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Zou C, Yi X, Li H, Bizic M, Berman-Frank I, Gao K. Correlation of methane production with physiological traits in Trichodesmium IMS 101 grown with methylphosphonate at different temperatures. Front Microbiol 2024; 15:1396369. [PMID: 38894967 PMCID: PMC11184136 DOI: 10.3389/fmicb.2024.1396369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
The diazotrophic cyanobacterium Trichodesmium has been recognized as a potentially significant contributor to aerobic methane generation via several mechanisms including the utilization of methylphophonate (MPn) as a source of phosphorus. Currently, there is no information about how environmental factors regulate methane production by Trichodesmium. Here, we grew Trichodesmium IMS101 at five temperatures ranging from 16 to 31°C, and found that its methane production rates increased with rising temperatures to peak (1.028 ± 0.040 nmol CH4 μmol POC-1 day-1) at 27°C, and then declined. Its specific growth rate changed from 0.03 ± 0.01 d-1 to 0.34 ± 0.02 d-1, with the optimal growth temperature identified between 27 and 31°C. Within the tested temperature range the Q10 for the methane production rate was 4.6 ± 0.7, indicating a high sensitivity to thermal changes. In parallel, the methane production rates showed robust positive correlations with the assimilation rates of carbon, nitrogen, and phosphorus, resulting in the methane production quotients (molar ratio of carbon, nitrogen, or phosphorus assimilated to methane produced) of 227-494 for carbon, 40-128 for nitrogen, and 1.8-3.4 for phosphorus within the tested temperature range. Based on the experimental data, we estimated that the methane released from Trichodesmium can offset about 1% of its CO2 mitigation effects.
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Affiliation(s)
- Chuze Zou
- State Key Laboratory of Marine Environmental Science, College of the Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xiangqi Yi
- Polar and Marine Research Institute, College of Harbor and Coastal Engineering, Jimei University, Xiamen, China
| | - He Li
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China
| | - Mina Bizic
- Department of Environmental Microbiomics, Institute of Environmental Technology, Technical University of Berlin, Berlin, Germany
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin, Germany
| | - Ilana Berman-Frank
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Kunshan Gao
- State Key Laboratory of Marine Environmental Science, College of the Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China
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Lai M, Qian Y, Wu YH, Han C, Liu Q. Devosia aquimaris sp. nov., isolated from seawater of the Changjiang River estuary of China. Antonie Van Leeuwenhoek 2024; 117:29. [PMID: 38280102 DOI: 10.1007/s10482-023-01924-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/27/2023] [Indexed: 01/29/2024]
Abstract
A gram-stain-negative, aerobic, rod-shaped bacterium strain CJK-A8-3T was isolated from a polyamine-enriched seawater sample collected from the Changjiang River estuary of China. The colonies were white and circular. Strain CJK-A8-3T grew optimally at 35 °C, pH 7.0 and 1.5% NaCl. Its polar lipids contained phosphatidylglycerol, phosphatidic acid, unidentified glycolipids, and a combination of phospholipids and glycolipids. The respiratory quinone was ubiquinone-10, and its main fatty acids were C16:0, 11-methyl C18:1ω7c and Summed Feature 8 (including C18:1ω7c/C18:1ω6c). The phylogenetic tree based on 16S rRNA genes placed strain CJK-A8-3T in a new linage within the genus Devosia. 16S rRNA gene sequence of strain CJK-A8-3T showed identities of 98.50% with Devosia beringensis S02T, 98.15% with D. oryziradicis, and 98.01% with D. submarina JCM 18935T. The genome size of strain CJK-A8-3T was 3.81 Mb with the DNA G + C content 63.9%, higher than those of the reference strains (60.4-63.8%). The genome contained genes functional in the metabolism of terrigenous aromatic compounds, alkylphosphonate and organic nitrogen, potentially beneficial for nutrient acquirement and environmental remediation. It also harbored genes functional in antibiotics resistance and balance of osmotic pressure, enhancing their adaptation to estuarine environments. Both genomic investigation and experimental verification showed that strain CJK-A8-3T could be versatile and efficient to use diverse organic nitrogen compounds as carbon and nitrogen sources. Based on phenotypic, chemotaxonomic, phylogenetic and genomic characteristics, strain CJK-A8-3T was identified as a novel Devosia species, named as Devosia aquimaris sp. nov. The type strain is CJK-A8-3T (= MCCC 1K06953T = KCTC 92162T).
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Affiliation(s)
- Mingyan Lai
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, Zhejiang, People's Republic of China
| | - Yurong Qian
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, Zhejiang, People's Republic of China
| | - Yue-Hong Wu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, Zhejiang, People's Republic of China
- Ocean College, Zhejiang University, Hangzhou, 310012, Zhejiang, People's Republic of China
| | - Chenhua Han
- Institute of Polar and Ocean Technology, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, People's Republic of China
| | - Qian Liu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, Zhejiang, People's Republic of China.
- Ocean College, Zhejiang University, Hangzhou, 310012, Zhejiang, People's Republic of China.
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Carvalho CR, Souza BCE, Bieluczyk W, Feitosa YB, Delbaje E, Camargo PB, Tsai SM, Fiore MF. Phosphonate consumers potentially contributing to methane production in Brazilian soda lakes. Extremophiles 2023; 28:4. [PMID: 37987855 DOI: 10.1007/s00792-023-01318-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 09/26/2023] [Indexed: 11/22/2023]
Abstract
Oxic methane production (OMP) has been reported to significantly contribute to methane emissions from oxic surface waters. Demethylation of organic compounds, photosynthesis-associated methane production, and (bacterio)chlorophyll reduction activity are some of the investigated mechanisms as potential OMP sources related to photosynthetic organisms. Recently, cyanobacteria have often been correlated with methane accumulation and emission in freshwater, marine, and saline systems. The Brazilian Pantanal is the world's largest wetland system, with approximately 10,000 shallow lakes, most of which are highly alkaline and saline extreme environments. We initiated this study with an overall investigation using genetic markers, from which we explored metagenomic and limnological data from the Pantanal soda for five potential OMP pathways. Our results showed a strong positive correlation between dissolved methane concentrations and bloom events. Metagenomic data and nutrients, mainly orthophosphate, nitrogen, iron, and methane concentrations, suggest that the organic phosphorous demethylation pathway has the most potential to drive OMP in lakes with blooms. A specialized bacterial community was identified, including the Cyanobacteria Raphidiopsis, although the bloom does not contain the genes to carry out this process. These data showed enough evidence to infer the occurrence of an OMP pathway at Pantanal soda lakes, including the microbial sources and their relation to the cyanobacterial blooms.
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Affiliation(s)
- C R Carvalho
- College of Agriculture 'Luiz de Queiroz', University of São Paulo, Piracicaba, São Paulo, Brazil
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - B C E Souza
- Department of Biological Sciences, State University of Feira de Santana, Feira de Santana, Bahia, Brazil
| | - W Bieluczyk
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Y B Feitosa
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - E Delbaje
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - P B Camargo
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - S M Tsai
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Marli F Fiore
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil.
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Wang W, Liu M, Cao B, Liu Y, Huang K, Ding Y, Xu Z, Sun F, Zhang Y, Niu W, Tian P, Huang D, Wang X, Xiao J. Vibrio methylphosphonaticus sp. nov., a methylphosphonate-decomposing bacterium isolated from surface seawater in the Xisha Islands, PR China. Int J Syst Evol Microbiol 2023; 73. [PMID: 37997883 DOI: 10.1099/ijsem.0.006183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023] Open
Abstract
A Gram-stain-negative, facultative anaerobic, methylphosphonate-decomposing, motile by a polar flagellum and rod-shaped marine bacterium, designated S4B1T, was isolated from the surface seawater collected from the Yongle Atoll (Xisha Islands, PR China). The pairwise alignment showed the highest sequence similarity of 97.5 and 96.6 % to Vibrio aestuarianus subsp. cardii 12_122_3T3T and Vibrio atypicus HHS02T, respectively. Phylogenetic analysis based on 16S rRNA gene and the phylogenomic analysis of single-copy genes showed that strain S4B1T belonged to the genus Vibrio and formed a close branch with Vibrio qingdaonensis ZSDZ65T. Growth of strain S4B1T occurred at 4-30 °C (optimum, 28 °C), at pH 6.0-8.0 (optimum, pH 7.0) and in the presence of 2-7 % (w/v) NaCl (optimum, 3 %). The predominant fatty acids (>10 %) were C16 : 0, iso-C16 : 0 and summed feature 3 (C16 : 1 ω7c or/and C16 : 1 ω6c). The DNA G+C content of the assembled genomic sequence was 44.3 mol%. Average nucleotide identity (ANI) values between S4B1T and its reference species were lower than the threshold for species delineation (95-96 %), in which its highest ANI value with V. qingdaonensis ZSDZ65T was 87.0 %. In silico DNA-DNA hybridization further showed that strain S4B1T had less than 70 % similarity to its relatives. On the basis of the polyphasic evidence, strain S4B1T is proposed to represent a novel species of the genus Vibrio, for which the name Vibrio methylphosphonaticus sp. nov. is proposed. The type strain is S4B1T (=KCTC 92311T=MCCC 1K06168T).
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Affiliation(s)
- Wei Wang
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Mei Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Bingbing Cao
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Yi Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Keyi Huang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Yunqi Ding
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Ziqing Xu
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Fucheng Sun
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Yunxiao Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Wentao Niu
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Peng Tian
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Dingyong Huang
- Key Laboratory of Marine Ecological Conservation and Restoration, Ministry of Natural Resources /Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration, Fujian, PR China
| | - Xiaolei Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Jiaguang Xiao
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
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von Arx JN, Kidane AT, Philippi M, Mohr W, Lavik G, Schorn S, Kuypers MMM, Milucka J. Methylphosphonate-driven methane formation and its link to primary production in the oligotrophic North Atlantic. Nat Commun 2023; 14:6529. [PMID: 37845220 PMCID: PMC10579326 DOI: 10.1038/s41467-023-42304-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/06/2023] [Indexed: 10/18/2023] Open
Abstract
Methylphosphonate is an organic phosphorus compound used by microorganisms when phosphate, a key nutrient limiting growth in most marine surface waters, becomes unavailable. Microbial methylphosphonate use can result in the formation of methane, a potent greenhouse gas, in oxic waters where methane production is traditionally unexpected. The extent and controlling factors of such aerobic methane formation remain underexplored. Here, we show high potential net rates of methylphosphonate-driven methane formation (median 0.4 nmol methane L-1 d-1) in the upper water column of the western tropical North Atlantic. The rates are repressed but still quantifiable in the presence of in-situ or added phosphate, suggesting that some methylphosphonate-driven methane formation persists in phosphate-replete waters. The genetic potential for methylphosphonate utilisation is present in and transcribed by key photo- and heterotrophic microbial taxa, such as Pelagibacterales, SAR116, and Trichodesmium. While the large cyanobacterial nitrogen-fixers dominate in the surface layer, phosphonate utilisation by Alphaproteobacteria appears to become more important in deeper depths. We estimate that at our study site, a substantial part (median 11%) of the measured surface carbon fixation can be sustained by phosphorus liberated from phosphonate utilisation, highlighting the ecological importance of phosphonates in the carbon cycle of the oligotrophic ocean.
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Affiliation(s)
- Jan N von Arx
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Abiel T Kidane
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Miriam Philippi
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Wiebke Mohr
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sina Schorn
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Jana Milucka
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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Li J, Liu H, Liu Z, Zhang X, Blake RE, Huang Z, Cai M, Wang F, Yu C. Transformation mechanism of methylphosphonate to methane by Burkholderia sp: Insight from multi-labeled water isotope probing and transcriptomic. ENVIRONMENTAL RESEARCH 2023; 218:114970. [PMID: 36470350 DOI: 10.1016/j.envres.2022.114970] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/25/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
Methylphosphonate (MPn), has been identified as a likely source of methane in aerobic ocean and may be responsible for the "ocean methane paradox", that is oversaturation of dissolved methane in oxic sea waters. However, the mechanism underlying the cleavage of C-P bonds during microbial degradation is not well understood. Using multi-labeled water isotope probing (MLWIP) and transcriptome analysis, we investigated the phosphate oxygen isotope systematics and mechanisms of microbial-mediated degradation of MPn in this study. In the aerobic culture containing MPn as the only phosphorus source, there was a significant release of inorganic phosphate (149.4 μmol/L) and free methane (268.3 mg/L). The oxygen isotopic composition of inorganic phosphorus (δ18OP) of accumulated released phosphate was 4.50‰, 23.96‰, and 40.88‰, respectively, in the corresponding 18O-labeled waters of -10.3‰, 9.9‰, and 30.6‰, and the slope obtained in plots of δ18OP versus the oxygen isotopic composition of water (δ18OW) was 0.89. Consequently, 89% of the oxygen atoms (Os) in phosphate (PO4) were exchanged with 18O-labeled waters in the medium, while the rest were exchanged with intracellular metabolic water. It has been confirmed that the C-P bond cleavage of MPn occurs in the cell with both ambient and metabolic water participation. Moreover, phn gene clusters play significant roles to cleave the C-P bond of MPn for Burkholderia sp. HQL1813, in which phnJ, phnM and phnI genes are significantly up-regulated during MPn decomposition to methane. In conclusion, the aerobic biotransformation of MPn to free methane by Burkholderia sp. HQL1813 has been elucidated, providing new insights into the mechanism that bio-cleaves C-P bonds to produce methane aerobically in aqueous environments for representative phosphonates.
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Affiliation(s)
- Junhong Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, 430062, Wuhan, China
| | - Houquan Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, 430062, Wuhan, China
| | - Zeqin Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, 430062, Wuhan, China
| | - Xianhua Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, 430062, Wuhan, China
| | - Ruth Elaine Blake
- Department of Earth and Planetary Sciences, Yale University, New Haven, CT, 06520-8109, USA
| | - Zhiyong Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, National Technology Innovation Center of Synthetic Biology, 300308, Tianjin, China
| | - Minmin Cai
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, National Engineering Research Centre of Microbial Pesticides, Huazhong Agricultural University, 430070, Wuhan, China
| | - Fei Wang
- School of Environment, Beijing Normal University, 19 Xinjiekouwai, Haidian District, 100875, Beijing, China.
| | - Chan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, 430062, Wuhan, China.
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Li J, Yu C, Liu Z, Wang Y, Wang F. Microplastic accelerate the phosphorus-related metabolism of bacteria to promote the decomposition of methylphosphonate to methane. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:160020. [PMID: 36356736 DOI: 10.1016/j.scitotenv.2022.160020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/08/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
Microplastic (MP) contaminants in marine water have become a global public health concern because of their persistence and potentially adverse effects on organisms. MP can affect the growth and metabolism of marine microorganisms and further impact the microbial environmental functions. The molecular impact mechanisms of MP on specific functional microbes with the capability of decomposing methylphosphonate (MPn) to release methane (CH4) in oxygenated water have rarely been reported upon. Herein, we investigated the effects of MP on microbes and concomitant methanogenesis via the microbial degradation of MPn. Furthermore, the specific perturbation was revealed at the molecular level combined with transcriptomics and metabolomics. The results showed that intracellular phosphorus utilization by MPn-degrading strain Burkholderia sp. HQL1813 was enhanced by accelerating the catabolism of MPn. Phosphorus transport-related genes (phnG-M, pstSCAB, phnCDE) were upregulated in the MP exposure groups. Amino acid metabolism, the phosphotransferase system and nucleotide metabolism were also perturbed after MP exposure. Notably, released CH4 increased by 24 %, 29 % and 14 % in the exposure group. In addition, the responses of the strain were dose-independent with increasing MP doses. These findings are beneficial for clarifying the effect of MP on specific functional microbes at the molecular level and their degradation of CH4 by MPn.
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Affiliation(s)
- Junhong Li
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, 100083 Beijing, China; School of Environment, Beijing Normal University, 19 Xinjiekouwai Street, 100875 Beijing, China
| | - Chan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, 430062 Wuhan, China
| | - Zeqin Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, 430062 Wuhan, China
| | - Yan Wang
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, 100083 Beijing, China
| | - Fei Wang
- School of Environment, Beijing Normal University, 19 Xinjiekouwai Street, 100875 Beijing, China.
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Lockwood S, Greening C, Baltar F, Morales SE. Global and seasonal variation of marine phosphonate metabolism. THE ISME JOURNAL 2022; 16:2198-2212. [PMID: 35739297 PMCID: PMC9381506 DOI: 10.1038/s41396-022-01266-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 05/17/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022]
Abstract
Marine microbial communities rely on dissolved organic phosphorus (DOP) remineralisation to meet phosphorus (P) requirements. We extensively surveyed the genomic and metagenomic distribution of genes directing phosphonate biosynthesis, substrate-specific catabolism of 2-aminoethylphosphonate (2-AEP, the most abundant phosphonate in the marine environment), and broad-specificity catabolism of phosphonates by the C-P lyase (including methylphosphonate, a major source of methane). We developed comprehensive enzyme databases by curating publicly available sequences and then screened metagenomes from TARA Oceans and Munida Microbial Observatory Time Series (MOTS) to assess spatial and seasonal variation in phosphonate metabolism pathways. Phosphonate cycling genes were encoded in diverse gene clusters by 35 marine bacterial and archaeal classes. More than 65% of marine phosphonate cycling genes mapped to Proteobacteria with production demonstrating wider taxonomic diversity than catabolism. Hydrolysis of 2-AEP was the dominant phosphonate catabolism strategy, enabling microbes to assimilate carbon and nitrogen alongside P. Genes for broad-specificity catabolism by the C-P lyase were far less widespread, though enriched in the extremely P-deplete environment of the Mediterranean Sea. Phosphonate cycling genes were abundant in marine metagenomes, particularly from the mesopelagic zone and winter sampling dates. Disparity between prevalence of substrate-specific and broad-specificity catabolism may be due to higher resource expenditure from the cell to build and retain the C-P lyase. This study is the most comprehensive metagenomic survey of marine microbial phosphonate cycling to date and provides curated databases for 14 genes involved in phosphonate cycling.
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Antiscalants Used in Seawater Desalination: Biodegradability and Effects on Microbial Diversity. Microorganisms 2022; 10:microorganisms10081580. [PMID: 36013998 PMCID: PMC9414044 DOI: 10.3390/microorganisms10081580] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 07/18/2022] [Indexed: 11/25/2022] Open
Abstract
Antiscalants are organic polymers widely used for scale inhibition in seawater desalination. While they are susceptible to biodegradation, they provide nutrients for bacterial cell growth and energy for the microbes that assimilate and degrade them. This paper shows the biodegradability of three commercial antiscalants (polyacrylate—CA, polyphosphonate—PP, and carboxylated dendrimers—DN) applied in seawater reverse osmosis desalination (SWRO) as well as analyzing the antiscalant’s effects on microbial diversity using microbial cultures grown in seawater, under semi-continuous batch conditions. Nutritional uptake and contribution of the antiscalants to microbial growth were investigated by measuring DOC, TDN, NO3−, NO2−, PO4−, NH4+, and TP of the filtered samples of the incubated batch, twice a month, for twelve months. The microbial community was estimated by 16S rRNA sequencing. The main changes in the microbial communities were determined by the incubation period. However, bacterial orders of the antiscalant treatments differed significantly from the control treatment, namely Planctomycetales, Clostridiales, Sphingobacteriales, Rhodobacterales, and Flavobacteriales, and other unclassified bacterial orders, which were found in various relative abundances dependent on incubation times. The results showed the PP antiscalant to be the least biodegradable and to have the least effect on the bacterial community composition compared to the control. This result emphasizes the need to reassess the suitability criteria of antiscalants, and to further monitor their long-term environmental effects.
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Urata S, Kurosawa Y, Yamasaki N, Yamamoto H, Nishiwaki N, Hongo Y, Adachi M, Yamaguchi H. Utilization of phosphonic acid compounds by marine bacteria of the genera Phaeobacter, Ruegeria, and Thalassospira (α-Proteobacteria). FEMS Microbiol Lett 2022; 369:6652134. [DOI: 10.1093/femsle/fnac065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/27/2022] [Accepted: 07/27/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Phosphonic acid (phosphonate) that possesses a carbon (C)-P bond is a chemically stable form of organic phosphorus (P). Various phosphonic acids are widely distributed in oceanic waters; in particular, methylphosphonic acid (namely methylphosphonate) is believed to be responsible for global methane production. To discuss the microbial degradation of phosphonic acids, we investigated the utilization of phosphonic acid compounds by cultures of marine bacteria, Phaeobacter sp., Ruegeria sp. (Rhodobacterales), and Thalassospira sp. (Rhodospirillales). These bacterial cultures were able to grow on methylphosphonic acid as well as on the tested alkyl-, carboxy-, aminoalkyl-, and hydroxyalkyl-phosphonic acid compounds. Cell yields and growth rates of Ruegeria and Thalassospira cultures grown on methyl-, ethyl-, propyl-, and butyl-phosphonic acid compounds tended to decrease with increasing alkyl chain length. In contrast, Phaeobacter sp. grew well on such alkyl phosphonic acids. Our results suggest that these marine bacteria, which exhibit varied utilization, are involved in microbial degradation of various phosphonic acid compounds.
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Affiliation(s)
- Shinnpei Urata
- Graduate School of Integrated Arts and Sciences, Kochi University , Monobe-Otsu, Nankoku , Kochi 783–8502, Japan
| | - Yuki Kurosawa
- Graduate School of Integrated Arts and Sciences, Kochi University , Monobe-Otsu, Nankoku , Kochi 783–8502, Japan
| | - Naoto Yamasaki
- Faculty of Pharmaceutical Science, Tokushima Bunri University , Yamashiro-cho, Tokushima 770–8514, Japan
| | - Hirofumi Yamamoto
- Faculty of Pharmaceutical Science, Tokushima Bunri University , Yamashiro-cho, Tokushima 770–8514, Japan
| | - Nagatoshi Nishiwaki
- School of Environmental Science and Engineering, Kochi University of Technology , Tosayamada , Kami, Kochi 782–8502, Japan
- Research Centre of Molecular Design, Kochi University of Technology , Tosayamada , Kami, Kochi 782–8502, Japan
| | - Yuki Hongo
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency , Fukuura, Yokohama , Kanagawa 236–8648, Japan
| | - Masao Adachi
- Faculty of Agriculture and Marine Science, Kochi University , Monobe-Otsu, Nankoku , Kochi 783–8502, Japan
| | - Haruo Yamaguchi
- Faculty of Agriculture and Marine Science, Kochi University , Monobe-Otsu, Nankoku , Kochi 783–8502, Japan
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Bueno de Mesquita CP, Zhou J, Theroux S, Tringe SG. Methylphosphonate Degradation and Salt-Tolerance Genes of Two Novel Halophilic Marivita Metagenome-Assembled Genomes from Unrestored Solar Salterns. Genes (Basel) 2022; 13:genes13010148. [PMID: 35052488 PMCID: PMC8774927 DOI: 10.3390/genes13010148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 12/30/2022] Open
Abstract
Aerobic bacteria that degrade methylphosphonates and produce methane as a byproduct have emerged as key players in marine carbon and phosphorus cycles. Here, we present two new draft genome sequences of the genus Marivita that were assembled from metagenomes from hypersaline former industrial salterns and compare them to five other Marivita reference genomes. Phylogenetic analyses suggest that both of these metagenome-assembled genomes (MAGs) represent new species in the genus. Average nucleotide identities to the closest taxon were <85%. The MAGs were assembled with SPAdes, binned with MetaBAT, and curated with scaffold extension and reassembly. Both genomes contained the phnCDEGHIJLMP suite of genes encoding the full C-P lyase pathway of methylphosphonate degradation and were significantly more abundant in two former industrial salterns than in nearby reference and restored wetlands, which have lower salinity levels and lower methane emissions than the salterns. These organisms contain a variety of compatible solute biosynthesis and transporter genes to cope with high salinity levels but harbor only slightly acidic proteomes (mean isoelectric point of 6.48).
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Affiliation(s)
- Clifton P. Bueno de Mesquita
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (C.P.B.d.M.); (J.Z.)
| | - Jinglie Zhou
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (C.P.B.d.M.); (J.Z.)
| | - Susanna Theroux
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA;
| | - Susannah G. Tringe
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (C.P.B.d.M.); (J.Z.)
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Correspondence:
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12
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Microbial drivers of methane emissions from unrestored industrial salt ponds. THE ISME JOURNAL 2022; 16:284-295. [PMID: 34321618 PMCID: PMC8692437 DOI: 10.1038/s41396-021-01067-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 02/07/2023]
Abstract
Wetlands are important carbon (C) sinks, yet many have been destroyed and converted to other uses over the past few centuries, including industrial salt making. A renewed focus on wetland ecosystem services (e.g., flood control, and habitat) has resulted in numerous restoration efforts whose effect on microbial communities is largely unexplored. We investigated the impact of restoration on microbial community composition, metabolic functional potential, and methane flux by analyzing sediment cores from two unrestored former industrial salt ponds, a restored former industrial salt pond, and a reference wetland. We observed elevated methane emissions from unrestored salt ponds compared to the restored and reference wetlands, which was positively correlated with salinity and sulfate across all samples. 16S rRNA gene amplicon and shotgun metagenomic data revealed that the restored salt pond harbored communities more phylogenetically and functionally similar to the reference wetland than to unrestored ponds. Archaeal methanogenesis genes were positively correlated with methane flux, as were genes encoding enzymes for bacterial methylphosphonate degradation, suggesting methane is generated both from bacterial methylphosphonate degradation and archaeal methanogenesis in these sites. These observations demonstrate that restoration effectively converted industrial salt pond microbial communities back to compositions more similar to reference wetlands and lowered salinities, sulfate concentrations, and methane emissions.
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Cai Z, Zhou L, Liu L, Wang D, Ren W, Long H, Zhang X, Xie Z. Bacterial epiphyte and endophyte communities of seagrass Thalassia hemprichii: the impact of feed extract solution. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:757-772. [PMID: 34713580 DOI: 10.1111/1758-2229.13019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 09/05/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
The global seagrass bed ecosystem acts as a natural ecological barrier in the littoral coastal zone. In recent years, this ecosystem has suffered from serious eutrophication and destruction caused by the continuous expansion of aquaculture. However, our understanding of the influence of aquaculture on the bacterial community remains limited. In this study, we used 16S amplicon sequencing to evaluate the impact of aquaculture feed extract solution on the composition and function of bacterial epiphytes and endophyte communities of the core seagrass from the seagrass bed ecosystem in Hainan, Thalassia hemprichii. The feed extract solution was the main factor that significantly affected the bacterial epiphyte and endophyte community structure of seagrass leaves but had no marked effect on alpha diversity was observed. Additionally, the bacterial epiphyte and endophyte community of the T. hemprichii leaves alleviated the effects of organic matter, sulfide, and nutrients caused by aquaculture wastewater. The feed extract solution promoted the proliferation of Bacteroidales, Vibrio, Desulfobulbaceae, Desulfobacteraceae, Pseudoalteromonas, Paludibacter, Marinomonas, and Pseudomonas in the leaves and root of T. hemprichii, which can effectively improve the digestibility of eutrophication. In fact, Desulfobacteraceae and Desulfobulbaceae can reduce sulfate to sulfide and oxidize sulfide to sulfur within seagrass, indicating that the increase in Desulfobulbaceae and Desulfobacteraceae facilitated the accumulation of sulfide with the treatment of feed extract solution, which may be the reason for the degradation of seagrass caused by aquaculture wastewater containing high concentrations of organic pollutants. These results suggest that although seagrass beds can withstand low concentrations of aquaculture pollutants, sulfide emissions should be minimized.
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Affiliation(s)
- Zefu Cai
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan Province, 570228, China
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, Hainan Province, 571126, China
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, Hainan Province, 570228, China
- College of Marine Sciences, Hainan University, Haikou, Hainan Province, 570228, China
| | - Lei Zhou
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan Province, 570228, China
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, Hainan Province, 570228, China
- College of Marine Sciences, Hainan University, Haikou, Hainan Province, 570228, China
| | - Lihua Liu
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan Province, 570228, China
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, Hainan Province, 570228, China
- College of Marine Sciences, Hainan University, Haikou, Hainan Province, 570228, China
| | - Daoru Wang
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, Hainan Province, 571126, China
| | - Wei Ren
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan Province, 570228, China
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, Hainan Province, 570228, China
- College of Marine Sciences, Hainan University, Haikou, Hainan Province, 570228, China
| | - Hao Long
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan Province, 570228, China
| | - Xiang Zhang
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan Province, 570228, China
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, Hainan Province, 570228, China
- College of Marine Sciences, Hainan University, Haikou, Hainan Province, 570228, China
| | - Zhenyu Xie
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan Province, 570228, China
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, Hainan Province, 570228, China
- College of Marine Sciences, Hainan University, Haikou, Hainan Province, 570228, China
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14
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Jin H, Wang Y, Fu Y, Bhaya D. The role of three-tandem Pho Boxes in the control of the C-P lyase operon in a thermophilic cyanobacterium. Environ Microbiol 2021; 23:6433-6449. [PMID: 34472186 DOI: 10.1111/1462-2920.15750] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/22/2021] [Accepted: 08/28/2021] [Indexed: 11/28/2022]
Abstract
Cyanobacteria have an inherited advantage in phosphonate phytoremediation. However, studies on phosphonate metabolism in cyanobacteria are rare and mostly focus on physiology and ecology. Here, C-P lyase gene cluster regulation in an undomesticated thermophilic Synechococcus OS-B' was examined in Synechocystis sp. PCC6803, a unicellular cyanobacterial model. Phylogenetic and cluster synteny analysis of C-P lyase genes revealed a closer relationship between Syn OS-B' and Thermus thermophilus, than with other cyanobacteria. Pho boxes were identified in the 5'-end-flanking region of the C-P lyase gene cluster, through which the downstream gene expression was regulated in a phosphate concentration-dependent manner. Unexpectedly, the phosphate concentration that thoroughly inhibited Pho boxes was almost two orders of magnitude higher than that of any natural or anthropogenic wastewater reported so far. The Pho boxes mediated regulation was achieved through the Pho regulon two-component system, and the absence of either SphS or SphR ablated the cell's ability to sense ambient phosphate changes. The three tandems of Pho boxes maintained inequivalent roles, of which the third tandem was not essential; however, it played a role in adjusting Pho boxes response in both positive and negative manner under phosphorus limitation.
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Affiliation(s)
- Haojie Jin
- College of Forestry, Beijing Forestry University, Beijing, 100083, China.,Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Yan Wang
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
| | - Yujie Fu
- College of Forestry, Beijing Forestry University, Beijing, 100083, China
| | - Devaki Bhaya
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
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15
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DeLong EF. Genome-enabled exploration of microbial ecology and evolution in the sea: a rising tide lifts all boats. Environ Microbiol 2021; 23:1301-1321. [PMID: 33459471 PMCID: PMC8049014 DOI: 10.1111/1462-2920.15403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/26/2022]
Abstract
As a young bacteriologist just launching my career during the early days of the 'microbial revolution' in the 1980s, I was fortunate to participate in some early discoveries, and collaborate in the development of cross-disciplinary methods now commonly referred to as "metagenomics". My early scientific career focused on applying phylogenetic and genomic approaches to characterize 'wild' bacteria, archaea and viruses in their natural habitats, with an emphasis on marine systems. These central interests have not changed very much for me over the past three decades, but knowledge, methodological advances and new theoretical perspectives about the microbial world certainly have. In this invited 'How we did it' perspective, I trace some of the trajectories of my lab's collective efforts over the years, including phylogenetic surveys of microbial assemblages in marine plankton and sediments, development of microbial community gene- and genome-enabled surveys, and application of genome-guided, cultivation-independent functional characterization of novel enzymes, pathways and their relationships to in situ biogeochemistry. Throughout this short review, I attempt to acknowledge, all the mentors, students, postdocs and collaborators who enabled this research. Inevitably, a brief autobiographical review like this cannot be fully comprehensive, so sincere apologies to any of my great colleagues who are not explicitly mentioned herein. I salute you all as well!
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Affiliation(s)
- Edward F DeLong
- Daniel K. Inouye Centre for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI, 96822, USA
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16
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DeLong EF. Exploring Marine Planktonic Archaea: Then and Now. Front Microbiol 2021; 11:616086. [PMID: 33519774 PMCID: PMC7838436 DOI: 10.3389/fmicb.2020.616086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 12/18/2020] [Indexed: 12/24/2022] Open
Abstract
In 1977, Woese and Fox leveraged molecular phylogenetic analyses of ribosomal RNAs and identified a new microbial domain of life on Earth, the Archaebacteria (now known as Archaea). At the time of their discovery, only one archaebacterial group, the strictly anaerobic methanogens, was known. But soon, other phenotypically unrelated microbial isolates were shown to belong to the Archaea, many originating from extreme habitats, including extreme halophiles, extreme thermophiles, and thermoacidophiles. Since most Archaea seemed to inhabit extreme or strictly anoxic habitats, it came as a surprise in 1992 when two new lineages of archaea were reported to be abundant in oxygen rich, temperate marine coastal waters and the deep ocean. Since that time, studies of marine planktonic archaea have revealed many more surprises, including their unexpected ubiquity, unusual symbiotic associations, unpredicted physiologies and biogeochemistry, and global abundance. In this Perspective, early work conducted on marine planktonic Archaea by my lab group and others is discussed in terms of the relevant historical context, some of the original research motivations, and surprises and discoveries encountered along the way.
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Affiliation(s)
- Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography Research and Education, University of Hawai'i at Mănoa, Honolulu, HI, United States
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17
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Sun X, Chen B, Xia B, Li Q, Zhu L, Zhao X, Gao Y, Qu K. Impact of mariculture-derived microplastics on bacterial biofilm formation and their potential threat to mariculture: A case in situ study on the Sungo Bay, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 262:114336. [PMID: 32443196 DOI: 10.1016/j.envpol.2020.114336] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/26/2020] [Accepted: 03/04/2020] [Indexed: 06/11/2023]
Abstract
Microplastics (MPs) pollution in the marine environment has attracted considerable global attention. However, the colonization of microorganisms on mariculture-derived MPs and their effects on mariculture remain poorly understood. In this study, the MPs (fishing nets, foams and floats) and a natural substrate, within size ranges (1-4 mm), were then incubated for 21 days in Sungo Bay (China), and the composition and diversity of bacterial communities attached on all substrates were investigated. Results showed that bacterial communities on MPs mainly originated from their surrounding seawater and sediment, with an average contribution on total MPs adherent population of 47.91% and 37.33%, respectively. Principle coordinate analysis showed that community similarity between MPs and surrounding seawater decreased with exposure time. In addition, lower average bacterial community diversity and higher relative abundances of bacteria from the genera Vibrio, Pseudoalteromonas and Alteromonas on MPs than those in their surrounding seawater and sediments indicated that MPs might enrich potential pathogens and bacteria related with carbohydrate metabolism. They are responsible for the significant differences in KEGG Orthology pathways (infectious disease and carbohydrate metabolism) between MPs and seawater. The KO pathway (Infectious Diseases) associated with MPs was also significantly higher than those with feathers in the nearshore area. MPs might be vectors for enrichment of potentially pathogenic Vibrio, and enhance the ecological risk of MPs to mariculture industry.
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Affiliation(s)
- Xuemei Sun
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Bijuan Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Bin Xia
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
| | - Qiufen Li
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Lin Zhu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Xinguo Zhao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Yaping Gao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Keming Qu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
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18
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Podell S, Blanton JM, Oliver A, Schorn MA, Agarwal V, Biggs JS, Moore BS, Allen EE. A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes. MICROBIOME 2020; 8:97. [PMID: 32576248 PMCID: PMC7313196 DOI: 10.1186/s40168-020-00877-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 05/28/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND Marine sponges and their microbiomes contribute significantly to carbon and nutrient cycling in global reefs, processing and remineralizing dissolved and particulate organic matter. Lamellodysidea herbacea sponges obtain additional energy from abundant photosynthetic Hormoscilla cyanobacterial symbionts, which also produce polybrominated diphenyl ethers (PBDEs) chemically similar to anthropogenic pollutants of environmental concern. Potential contributions of non-Hormoscilla bacteria to Lamellodysidea microbiome metabolism and the synthesis and degradation of additional secondary metabolites are currently unknown. RESULTS This study has determined relative abundance, taxonomic novelty, metabolic capacities, and secondary metabolite potential in 21 previously uncharacterized, uncultured Lamellodysidea-associated microbial populations by reconstructing near-complete metagenome-assembled genomes (MAGs) to complement 16S rRNA gene amplicon studies. Microbial community compositions aligned with sponge host subgroup phylogeny in 16 samples from four host clades collected from multiple sites in Guam over a 3-year period, including representatives of Alphaproteobacteria, Gammaproteobacteria, Oligoflexia, and Bacteroidetes as well as Cyanobacteria (Hormoscilla). Unexpectedly, microbiomes from one host clade also included Cyanobacteria from the prolific secondary metabolite-producer genus Prochloron, a common tunicate symbiont. Two novel Alphaproteobacteria MAGs encoded pathways diagnostic for methylotrophic metabolism as well as type III secretion systems, and have been provisionally assigned to a new order, designated Candidatus Methylospongiales. MAGs from other taxonomic groups encoded light-driven energy production pathways using not only chlorophyll, but also bacteriochlorophyll and proteorhodopsin. Diverse heterotrophic capabilities favoring aerobic versus anaerobic conditions included pathways for degrading chitin, eukaryotic extracellular matrix polymers, phosphonates, dimethylsulfoniopropionate, trimethylamine, and benzoate. Genetic evidence identified an aerobic catabolic pathway for halogenated aromatics that may enable endogenous PBDEs to be used as a carbon and energy source. CONCLUSIONS The reconstruction of high-quality MAGs from all microbial taxa comprising greater than 0.1% of the sponge microbiome enabled species-specific assignment of unique metabolic features that could not have been predicted from taxonomic data alone. This information will promote more representative models of marine invertebrate microbiome contributions to host bioenergetics, the identification of potential new sponge parasites and pathogens based on conserved metabolic and physiological markers, and a better understanding of biosynthetic and degradative pathways for secondary metabolites and halogenated compounds in sponge-associated microbiota. Video Abstract.
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Affiliation(s)
- Sheila Podell
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Jessica M Blanton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Aaron Oliver
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Michelle A Schorn
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jason S Biggs
- University of Guam Marine Laboratory, UoG Station, Mangilao, GU, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Eric E Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
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19
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Cieslak MC, Castelfranco AM, Roncalli V, Lenz PH, Hartline DK. t-Distributed Stochastic Neighbor Embedding (t-SNE): A tool for eco-physiological transcriptomic analysis. Mar Genomics 2020; 51:100723. [DOI: 10.1016/j.margen.2019.100723] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/20/2019] [Accepted: 11/01/2019] [Indexed: 01/19/2023]
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20
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Defining the Environmental Adaptations of Genus Devosia: Insights into its Expansive Short Peptide Transport System and Positively Selected Genes. Sci Rep 2020; 10:1151. [PMID: 31980727 PMCID: PMC6981132 DOI: 10.1038/s41598-020-58163-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/19/2019] [Indexed: 12/21/2022] Open
Abstract
Devosia are well known for their dominance in soil habitats contaminated with various toxins and are best characterized for their bioremediation potential. In this study, we compared the genomes of 27 strains of Devosia with aim to understand their metabolic abilities. The analysis revealed their adaptive gene repertoire which was bared from 52% unique pan-gene content. A striking feature of all genomes was the abundance of oligo- and di-peptide permeases (oppABCDF and dppABCDF) with each genome harboring an average of 60.7 ± 19.1 and 36.5 ± 10.6 operon associated genes respectively. Apart from their primary role in nutrition, these permeases may help Devosia to sense environmental signals and in chemotaxis at stressed habitats. Through sequence similarity network analyses, we identified 29 Opp and 19 Dpp sequences that shared very little homology with any other sequence suggesting an expansive short peptidic transport system within Devosia. The substrate determining components of these permeases viz. OppA and DppA further displayed a large diversity that separated into 12 and 9 homologous clusters respectively in addition to large number of isolated nodes. We also dissected the genome scale positive evolution and found genes associated with growth (exopolyphosphatase, HesB_IscA_SufA family protein), detoxification (moeB, nifU-like domain protein, alpha/beta hydrolase), chemotaxis (cheB, luxR) and stress response (phoQ, uspA, luxR, sufE) were positively selected. The study highlights the genomic plasticity of the Devosia spp. for conferring adaptation, bioremediation and the potential to utilize a wide range of substrates. The widespread toxin-antitoxin loci and ‘open’ state of the pangenome provided evidence of plastic genomes and a much larger genetic repertoire of the genus which is yet uncovered.
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21
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Xia C, Geng H, Li X, Zhang Y, Wang F, Tang X, Blake RE, Li H, Chang SJ, Yu C. Mechanism of methylphosphonic acid photo-degradation based on phosphate oxygen isotopes and density functional theory. RSC Adv 2019; 9:31325-31332. [PMID: 35527942 PMCID: PMC9072446 DOI: 10.1039/c9ra05169d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/06/2019] [Indexed: 11/21/2022] Open
Abstract
Methylphosphonic acid (MPn) is an intermediate in the synthesis of the phosphorus-containing nerve agents, such as sarin and VX, and a biosynthesis product of marine microbes with ramifications to global climate change and eutrophication. Here, we applied the multi-labeled water isotope probing (MLWIP) approach to investigate the C-P bond cleavage mechanism of MPn under UV irradiation and density functional theory (DFT) to simulate the photo-oxidation reaction process involving reactive oxygen species (ROS). The results contrasted with those of the addition of the ROS-quenching compounds, 2-propanol and NaN3. The degradation kinetics results indicated that the extent of MPn degradation was more under alkaline conditions and that the degradation process was more rapid at the initial stage of the reaction. The phosphate oxygen isotope data confirmed that one exogenous oxygen atom was incorporated into the product orthophosphate (PO4) following the C-P bond cleavage, and the oxygen isotopic composition of this free PO4 was found to vary with pH. The combined results of the ROS-quenching experiments and DFT indicate that the C-P bond was cleaved by OH-/˙OH and not by other reactive oxygen species. Based on these results, we have established a mechanistic model for the photolysis of MPn, which provides new insights into the fate of MPn and other phosphonate/organophosphate compounds in the environment.
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Affiliation(s)
- Congcong Xia
- Jiangxi Transportation Institute China 809 Jinsha Road 330038 Nanchang China
- School of Energy & Environmental Engineering, University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Huanhuan Geng
- School of Energy & Environmental Engineering, University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Xiaobao Li
- Jiangxi Transportation Institute China 809 Jinsha Road 330038 Nanchang China
| | - Yiyue Zhang
- School of Energy & Environmental Engineering, University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Fei Wang
- School of Energy & Environmental Engineering, University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
| | - Xiaowen Tang
- School of Pharmaceutical Sciences, Sun Yet-sen University 510006 Guangzhou China
| | - R E Blake
- School of Energy & Environmental Engineering, University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
- Department of Geology and Geophysics, Yale University P.O. Box 208109 New Haven CT 06520-8109 USA
| | - Hui Li
- Department of Geology and Geophysics, Yale University P.O. Box 208109 New Haven CT 06520-8109 USA
| | - Sae Jung Chang
- Department of Geology and Geophysics, Yale University P.O. Box 208109 New Haven CT 06520-8109 USA
| | - Chan Yu
- School of Energy & Environmental Engineering, University of Science and Technology Beijing 30 Xueyuan Road 100083 Beijing China
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Gama SR, Vogt M, Kalina T, Hupp K, Hammerschmidt F, Pallitsch K, Zechel DL. An Oxidative Pathway for Microbial Utilization of Methylphosphonic Acid as a Phosphate Source. ACS Chem Biol 2019; 14:735-741. [PMID: 30810303 DOI: 10.1021/acschembio.9b00024] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Methylphosphonic acid is synthesized by marine bacteria and is a prominent component of dissolved organic phosphorus. Consequently, methylphosphonic acid also serves as a source of inorganic phosphate (Pi) for marine bacteria that are starved of this nutrient. Conversion of methylphosphonic acid into Pi is currently only known to occur through the carbon-phosphorus lyase pathway, yielding methane as a byproduct. In this work, we describe an oxidative pathway for the catabolism of methylphosphonic acid in Gimesia maris DSM8797. G. maris can use methylphosphonic acid as Pi sources despite lacking a phn operon encoding a carbon-phosphorus lyase pathway. Instead, the genome contains a locus encoding homologues of the non-heme Fe(II) dependent oxygenases HF130PhnY* and HF130PhnZ, which were previously shown to convert 2-aminoethylphosphonic acid into glycine and Pi. GmPhnY* and GmPhnZ1 were produced in E. coli and purified for characterization in vitro. The substrate specificities of the enzymes were evaluated with a panel of synthetic phosphonates. Via 31P NMR spectroscopy, it is demonstrated that the GmPhnY* converts methylphosphonic acid to hydroxymethylphosphonic acid, which in turn is oxidized by GmPhnZ1 to produce formic acid and Pi. In contrast, 2-aminoethylphosphonic acid is not a substrate for GmPhnY* and is therefore not a substrate for this pathway. These results thus reveal a new metabolic fate for methylphosphonic acid.
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Affiliation(s)
- Simanga R. Gama
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada
| | - Margret Vogt
- Institute of Organic Chemistry, University of Vienna, Vienna, Austria
| | - Thomas Kalina
- Institute of Organic Chemistry, University of Vienna, Vienna, Austria
| | - Kendall Hupp
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada
| | | | | | - David L. Zechel
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada
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Hook JL, Islam MN, Parker D, Prince AS, Bhattacharya S, Bhattacharya J. Disruption of staphylococcal aggregation protects against lethal lung injury. J Clin Invest 2018; 128:1074-1086. [PMID: 29431734 DOI: 10.1172/jci95823] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 01/04/2018] [Indexed: 01/23/2023] Open
Abstract
Infection by Staphylococcus aureus strain USA300 causes tissue injury, multiorgan failure, and high mortality. However, the mechanisms by which the bacteria adhere to, then stabilize on, mucosal surfaces before causing injury remain unclear. We addressed these issues through the first real-time determinations of USA300-alveolar interactions in live lungs. We found that within minutes, inhaled USA300 established stable, self-associated microaggregates in niches at curved, but not at flat, regions of the alveolar wall. The microaggregates released α-hemolysin toxin, causing localized alveolar injury, as indicated by epithelial dye loss, mitochondrial depolarization, and cytosolic Ca2+ increase. Spread of cytosolic Ca2+ through intercellular gap junctions to adjoining, uninfected alveoli caused pulmonary edema. Systemic pretreatment with vancomycin, a USA300-cidal antibiotic, failed to protect mice infected with inhaled WT USA300. However, vancomycin pretreatment markedly abrogated mortality in mice infected with mutant USA300 that lacked the aggregation-promoting factor PhnD. We interpret USA300-induced mortality as having resulted from rapid bacterial aggregation in alveolar niches. These findings indicate, for the first time to our knowledge, that alveolar microanatomy is critical in promoting the aggregation and, hence, in causing USA300-induced alveolar injury. We propose that in addition to antibiotics, strategies for bacterial disaggregation may constitute novel therapy against USA300-induced lung injury.
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Affiliation(s)
- Jaime L Hook
- Lung Biology Laboratory, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine
| | - Mohammad N Islam
- Lung Biology Laboratory, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine
| | | | | | - Sunita Bhattacharya
- Lung Biology Laboratory, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine.,Department of Pediatrics, and
| | - Jahar Bhattacharya
- Lung Biology Laboratory, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine.,Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University Medical Center, New York, New York, USA
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Phosphate insensitive aminophosphonate mineralisation within oceanic nutrient cycles. ISME JOURNAL 2018; 12:973-980. [PMID: 29339823 DOI: 10.1038/s41396-017-0031-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 08/25/2017] [Accepted: 11/29/2017] [Indexed: 11/08/2022]
Abstract
Many areas of the ocean are nutrient-poor yet support large microbial populations, leading to intense competition for and recycling of nutrients. Organic phosphonates are frequently found in marine waters, but require specialist enzymes for catabolism. Previous studies have shown that the genes that encode these enzymes in marine systems are under Pho regulon control and so are repressed by inorganic phosphate. This has led to the conclusion that phosphonates are recalcitrant in much of the ocean, where phosphorus is not limiting despite the degradative genes being common throughout the marine environment. Here we challenge this paradigm and show, for the first time, that bacteria isolated from marine samples have the ability to mineralise 2-aminoethylphosphonate, the most common biogenic marine aminophosphonate, via substrate-inducible gene regulation rather than via Pho-regulated metabolism. Substrate-inducible, Pho-independent 2-aminoethylphosphonate catabolism therefore represents a previously unrecognised component of the oceanic carbon, nitrogen and phosphorus cycles.
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Ulrich EC, Kamat SS, Hove-Jensen B, Zechel DL. Methylphosphonic Acid Biosynthesis and Catabolism in Pelagic Archaea and Bacteria. Methods Enzymol 2018; 605:351-426. [DOI: 10.1016/bs.mie.2018.01.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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26
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Li F, Neves ALA, Ghoshal B, Guan LL. Symposium review: Mining metagenomic and metatranscriptomic data for clues about microbial metabolic functions in ruminants. J Dairy Sci 2017; 101:5605-5618. [PMID: 29274958 DOI: 10.3168/jds.2017-13356] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/27/2017] [Indexed: 12/22/2022]
Abstract
Metagenomics and metatranscriptomics can capture the whole genome and transcriptome repertoire of microorganisms through sequencing total DNA/RNA from various environmental samples, providing both taxonomic and functional information with high resolution. The unique and complex rumen microbial ecosystem is receiving great research attention because the rumen microbiota coevolves with the host and equips ruminants with the ability to convert cellulosic plant materials to high-protein products for human consumption. To date, hundreds to thousands of microbial phylotypes have been identified in the rumen using culture-independent molecular-based approaches, and genomic information of rumen microorganisms is rapidly accumulating through the single genome sequencing. However, functional characteristics of the rumen microbiome have not been well described because there are numerous uncultivable microorganisms in the rumen. The advent of metagenomics and metatranscriptomics along with advanced bioinformatics methods can help us better understand mechanisms of the rumen fermentation, which is vital for improving nutrient utilization and animal productivity. Therefore, in this review, we summarize a general workflow to conduct rumen metagenomics and metatranscriptomics and discuss how the data can be interpreted to be useful information. Moreover, we review recent literatures studying associations between the rumen microbiome and host phenotypes (e.g., feed efficiency and methane emissions) using these approaches, aiming to provide a useful guide to include studying the rumen microbiome as one of the research objectives using these 2 approaches.
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Affiliation(s)
- Fuyong Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5
| | - Andre L A Neves
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5
| | - Bibaswan Ghoshal
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5.
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Sosa OA, Repeta DJ, Ferrón S, Bryant JA, Mende DR, Karl DM, DeLong EF. Isolation and Characterization of Bacteria That Degrade Phosphonates in Marine Dissolved Organic Matter. Front Microbiol 2017; 8:1786. [PMID: 29085339 PMCID: PMC5649143 DOI: 10.3389/fmicb.2017.01786] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 09/05/2017] [Indexed: 11/13/2022] Open
Abstract
Semi-labile dissolved organic matter (DOM) accumulates in surface waters of the oligotrophic ocean gyres and turns over on seasonal to annual timescales. This reservoir of DOM represents an important source of carbon, energy, and nutrients to marine microbial communities but the identity of the microorganisms and the biochemical pathways underlying the cycling of DOM remain largely uncharacterized. In this study we describe bacteria isolated from the North Pacific Subtropical Gyre (NPSG) near Hawaii that are able to degrade phosphonates associated with high molecular weight dissolved organic matter (HMWDOM), which represents a large fraction of semi-labile DOM. We amended dilution-to-extinction cultures with HMWDOM collected from NPSG surface waters and with purified HMWDOM enriched with polysaccharides bearing alkylphosphonate esters. The HMWDOM-amended cultures were enriched in Roseobacter isolates closely related to Sulfitobacter and close relatives of hydrocarbon-degrading bacteria of the Oceanospirillaceae family, many of which encoded phosphonate degradation pathways. Sulfitobacter cultures encoding C-P lyase were able to catabolize methylphosphonate and 2-hydroxyethylphosphonate, as well as the esters of these phosphonates found in native HMWDOM polysaccharides to acquire phosphorus while producing methane and ethylene, respectively. Conversely, growth of these isolates on HMWDOM polysaccharides as carbon source did not support robust increases in cell yields, suggesting that the constituent carbohydrates in HMWDOM were not readily available to these individual isolates. We postulate that the complete remineralization of HMWDOM polysaccharides requires more complex microbial inter-species interactions. The degradation of phosphonate esters and other common substitutions in marine polysaccharides may be key steps in the turnover of marine DOM.
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Affiliation(s)
- Oscar A Sosa
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, United States.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii, Honolulu, HI, United States
| | - Daniel J Repeta
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Sara Ferrón
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, United States.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii, Honolulu, HI, United States
| | - Jessica A Bryant
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, United States.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii, Honolulu, HI, United States
| | - Daniel R Mende
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, United States.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii, Honolulu, HI, United States
| | - David M Karl
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, United States.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii, Honolulu, HI, United States
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, United States.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii, Honolulu, HI, United States
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Belkin N, Rahav E, Elifantz H, Kress N, Berman-Frank I. The effect of coagulants and antiscalants discharged with seawater desalination brines on coastal microbial communities: A laboratory and in situ study from the southeastern Mediterranean. WATER RESEARCH 2017; 110:321-331. [PMID: 28063294 DOI: 10.1016/j.watres.2016.12.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 12/05/2016] [Accepted: 12/10/2016] [Indexed: 06/06/2023]
Abstract
Desalination outflows frequently discharge brine containing coagulants and antiscalants (e.g. Iron-hydroxides and polyphosphonates) to the coastal environment. Here we examined changes in composition and productivity of natural microbial coastal communities in experimental mesocosms treated with either iron-hydroxide (Fe), polyphosphonate (Pn), or a combination of high salinities with both chemicals (All). Within 2 h of addition Fe already altered the microbial community composition, enhanced the bacterial production (BP) and cell specific production (BP/BA), and decreased primary production. Addition of Pn, relieved phosphorus stress as demonstrated by the immediate (within 2 h) and significant reduction in the ecto-enzyme alkaline phosphatase activity (APA). Synergistic effects were observed in the All treatment, reflected by increased production of both primary and bacterial producers as P-stress was relieved. After 10 days of incubation, the microbial community composition changed significantly only in the All treatment. The Fe-only treatment caused a significant decline in autotrophic biomass and in the assimilation number (AN), while in both the Pn and the All treatments the BP/BA increased with the added P. We also examined the microbial community responses in a natural impacted environment at the Ashkelon seawater desalination plant brine discharge site during summer and winter. The community composition differed in elevated-salinity compared with non-impacted stations with higher AN and bacterial efficiencies (BP/BA) measured in summer in the elevated-salinity stations. The seasonal differences in responses may reflect both biotic (i.e. initial community composition) and abiotic factors (currents and residence time of salinity gradients). Our results emphasize that desalination brine discharges that include chemicals such as iron-hydroxide and polyphosphonates can induce physiological and compositional changes in the microbial community. With the expansion of desalination facilities worldwide such shifts in composition and function of the microbial communities may destabilize and change local aquatic food webs and should thus be monitored.
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Affiliation(s)
- Natalia Belkin
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Eyal Rahav
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa 31080, Israel
| | - Hila Elifantz
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Nurit Kress
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa 31080, Israel
| | - Ilana Berman-Frank
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel.
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29
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Abstract
Organophosphonic acids are unique as natural products in terms of stability and mimicry. The C-P bond that defines these compounds resists hydrolytic cleavage, while the phosphonyl group is a versatile mimic of transition-states, intermediates, and primary metabolites. This versatility may explain why a variety of organisms have extensively explored the use organophosphonic acids as bioactive secondary metabolites. Several of these compounds, such as fosfomycin and bialaphos, figure prominently in human health and agriculture. The enzyme reactions that create these molecules are an interesting mix of chemistry that has been adopted from primary metabolism as well as those with no chemical precedent. Additionally, the phosphonate moiety represents a source of inorganic phosphate to microorganisms that live in environments that lack this nutrient; thus, unusual enzyme reactions have also evolved to cleave the C-P bond. This review is a comprehensive summary of the occurrence and function of organophosphonic acids natural products along with the mechanisms of the enzymes that synthesize and catabolize these molecules.
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Affiliation(s)
- Geoff P Horsman
- Department of Chemistry and Biochemistry, Wilfrid Laurier University , Waterloo, Ontario N2L 3C5, Canada
| | - David L Zechel
- Department of Chemistry, Queen's University , Kingston, Ontario K7L 3N6, Canada
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30
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Freshwater bacteria release methane as a byproduct of phosphorus acquisition. Appl Environ Microbiol 2016; 82:6994-7003. [PMID: 27694233 DOI: 10.1128/aem.02399-16] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Freshwater lakes emit large amounts of methane, some of which is produced in oxic surface waters. Two potential pathways for aerobic methane production exist: methanogenesis in oxygenated water, which has been observed in some lakes, or demethylation of small organic molecules. Although methane is produced via demethylation in oxic marine environments, this mechanism of methane release has not yet been demonstrated in freshwater systems. Genes related to the C-P lyase pathway, which cleaves C-P bonds in phosphonate compounds, were found in a metagenomic survey of the surface water of Lake Matano, which is chronically P-starved and methane-rich. We demonstrate that four bacterial isolates from Lake Matano obtain P from methylphosphonate and release methane, and that this activity is repressed by phosphate. We further demonstrate that expression of phnJ, which encodes the enzyme that releases methane, is higher in the presence of methylphosphonate and lower when both methylphosphonate and phosphate are added. This gene is also found in most of the metagenomic data sets from freshwater environments. These experiments link methylphosphonate degradation and methane production with gene expression and phosphate availability in freshwater organisms, and suggest that some of the excess methane in the Lake Matano surface water, and in other methane-rich lakes, may be produced by P-starved bacteria. IMPORTANCE Methane is an important greenhouse gas, and contributes substantially to global warming. Although freshwater environments are known to release methane into the atmosphere, estimates of the amount of methane emitted by freshwater lakes vary from 8 to 73 Tg per year. Methane emissions are difficult to predict in part because the source of the methane can vary: it is the end product of the energy-conserving pathway in methanogenic archaea, which predominantly live in anoxic sediments or waters, but have also been identified in some oxic freshwater environments. More recently, methane release from small organic molecules has been observed in oxic marine environments. Here we show that demethylation of methylphosphonate may also contribute to methane release from lakes, and that phosphate can repress this activity. Since lakes are typically phosphorus-limited, some methane release in these environments may be a byproduct of phosphorus metabolism, rather than carbon or energy metabolism. Methane emissions from lakes are currently predicted using primary production, eutrophication status, extent of anoxia, and the shape and size of the lake; to improve prediction of methane emissions, phosphorus availability and sources may also need to be included in these models.
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Chin JP, McGrath JW, Quinn JP. Microbial transformations in phosphonate biosynthesis and catabolism, and their importance in nutrient cycling. Curr Opin Chem Biol 2016; 31:50-7. [DOI: 10.1016/j.cbpa.2016.01.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 01/11/2016] [Accepted: 01/15/2016] [Indexed: 11/24/2022]
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Abstract
Dissolved organic matter (DOM) in the oceans is one of the largest pools of reduced carbon on Earth, comparable in size to the atmospheric CO2 reservoir. A vast number of compounds are present in DOM, and they play important roles in all major element cycles, contribute to the storage of atmospheric CO2 in the ocean, support marine ecosystems, and facilitate interactions between organisms. At the heart of the DOM cycle lie molecular-level relationships between the individual compounds in DOM and the members of the ocean microbiome that produce and consume them. In the past, these connections have eluded clear definition because of the sheer numerical complexity of both DOM molecules and microorganisms. Emerging tools in analytical chemistry, microbiology, and informatics are breaking down the barriers to a fuller appreciation of these connections. Here we highlight questions being addressed using recent methodological and technological developments in those fields and consider how these advances are transforming our understanding of some of the most important reactions of the marine carbon cycle.
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Environmental Filtering of Microbial Communities in Agricultural Soil Shifts with Crop Growth. PLoS One 2015; 10:e0134345. [PMID: 26226508 PMCID: PMC4520589 DOI: 10.1371/journal.pone.0134345] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 07/08/2015] [Indexed: 11/19/2022] Open
Abstract
Plant and soil properties cooperatively structure soil microbial communities, with implications for ecosystem functioning. However, the extent to which each factor contributes to community structuring is not fully understood. To quantify the influence of plants and soil properties on microbial diversity and composition in an agricultural context, we conducted an experiment within a corn-based annual cropping system and a perennial switchgrass cropping system across three topographic positions. We sequenced barcoded 16S ribosomal RNA genes from whole soil three times throughout a single growing season and across two years in July. To target the belowground effects of plants, we also sampled rhizosphere soil in July. We hypothesized that microbial community α-diversity and composition (β-diversity) would be more sensitive to cropping system effects (annual vs. perennial inputs) than edaphic differences among topographic positions, with greater differences occurring in the rhizosphere compared to whole soil. We found that microbial community composition consistently varied with topographic position, and cropping system and the rhizosphere influenced α-diversity. In July, cropping system and rhizosphere structured a small but specific group of microbes implying a subset of microbial taxa, rather than broad shifts in community composition, may explain previously observed differences in resource cycling between treatments. Using rank abundance analysis, we detected enrichment of Saprospirales and Actinomycetales, including cellulose and chitin degraders, in the rhizosphere soil and enrichment of Nitrospirales, Syntrophobacterales, and MND1 in the whole soil. Overall, these findings support environmental filtering for the soil microbial community first by soil and second by the rhizosphere. Across cropping systems, plants selected for a general rhizosphere community with evidence for plant-specific effects related to time of sampling.
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Wang Z, Robertson KL, Liu C, Liu JL, Johnson BJ, Leary DH, Compton JR, Vuddhakul V, Legler PM, Vora GJ. A novelVibriobeta-glucosidase (LamN) that hydrolyzes the algal storage polysaccharide laminarin. FEMS Microbiol Ecol 2015. [DOI: 10.1093/femsec/fiv087] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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35
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Lim YW, Cuevas DA, Silva GGZ, Aguinaldo K, Dinsdale EA, Haas AF, Hatay M, Sanchez SE, Wegley-Kelly L, Dutilh BE, Harkins TT, Lee CC, Tom W, Sandin SA, Smith JE, Zgliczynski B, Vermeij MJA, Rohwer F, Edwards RA. Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition. PeerJ 2014; 2:e520. [PMID: 25177534 PMCID: PMC4145072 DOI: 10.7717/peerj.520] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 07/23/2014] [Indexed: 11/20/2022] Open
Abstract
Genomics and metagenomics have revolutionized our understanding of marine microbial ecology and the importance of microbes in global geochemical cycles. However, the process of DNA sequencing has always been an abstract extension of the research expedition, completed once the samples were returned to the laboratory. During the 2013 Southern Line Islands Research Expedition, we started the first effort to bring next generation sequencing to some of the most remote locations on our planet. We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the Ion Torrent PGM platform on the Merchant Yacht Hanse Explorer. Onboard sequence assembly, annotation, and analysis enabled us to investigate the role of the microbes in the coral reef ecology of these islands and atolls. This analysis identified phosphonate as an important phosphorous source for microbes growing in the Line Islands and reinforced the importance of L-serine in marine microbial ecosystems. Sequencing in the field allowed us to propose hypotheses and conduct experiments and further sampling based on the sequences generated. By eliminating the delay between sampling and sequencing, we enhanced the productivity of the research expedition. By overcoming the hurdles associated with sequencing on a boat in the middle of the Pacific Ocean we proved the flexibility of the sequencing, annotation, and analysis pipelines.
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Affiliation(s)
- Yan Wei Lim
- Department of Biology, San Diego State University , San Diego, CA , USA
| | - Daniel A Cuevas
- Computational Sciences Research Center, San Diego State University , San Diego, CA , USA
| | | | - Kristen Aguinaldo
- Department of Biology, San Diego State University , San Diego, CA , USA ; Ion Torrent Research & Development Group, Thermo Fisher Scientific , Carlsbad, CA , USA
| | | | - Andreas F Haas
- Department of Biology, San Diego State University , San Diego, CA , USA
| | - Mark Hatay
- Department of Biology, San Diego State University , San Diego, CA , USA
| | | | | | - Bas E Dutilh
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre , Geert Grooteplein, GA, Nijmegen , The Netherlands ; Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro , Brazil
| | - Timothy T Harkins
- Advanced Applications Group, Life Technologies, Inc. , Beverly, MA , USA
| | - Clarence C Lee
- Advanced Applications Group, Life Technologies, Inc. , Beverly, MA , USA ; Life Sciences Group, Thermo Fisher Scientific , South San Francisco, CA , USA
| | - Warren Tom
- Advanced Applications Group, Life Technologies, Inc. , Beverly, MA , USA
| | - Stuart A Sandin
- Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California San Diego , La Jolla, CA , USA
| | - Jennifer E Smith
- Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California San Diego , La Jolla, CA , USA
| | - Brian Zgliczynski
- Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California San Diego , La Jolla, CA , USA
| | - Mark J A Vermeij
- Caribbean Research and Management of Biodiversity (CARMABI) , Willemstad , Curacao ; Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam , Amsterdam , The Netherlands
| | - Forest Rohwer
- Department of Biology, San Diego State University , San Diego, CA , USA
| | - Robert A Edwards
- Department of Biology, San Diego State University , San Diego, CA , USA ; Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro , Brazil ; Division of Mathematics and Computer Science, Argonne National Laboratory , Argonne, IL , USA
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Methane production by phosphate-starved SAR11 chemoheterotrophic marine bacteria. Nat Commun 2014; 5:4346. [PMID: 25000228 DOI: 10.1038/ncomms5346] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 06/09/2014] [Indexed: 11/08/2022] Open
Abstract
The oxygenated surface waters of the world's oceans are supersaturated with methane relative to the atmosphere, a phenomenon termed the 'marine methane paradox'. The production of methylphosphonic acid (MPn) by marine archaea related to Nitrosopumilus maritimus and subsequent decomposition of MPn by phosphate-starved bacterioplankton may partially explain the excess methane in surface waters. Here we show that Pelagibacterales sp. strain HTCC7211, an isolate of the SAR11 clade of marine α-proteobacteria, produces methane from MPn, stoichiometric to phosphorus consumption, when starved for phosphate. Gene transcripts encoding phosphonate transport and hydrolysis proteins are upregulated under phosphate limitation, suggesting a genetic basis for the methanogenic phenotype. Strain HTCC7211 can also use 2-aminoethylphosphonate and assorted phosphate esters for phosphorus nutrition. Despite strain-specific differences in phosphorus utilization, these findings identify Pelagibacterales bacteria as a source of biogenic methane and further implicate phosphate starvation of chemoheterotrophic bacteria in the long-observed methane supersaturation in oxygenated waters.
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37
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Emerging strategies and integrated systems microbiology technologies for biodiscovery of marine bioactive compounds. Mar Drugs 2014; 12:3516-59. [PMID: 24918453 PMCID: PMC4071589 DOI: 10.3390/md12063516] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 12/30/2022] Open
Abstract
Marine microorganisms continue to be a source of structurally and biologically novel compounds with potential use in the biotechnology industry. The unique physiochemical properties of the marine environment (such as pH, pressure, temperature, osmolarity) and uncommon functional groups (such as isonitrile, dichloroimine, isocyanate, and halogenated functional groups) are frequently found in marine metabolites. These facts have resulted in the production of bioactive substances with different properties than those found in terrestrial habitats. In fact, the marine environment contains a relatively untapped reservoir of bioactivity. Recent advances in genomics, metagenomics, proteomics, combinatorial biosynthesis, synthetic biology, screening methods, expression systems, bioinformatics, and the ever increasing availability of sequenced genomes provides us with more opportunities than ever in the discovery of novel bioactive compounds and biocatalysts. The combination of these advanced techniques with traditional techniques, together with the use of dereplication strategies to eliminate known compounds, provides a powerful tool in the discovery of novel marine bioactive compounds. This review outlines and discusses the emerging strategies for the biodiscovery of these bioactive compounds.
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