes for reducing the external nitrogen loads delivered to coastal ecosystems, and these processes can be affected by pollutants. In this study, we investigated the effect of crude oil on denitrification and anammox. Controlled laboratory experiments were performed using sediment slurries from the Lima Estuary (NW Portugal). Anammox and denitrification rates were measured using (15)N-labeled NO3(-), and the production of (29)N2 and (30)N2 quantified by membrane inlet mass spectrometry. Results revealed that while denitrification rates were stimulated between 10 and 25 000 times after crude oil amendment, anammox activity was partially (between 2 and 5 times) or completely inhibited by the addition of crude oil when comparing to rates in unamended controls. Similar results were observed across four estuarine sediment types, despite their different physical-chemical characteristics. Moreover, N2O production was reduced by 2-36 times following crude oil addition. Further work is required to fully understand the mechanism(s) of the observed reduction in N2O production. This study represents one of the first contributions to the understanding of the impact of crude oil pollution on denitrification and anammox, with profound implications for the management of aquatic ecosystems regarding eutrophication (N-removal).
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Affiliation(s)
- Hugo Ribeiro
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal.
| | - Ana P Mucha
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal
| | - Isabel Azevedo
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal
| | - Paula Salgado
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas de Abel Salazar (ICBAS-UP), Universidade do Porto, Porto, Portugal
| | - Catarina Teixeira
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas de Abel Salazar (ICBAS-UP), Universidade do Porto, Porto, Portugal
| | - C Marisa R Almeida
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal
| | - Samantha B Joye
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Catarina Magalhães
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal
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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: 238] [Impact Index Per Article: 29.8] [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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Chen J, Zhou HC, Pan Y, Shyla FS, Tam NFY. Effects of polybrominated diphenyl ethers and plant species on nitrification, denitrification and anammox in mangrove soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 553:60-70. [PMID: 26901803 DOI: 10.1016/j.scitotenv.2016.02.052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 01/31/2016] [Accepted: 02/07/2016] [Indexed: 05/26/2023]
Abstract
Little is known about polybrominated diphenyl ethers (PBDEs) and planting affect biogeochemical processes, and their impact on microbial nitrogen (N) transformation in soil. A 12-month microcosm experiment was conducted to understand the effects of a mixture of PBDEs at two contamination levels, 2 and 20 mg kg(-1)dry weight representing low and high soil contamination, respectively, using two mangrove plant species, namely Kandelia obovata (Ko) and Bruguiera gymnorrhiza (Bg), on nitrification, denitrification and anammox in mangrove soils. No significant changes in these N transformation processes were found at month 3 and at a low level of PBDEs in both plant species, suggesting that short-term exposure to 2 mg kg(-1) contamination did not affect microbial N transformation. At month 12, a high level of PBDE contamination significantly decreased the nitrification potential activity and the copy numbers of archaeal amoA and bacterial amoA gene in Ko soil, but such inhibitory effect was not significant in Bg soil. On the contrary, the denitrification-related parameters, including the activities of nitrate reductase and nitrite reductase, potential denitrification activity and copy numbers of nirK, nirS and nosZ gene, were stimulated by a high level of PBDE contamination in both Ko and Bg soils, and the stimulation was higher in the more anaerobic Bg soil. Different from denitrification, a high level of PBDE contamination decreased the copy numbers of anammox bacterial 16S rRNA gene in Bg soil but not in Ko soil; this was possibly related to the lower nitrate concentration in Bg soil that might inhibit the growth of anammox bacteria. These results indicated that the effects of PBDEs on microbial N transformation were plant species-specific, with the nitrifying microorganisms in Ko soil more susceptible to PBDE contamination, while denitrification and anammox in Bg soil were more sensitive.
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Affiliation(s)
- Juan Chen
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Hai Chao Zhou
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Ying Pan
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Farzana Shazia Shyla
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Nora Fung-Yee Tam
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China.
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36
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Acosta-González A, Marqués S. Bacterial diversity in oil-polluted marine coastal sediments. Curr Opin Biotechnol 2016; 38:24-32. [PMID: 26773654 DOI: 10.1016/j.copbio.2015.12.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 11/27/2022]
Abstract
Marine environments harbour a persistent microbial seed which can be shaped by changes of the environmental conditions such as contamination by petroleum components. Oil spills, together with small but continuous discharges of oil from transportation and recreational activities, are important sources of hydrocarbon pollution within the marine realm. Consequently, prokaryotic communities have become well pre-adapted toward oil pollution, and many microorganisms that are exposed to its presence develop an active degradative response. The natural attenuation of oil pollutants, as has been demonstrated in many sites, is modulated according to the intrinsic environmental properties such as the availability of terminal electron acceptors and elemental nutrients, together with the degree of pollution and the type of hydrocarbon fractions present. Whilst dynamics in the bacterial communities in the aerobic zones of coastal sediments are well characterized and the key players in hydrocarbon biodegradation have been identified, the subtidal ecology of the anaerobic community is still not well understood. However, current data suggest common patterns of response in these ecosystems.
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Affiliation(s)
- Alejandro Acosta-González
- Grupo de Investigación en Bioprospección (GIBP), Facultad de Ingeniería, Universidad de La Sabana, Autopista Norte km 7, Chía, Cundinamarca, Colombia
| | - Silvia Marqués
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Department of Environmental Protection, Profesor Albareda 1, E-18008 Granada, Spain.
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37
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Zhao D, Lu F, Qiu M, DING YUTING, Zhou X. Dynamics and Diversity of Microbial Community Succession of Surimi During Fermentation with Next-Generation Sequencing. J Food Saf 2015. [DOI: 10.1111/jfs.12245] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Dandan Zhao
- College of Biological and Environmental Engineering; Zhejiang University of Technology; Hangzhou China
| | - Fei Lu
- Department of Food Science and Technology; Ocean College, Zhejiang University of Technology; Hangzhou China
| | - Mengting Qiu
- Department of Food Science and Technology; Ocean College, Zhejiang University of Technology; Hangzhou China
| | - YUTING DING
- Department of Food Science and Technology; Ocean College, Zhejiang University of Technology; Hangzhou China
| | - Xuxia Zhou
- Department of Food Science and Technology; Ocean College, Zhejiang University of Technology; Hangzhou China
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38
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Bargiela R, Gertler C, Magagnini M, Mapelli F, Chen J, Daffonchio D, Golyshin PN, Ferrer M. Degradation Network Reconstruction in Uric Acid and Ammonium Amendments in Oil-Degrading Marine Microcosms Guided by Metagenomic Data. Front Microbiol 2015; 6:1270. [PMID: 26635742 PMCID: PMC4656828 DOI: 10.3389/fmicb.2015.01270] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 10/30/2015] [Indexed: 11/13/2022] Open
Abstract
Biostimulation with different nitrogen sources is often regarded as a strategy of choice in combating oil spills in marine environments. Such environments are typically depleted in nitrogen, therefore limiting the balanced microbial utilization of carbon-rich petroleum constituents. It is fundamental, yet only scarcely accounted for, to analyze the catabolic consequences of application of biostimulants. Here, we examined such alterations in enrichment microcosms using sediments from chronically crude oil-contaminated marine sediment at Ancona harbor (Italy) amended with natural fertilizer, uric acid (UA), or ammonium (AMM). We applied the web-based AromaDeg resource using as query Illumina HiSeq meta-sequences (UA: 27,893 open reading frames; AMM: 32,180) to identify potential catabolic differences. A total of 45 (for UA) and 65 (AMM) gene sequences encoding key catabolic enzymes matched AromaDeg, and their participation in aromatic degradation reactions could be unambiguously suggested. Genomic signatures for the degradation of aromatics such as 2-chlorobenzoate, indole-3-acetate, biphenyl, gentisate, quinoline and phenanthrene were common for both microcosms. However, those for the degradation of orcinol, ibuprofen, phenylpropionate, homoprotocatechuate and benzene (in UA) and 4-aminobenzene-sulfonate, p-cumate, dibenzofuran and phthalate (in AMM), were selectively enriched. Experimental validation was conducted and good agreement with predictions was observed. This suggests certain discrepancies in action of these biostimulants on the genomic content of the initial microbial community for the catabolism of petroleum constituents or aromatics pollutants. In both cases, the emerging microbial communities were phylogenetically highly similar and were composed by very same proteobacterial families. However, examination of taxonomic assignments further revealed different catabolic pathway organization at the organismal level, which should be considered for designing oil spill mitigation strategies in the sea.
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Affiliation(s)
- Rafael Bargiela
- Systems Biotechnology, Department of Biocatalysis, Institute of Catalysis, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | | | | | - Francesca Mapelli
- Department of Food, Environmental and Nutritional Sciences, University of Milan Milan, Italy
| | | | - Daniele Daffonchio
- Department of Food, Environmental and Nutritional Sciences, University of Milan Milan, Italy ; Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | | | - Manuel Ferrer
- Systems Biotechnology, Department of Biocatalysis, Institute of Catalysis, Consejo Superior de Investigaciones Científicas Madrid, Spain
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Sanni GO, Coulon F, McGenity TJ. Dynamics and distribution of bacterial and archaeal communities in oil-contaminated temperate coastal mudflat mesocosms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15230-15247. [PMID: 25869427 DOI: 10.1007/s11356-015-4313-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/02/2015] [Indexed: 06/04/2023]
Abstract
Mudflats are ecologically important habitats that are susceptible to oil pollution, but intervention is difficult in these fine-grained sediments, and so clean-up usually relies on natural attenuation. Therefore, we investigated the impact of crude oil on the bacterial, diatom and archaeal communities within the upper parts of the diatom-dominated sediment and the biofilm that detached from the surface at high tide. Biodegradation of petroleum hydrocarbons was rapid, with a 50 % decrease in concentration in the 0-2-mm section of sediment by 3 days, indicating the presence of a primed hydrocarbon-degrading community. The biggest oil-induced change was in the biofilm that detached from the sediment, with increased relative abundance of several types of diatom and of the obligately hydrocarbonoclastic Oleibacter sp., which constituted 5 % of the pyrosequences in the oiled floating biofilm on day 3 compared to 0.6 % in the non-oiled biofilm. Differences in bacterial community composition between oiled and non-oiled samples from the 0-2-mm section of sediment were only significant at days 12 to 28, and the 2-4-mm-sediment bacterial communities were not significantly affected by oil. However, specific members of the Chromatiales were detected (1 % of sequences in the 2-4-mm section) only in the oiled sediment, supporting other work that implicates them in anaerobic hydrocarbon degradation. Unlike the Bacteria, the archaeal communities were not significantly affected by oil. In fact, changes in community composition over time, perhaps caused by decreased nutrient concentration and changes in grazing pressure, overshadowed the effect of oil for both Bacteria and Archaea. Many obligate hydrocarbonoclastic and generalist oil-degrading bacteria were isolated, and there was little correspondence between the isolates and the main taxa detected by pyrosequencing of sediment-extracted DNA, except for Alcanivorax, Thalassolituus, Cycloclasticus and Roseobacter spp., which were detected by both methods.
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Affiliation(s)
- Gbemisola O Sanni
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Frédéric Coulon
- School of Energy, Environment and Agrifood, Cranfield University, Building 40, Cranfield, Bedfordshire, MK43 0AL, UK
| | - Terry J McGenity
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
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40
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Larsen PE, Collart FR, Dai Y. Predicting Ecological Roles in the Rhizosphere Using Metabolome and Transportome Modeling. PLoS One 2015; 10:e0132837. [PMID: 26332409 PMCID: PMC4557938 DOI: 10.1371/journal.pone.0132837] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 06/18/2015] [Indexed: 12/17/2022] Open
Abstract
The ability to obtain complete genome sequences from bacteria in environmental samples, such as soil samples from the rhizosphere, has highlighted the microbial diversity and complexity of environmental communities. However, new algorithms to analyze genome sequence information in the context of community structure are needed to enhance our understanding of the specific ecological roles of these organisms in soil environments. We present a machine learning approach using sequenced Pseudomonad genomes coupled with outputs of metabolic and transportomic computational models for identifying the most predictive molecular mechanisms indicative of a Pseudomonad's ecological role in the rhizosphere: a biofilm, biocontrol agent, promoter of plant growth, or plant pathogen. Computational predictions of ecological niche were highly accurate overall with models trained on transportomic model output being the most accurate (Leave One Out Validation F-scores between 0.82 and 0.89). The strongest predictive molecular mechanism features for rhizosphere ecological niche overlap with many previously reported analyses of Pseudomonad interactions in the rhizosphere, suggesting that this approach successfully informs a system-scale level understanding of how Pseudomonads sense and interact with their environments. The observation that an organism's transportome is highly predictive of its ecological niche is a novel discovery and may have implications in our understanding microbial ecology. The framework developed here can be generalized to the analysis of any bacteria across a wide range of environments and ecological niches making this approach a powerful tool for providing insights into functional predictions from bacterial genomic data.
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Affiliation(s)
- Peter E. Larsen
- Argonne National Laboratory, Biosciences Division, Argonne, IL, United States of America
- University of Illinois at Chicago, Department of Bioengineering, Chicago, IL, United States of America
| | - Frank R. Collart
- Argonne National Laboratory, Biosciences Division, Argonne, IL, United States of America
| | - Yang Dai
- University of Illinois at Chicago, Department of Bioengineering, Chicago, IL, United States of America
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Verma H, Kumar R, Oldach P, Sangwan N, Khurana JP, Gilbert JA, Lal R. Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways. BMC Genomics 2014; 15:1014. [PMID: 25418849 PMCID: PMC4289293 DOI: 10.1186/1471-2164-15-1014] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 10/23/2014] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Sphingobium spp. are efficient degraders of a wide range of chlorinated and aromatic hydrocarbons. In particular, strains which harbour the lin pathway genes mediating the degradation of hexachlorocyclohexane (HCH) isomers are of interest due to the widespread persistence of this contaminant. Here, we examined the evolution and diversification of the lin pathway under the selective pressure of HCH, by comparing the draft genomes of six newly-sequenced Sphingobium spp. (strains LL03, DS20, IP26, HDIPO4, P25 and RL3) isolated from HCH dumpsites, with three existing genomes (S. indicum B90A, S. japonicum UT26S and Sphingobium sp. SYK6). RESULTS Efficient HCH degraders phylogenetically clustered in a closely related group comprising of UT26S, B90A, HDIPO4 and IP26, where HDIPO4 and IP26 were classified as subspecies with ANI value >98%. Less than 10% of the total gene content was shared among all nine strains, but among the eight HCH-associated strains, that is all except SYK6, the shared gene content jumped to nearly 25%. Genes associated with nitrogen stress response and two-component systems were found to be enriched. The strains also housed many xenobiotic degradation pathways other than HCH, despite the absence of these xenobiotics from isolation sources. Additionally, these strains, although non-motile, but posses flagellar assembly genes. While strains HDIPO4 and IP26 contained the complete set of lin genes, DS20 was entirely devoid of lin genes (except linKLMN) whereas, LL03, P25 and RL3 were identified as lin deficient strains, as they housed incomplete lin pathways. Further, in HDIPO4, linA was found as a hybrid of two natural variants i.e., linA1 and linA2 known for their different enantioselectivity. CONCLUSION The bacteria isolated from HCH dumpsites provide a natural testing ground to study variations in the lin system and their effects on degradation efficacy. Further, the diversity in the lin gene sequences and copy number, their arrangement with respect to IS6100 and evidence for potential plasmid content elucidate possible evolutionary acquisition mechanisms for this pathway. This study further opens the horizon for selection of bacterial strains for inclusion in an HCH bioremediation consortium and suggests that HDIPO4, IP26 and B90A would be appropriate candidates for inclusion.
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Affiliation(s)
- Helianthous Verma
- />Molecular Biology Laboratory, Department of Zoology, University of Delhi, Room No. 115, Delhi, 110007 India
| | - Roshan Kumar
- />Molecular Biology Laboratory, Department of Zoology, University of Delhi, Room No. 115, Delhi, 110007 India
| | - Phoebe Oldach
- />Molecular Biology Laboratory, Department of Zoology, University of Delhi, Room No. 115, Delhi, 110007 India
| | - Naseer Sangwan
- />Molecular Biology Laboratory, Department of Zoology, University of Delhi, Room No. 115, Delhi, 110007 India
| | - Jitendra P Khurana
- />Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, India
| | - Jack A Gilbert
- />Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439 USA
- />Department of Ecology and Evolution, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637 USA
| | - Rup Lal
- />Molecular Biology Laboratory, Department of Zoology, University of Delhi, Room No. 115, Delhi, 110007 India
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Kimes NE, Callaghan AV, Suflita JM, Morris PJ. Microbial transformation of the Deepwater Horizon oil spill-past, present, and future perspectives. Front Microbiol 2014; 5:603. [PMID: 25477866 PMCID: PMC4235408 DOI: 10.3389/fmicb.2014.00603] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/23/2014] [Indexed: 01/24/2023] Open
Abstract
The Deepwater Horizon blowout, which occurred on April 20, 2010, resulted in an unprecedented oil spill. Despite a complex effort to cap the well, oil and gas spewed from the site until July 15, 2010. Although a large proportion of the hydrocarbons was depleted via natural processes and human intervention, a substantial portion of the oil remained unaccounted for and impacted multiple ecosystems throughout the Gulf of Mexico. The depth, duration and magnitude of this spill were unique, raising many questions and concerns regarding the fate of the hydrocarbons released. One major question was whether or not microbial communities would be capable of metabolizing the hydrocarbons, and if so, by what mechanisms and to what extent? In this review, we summarize the microbial response to the oil spill as described by studies performed during the past four years, providing an overview of the different responses associated with the water column, surface waters, deep-sea sediments, and coastal sands/sediments. Collectively, these studies provide evidence that the microbial response to the Deepwater Horizon oil spill was rapid and robust, displaying common attenuation mechanisms optimized for low molecular weight aliphatic and aromatic hydrocarbons. In contrast, the lack of evidence for the attenuation of more recalcitrant hydrocarbon components suggests that future work should focus on both the environmental impact and metabolic fate of recalcitrant compounds, such as oxygenated oil components.
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Affiliation(s)
- Nikole E. Kimes
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel HernándezSan Juan, Spain
| | - Amy V. Callaghan
- Department of Microbiology and Plant Biology, University of OklahomaNorman, OK, USA
| | - Joseph M. Suflita
- Department of Microbiology and Plant Biology, University of OklahomaNorman, OK, USA
| | - Pamela J. Morris
- Belle W. Baruch Institute for Marine and Coastal Sciences, University of South CarolinaGeorgetown, SC, USA
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Kostka JE, Teske AP, Joye SB, Head IM. The metabolic pathways and environmental controls of hydrocarbon biodegradation in marine ecosystems. Front Microbiol 2014; 5:471. [PMID: 25237309 PMCID: PMC4154464 DOI: 10.3389/fmicb.2014.00471] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 08/19/2014] [Indexed: 11/20/2022] Open
Affiliation(s)
- Joel E Kostka
- School of Biology and Earth and Atmospheric Sciences, Georgia Institute of Technology Atlanta, GA, USA
| | - Andreas P Teske
- Department of Marine Sciences, University of North Carolina Chapel Hill, NC, USA
| | - Samantha B Joye
- Department of Marine Sciences, University of Georgia Athens, GA, USA
| | - Ian M Head
- School of Civil Engineering and Geosciences, Newcastle University Newcastle upon Tyne, UK
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Gilbert JA, Jansson JK, Knight R. The Earth Microbiome project: successes and aspirations. BMC Biol 2014; 12:69. [PMID: 25184604 PMCID: PMC4141107 DOI: 10.1186/s12915-014-0069-1] [Citation(s) in RCA: 486] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 08/06/2014] [Indexed: 11/11/2022] Open
Affiliation(s)
- Jack A Gilbert
- />Institute for Genomics and Systems Biology, Argonne National Laboratory, Lemont, IL 60439 USA
- />Department of Ecology and Evolution, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637 USA
- />College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Janet K Jansson
- />Pacific Northwest National Laboratory, PO Box 999, MSIN: J4-18, Richland, WA 99352 USA
| | - Rob Knight
- />Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309 USA
- />Howard Hughes Medical Institute, Boulder, CO 80309 USA
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Larsen PE, Scott N, Post AF, Field D, Knight R, Hamada Y, Gilbert JA. Satellite remote sensing data can be used to model marine microbial metabolite turnover. ISME JOURNAL 2014; 9:166-79. [PMID: 25072414 PMCID: PMC4274419 DOI: 10.1038/ismej.2014.107] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/25/2014] [Accepted: 05/28/2014] [Indexed: 11/09/2022]
Abstract
Sampling ecosystems, even at a local scale, at the temporal and spatial resolution necessary to capture natural variability in microbial communities are prohibitively expensive. We extrapolated marine surface microbial community structure and metabolic potential from 72 16S rRNA amplicon and 8 metagenomic observations using remotely sensed environmental parameters to create a system-scale model of marine microbial metabolism for 5904 grid cells (49 km(2)) in the Western English Chanel, across 3 years of weekly averages. Thirteen environmental variables predicted the relative abundance of 24 bacterial Orders and 1715 unique enzyme-encoding genes that encode turnover of 2893 metabolites. The genes' predicted relative abundance was highly correlated (Pearson Correlation 0.72, P-value <10(-6)) with their observed relative abundance in sequenced metagenomes. Predictions of the relative turnover (synthesis or consumption) of CO2 were significantly correlated with observed surface CO2 fugacity. The spatial and temporal variation in the predicted relative abundances of genes coding for cyanase, carbon monoxide and malate dehydrogenase were investigated along with the predicted inter-annual variation in relative consumption or production of ∼3000 metabolites forming six significant temporal clusters. These spatiotemporal distributions could possibly be explained by the co-occurrence of anaerobic and aerobic metabolisms associated with localized plankton blooms or sediment resuspension, which facilitate the presence of anaerobic micro-niches. This predictive model provides a general framework for focusing future sampling and experimental design to relate biogeochemical turnover to microbial ecology.
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Affiliation(s)
- Peter E Larsen
- Argonne National Laboratory, Biosciences Division, Argonne, IL, USA
| | - Nicole Scott
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Anton F Post
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Dawn Field
- NERC Centre for Ecology and Hydrology, Wallingford, UK
| | - Rob Knight
- Department of Chemistry and Biochemistry, BioFrontiers Institute, University of Colorado at Boulder, Boulder, CO, USA
| | - Yuki Hamada
- Argonne National Laboratory, Environmental Science Division, Argonne, IL, USA
| | - Jack A Gilbert
- 1] Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA [2] Argonne National Laboratory, Institute for Genomic and Systems Biology, Argonne, IL, USA
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