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2024

  • Torcello-Requena A, Murphy A, Lidbury IDE, Pitt FD, Stark R, Millard AD, Puxty RJ, Chen Y, Scanlan DJ (2024). A distinct high affinity alkaline phosphatase facilitates occupation of P-depleted environments by marine picocyanobacteria. Proc Natl Acad Sci, doi/10.1073/pnas.2312892121.

  • Chen Y 2024 Beyond meta-omics: functional genomics in future marine microbiome research. Annual Review of Marine Science. in press. 

  • Dang YR et al., 2024 Phytoplankton-derived polysaccharides and microbial peptidoglycans are key nutrients for deep-sea microbes in the Mariana Trench. Microbiome, 12, 77 (2024). https://doi.org/10.1186/s40168-024-01789-x. 

  • Roman D et al., 2024 Structure Revision of a Widespread Marine Sulfonolipid Class Based on their Isolation and Total Synthesis. Angewandte Chemie. doi.org/10.1002/anie.202401195

  • S Tsola, Y Zhu, Y Chen, I Sanders, C Economou, V Bruchert, O Eyice (2024) Methanolobus use unspecific methyltransferasees to produce methane from dimethylsulfide. Microbiome 12, 3. https://doi.org/10.1186/s40168-023-01720-w.

  • Cook et al (2024) The long and short of it: Benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies. Microbial Genomics https://doi.org/10.1101/2023.02.12.527533 

2023​

  • He, NH Liu, JQ Liu, M Peng, ZJ Teng, TJ Gu, XL Chen, Y Chen, P Wang, CY Li, J Todd, YZ Zhang, XY Zhang (2023) SAR92 bacteria are potentially import DMSP degraders and sources of climate-active gases in marine environment. mBio. In press.

  • F Zhao, CM Yu, HN Sun, QL Qin, LS Zhao, P Wang, CY Li, HT Ding, HY Cao, ZZ Sun, Y Chen, QT Shen, XL Chen, PY Li, YZ Zhang (2023) Catabolism of red algal mixed-linkage xylan by marine Bacteroidetes: identification of a novel xylanase. J Biol Chem. 105116. doi: 10.1016/j.jbc.2023.105116.

  • D Tebbe et al., 2023 Microbial drivers of DMSO reduction and DMS-dependent methanogenesis in saltmarsh sediments. The ISME J, https://doi.org/10.1038/s41396-023-01539-1. 

  • Q Sheng, et al., 2023 The FilZ Protein Contains a Single PilZ Domain and Facilitates the Swarming Motility of Pseudoalteromonas sp. SM9913 Microorganisms 11 (6), 1566

  • Joshua Williams, Jaimee Kerven, Yin Chen, and Antonia P. Sagona 2023 Genetic Engineering of Bacteriophage K1F with Human Epidermal Growth Factor to Enhance Killing of Intracellular E. coli K1. ACS Synthetic Biology. https://doi.org/10.1021/acssynbio.3c00135

  • Holly Shropshire, & Richard Guillonneau et al 2023 Glyceroglycolipids are essential for Burkholderia cenocepacia intracellular survival by preventing phagolysosome acidification. BioRxiv https://www.biorxiv.org/content/10.1101/2023.05.30.542800v1.abstract

  • Westermann et al 2023 Bacterial catabolism of membrane phospholipids links marine biogeochemical cycles. Science Advances https://www.science.org/doi/10.1126/sciadv.adf5122 

  • Li CY, Mausz MA, Murphy A, Zhang N et al., (2023) Ubiquitous occurrence of a dimethylsulfoniopropionate ABC transporter in abundant marine bacteria. ISME Journal 17, 579–587  

  • Quareshy M, Shanmugam M, Cameron AD, Bugg TD, Chen Y (2023) Characterisation of an unusual cysteine pair in the Rieske carnitine monooxygenase CntA catalytic site. FEBS Journal  doi/10.1111/febs.16722 

  • Yu, HY Cao, ZJ Teng, M Wang, A McMinn, Y Chen, QT Shen, XL Chen, P Wang, YZ Zhang (2023) A novel D-glutamate catabolic pathway in marine proteobacteria and halophilic archaea. ISME Journal doi s41396-023-01364-6 

 

2022

  • Airs et al., (2022) Seasonal measurements of the nitrogenous osmolyte glycine betaine in marine temperate coastal waters. Biogeochemistry, in press 

  • Stirrup R & Mausz MA et al (2022) Aminolipids elicit functional trade-offs between competitiveness and bacteriophage attachment in Ruegeria pomeroyi. ISME Journal, in press 

  • Jameson et al (2023). DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms. Methods Mol Biol. 2023;2555:261-282.

  • Jiang et al (2022) A pathway for chitin oxidation in marine bacteria. Nature Communications 13(1):5899. doi: 10.1038/s41467-022-33566-5. 

  •  R Guillonneau, A Murphy, ZJ Teng, P Wang, YZ Zhang, DJ Scanlan, Y Chen (2022) Trade-offs of lipid remodelling in a marine predator-prey interaction in response to phosphorus limitation. Proc Natl Acad Sci, 119 (36) e2203057119 

  •  Lyon R, Jones RA, Shropshire H, Aberdeen I, Scanlan DJ, Millard A, Chen Y (2022) Membrane lipid renovation in Pseudomonas aeruginosa - implications for phage therapy? Environ Microbiol. doi.org/10.1111/1462-2920.16136

  •  Li CY, Crack JC, Newton-Payne S, Murphy A, Chen XL, Pinchbeck BJ, Zhou S, Peng M, Zhang XH, Chen Y, Brun NE, Todd JD, Zhang YZ. (2021) Mechanistic insight into Dsyb/DSYB, key enzymes in marine dimethylsulfoniopropionate synthesis, mLife, doi.org/10.1002/mlf2.12030 

  • Zhang LM, Silvano E, Rithman B, Ferretjans MA, Chen Y* (2022) Lipidomics and proteomics analyses of the N2-fixing bacterium Klebsiella variicola W12 in response to phosphorus stress. Journal of Sustainable Agriculture and Environment, doi.org/10.1002/sae2.12024.

  • 100 Scanlan J, Guillonneau R, Najmin S, Mausz MA, Murphy A, Cunningham M, Murray L, Kumaresan D, Zhang LM, Chen Y* (2022) the proteobacterial methanotroph Methylosinus trichosporium OB3b remodels membrane lipids in response to phosphate limitation. mBio doi.org/10.1128/mbio.00247-22

  • 99 Naguib M, Feldman N, Zarodkiewicz P, Shropshire H, Biamis C, EI-Halfawy OM, McCain J, Dezanet C, Decout JL, Chen Y, Cosa G, Valvano MA (2022) An evolutionary conserved detoxification system for membrane lipid–derived peroxyl radicals in Gram-negative bacteria. PloS Biolology doi.org/10.1371/journal.pbio.3001610.

  • 98 Murphy A, Scanlan DJ, Chen Y, Bending GD, Hammond JP, Wellington EMH, Lidbury I (2022) 2-aminoethylphosphonate utilisation in Pseudomonas putida BIRD-1 is controlled by multiple master regulators. Environ Microbiol. 24(4), 1902–1917 

  • 97 Mausz MA*, Airs RL, Dixon JL, Widdicome CE, Tarran G, Polimene L, Dashfield S, Beale R, Scanlan DJ, Chen Y *(2022) Microbial uptake dynamics of glycine betaine and choline in coastal seawater. Limnology and Oceanography. 67, 2022, 1052–1064. 

  • 96 Wang Y, Wang P, Cao HY, Ding HT, Su HN, Liu SC, Liu GF, Zhang X, Li CY, Peng M, Li FC, Li SY, Chen Y, Chen XL, Zhang YZ (2021) Structure of Vibrio collagenase VhaC provides new insight into the mechanism of bacterial collagenolysis. Nature Communications, 13, 566 (2022). https://doi.org/10.1038/s41467-022-28264-1 

 

2021

  • 95 Qin QL, Wang ZB, Cha QQ, Liu SS, Ren XB, Fu HH, Sun ML, Zhao DL, McMinn A, Chen Y, Chen XL, Zhang YZ, Li PY (2021). Biogeography of culturable marine bacteria from both poles reveals that 'everything is not everywhere' at the genomic level. Environ Microbiol. doi: 10.1111/1462-2920.15870.  

  • 94 Yu Y, Yang J, Zheng LY, Sheng Q, Li PY, Fu HH, L CY, Y Chen, Zhang YZ, Chen XL (2021) D-alanine metabolism by abundant marine heterotrophic bacteria. Applied and Environmental Microbiology, 88(3):e0221921. 

  • 93 Teng ZJ, Wang P, Chen XL, Guillonneau R, Li CY, Zou SB, Gong J, Xu KW, Han L, Wang C, Scanlan DJ, Chen Y, Zhang YZ (2021) Acrylate protects a marine bacterium from grazing by a ciliate predator. Nature Microbiology, 6(11):1351-1356. 

  • 92 Wang XJ, Ten ZJ, Wang P, Fu HH, Zhang WP, Chen XL, Zhang YZ, Y Chen, Zhang N, Li CY (2021) Molecular Insight into Dimethylsulfoxide Formation through Dimethylsulfide Oxidation Catalyzed by Bacterial Trimethylamine Monooxygenase. Frontiers in Microbiology, 12:735793. doi: 10.3389/fmicb.2021.735793 

  • 91 Teng ZJ, Qin QL, Zhang. WP, Li J, Fu HH, Wang P, Lan MS, Lu GF, He JF, McMinn A, Wang M, Chen XL, Zhang YZ, Chen Y, Li CY (2021) Biogeographic traits of dimethyl sulfide and dimethylsulfoniopropionate cycling in polar oceans. Microbiome, 9, 207. https://doi.org/10.1186/s40168-021-01153-3 

  • 90 Murphy AR, Scanlan DJ, Chen Y, Adams NB, Cadman WA, Boottrill A, Bending G, Hammond JP, Hitchcoock. A, Wellington EMH, Lidbury IDEA (2021) Aminophosphonate mineralisation is a major process in oceanic nitrogen and phosphorus cycling. Nature Communications, 12, 4554 (2021). doi.org/10.1038/s41467-021-24646-z. 

  • 89 W Shi, H-Y Zhao, Y Chen, J-S Wang, B Han, C-P Li, J-Y Lu, L-M Zhang (2021) Organic manure rather than phosphorus fertilization primarily determined asymbiotic nitrogen fixation rate and the stability of diazotrophic community in an upland red soil. Agriculture, Ecosystems and Environment in press 

  • 88 Rihtman B, Puxty RJ, Hapeshi A, Lee Y-J, Zhan Y, Michniewski S, Waterfield NR, Chen F, Weigele P, Millard AD, Scanlan DJ, Chen Y* (2021) A new family of globally distributed lytic roseophage, the Naomiviridae, has unusual thymidine to deoxyuridine substitution. Current Biology, 31, 3199–3206 

  • 87 CY Li, XJ Wang, XL Chen, Q Sheng, P Wang, M Quareshy, B Rihtman, X Shao, C Gao, J Todd, Y Chen, YZ Zhang (2021) A novel ATP dependent dimethylsulfoniopropionate lyase in bacteria that releases dimethyl sulfide and acryloyl-CoA. eLife 10:e64045 

  • 86 Jones RA, Shropshire H, Zhao C, Wei T, Murphy A, Lidbury I, Scanlan DJ, Y Chen* (2021) Phosphorus stress induces the synthesis of novel glycolipids in Pseudomonas aeruginosa that confer protection against a last-resort antibiotic. ISME Journal, 15(11):3303-3314 

  • 85 Wei T, Zhao C, Quareshy M, Wu N, Huang S, Zhao Y, Yang P, Mao D, Y Chen* (2021) Characterization of a glycolipid glycosyltransferase with broad substrate specificity from the marine bacterium Candidatus Pelagibacter sp. HTCC7211. Applied and Environmental Microbiology, 87:e00326-21 

  • 84 Shropshire H, Jones RA, Aguilo-Ferretjans M, Scanlan DJ, Chen Y* (2021) Proteomics insights into Burkholderia cenocepacia phosphorus stress response. Environmental Microbiology, in press 

  • 83 Smith AF, Silvano E, Pauker O, Guillonneau R, Quareshy M, Mausz MA, Murphy A, Stirrup R, Rihtman B, Feretjans MA, Brandsma J, Petersen J, Scanlan DJ, Chen Y* (2021) A novel class of sulfur-containing aminolipid widespread in marine roseobacters. ISME Journal 15, 2440–2453 

  • 82 Qin QL, Wang ZB, SU HN, Chen XL, Miao J, Wang XJ, Li CY, Zhang XY, Li PY, Wang M, Fang JS, Lidbury I, Zhang WP, Zhang XH, Yang GP, Chen Y, Zhang YZ (2021) Oxidation of trimethylamine to trimethylamine N-oxide facilitates bacterial adaptation to high hydrostatic pressure. Science Advances, https://advances.sciencemag.org/content/7/13/eabf9941 

  • 81 Xie BB, Rong JC, Tang BL, Wang SH, Liu GM, Qin QL, Zhang XY, Zhang WP, She QX, Y Chen, Liu FC, Li SY, Chen XL, Luo HW, Zhang YZ (2021) Evolutionary trajectory of the replication mode of bacterial replicons. mBio, 12:e02745- 20. 

  • 80. Li Y, Wang ZB, Zhang XY, Dang YR, Sun LL, Zhang WP, Fu HH, Yang GP, Wang M, McMinn A, Chen XL, Chen Y, Wang S, Zhang YZ, Qin QL (2021) Experimental evidence for long-term coexistence of copiotrophic and oligotrophic bacteria in pelagic surface seawater. Environmental Microbiology. 23(2), 1162–1173. 

  • 79. Wang N, Chen XL, Gao C, Peng M, Wang P, Zhang N, Li FC, Yang GP, Shen QT, Chen Y, Zhang YZ, Li CY (2021) Crystal structure of gamma-glytamylmethylamide synthetase provide insight into bacterial metabolism of oceanic monomethylamine. J Biol Chem in press 

  • 78. Shanmugam M, Quareshy M, Cameron AD, Bugg TDH, Chen Y (2021). Light-Activated Electron Transfer and Catalytic Mechanism of Carnitine Oxidation by Rieske-type Oxygenase from Human Microbiota, Angewandte Chemie 60, 4529 – 4534 

  • 77. Quareshy M, Shanmugam M, Townsend E, Jameson E, Bugg TDH, Cameron AD, Chen Y (2021). Structural basis of carnitine monooxygenase CntA substrate specificity, inhibition and inter-subunit electron transfer. J Biol Chem. in press 

  • 76. Lidbury I DAE, Borsetto C, Murphy AR, Bottrill A, Jones A, Bending GD, Hammond JP, Chen Y, Wellington EMH, Scanlan DJ (2021) Niche-adaptation in plant-associated Bacteroidetes favours specialisation in organic phophorus mineralisation. ISME Journal, 15:1040–1055 

  • 75. Ma RC, Chu YX, Wang J, Wang C, Leign MB, Chen Y, He R (2021) Stable-isotopic and metagenomic analyses reveal metabolic and microbial link of aerobic methane oxidation coupled to denitrification at different O2 levels. Science of the Total Environment, 764,142901 

 

2020

  • 74. E Silvano, M Yang, M Wolterink, H-A Giebel, M Simon, D J Scanlan, Y Zhao, Y Chen (2020) Lipidomic analysis of roseobacters of the pelagic RCA cluster and their response to phosphorus limitation, Frontiers In Microbiology doi.org/10.3389/fmicb.2020.552135

  • 73. F Xu, XL Chen, XH Sun, F Dong, CY Li, PY Li, HT Ding, Y Chen, YZ Zhang, P Wang (2020) Structural and molecular basis for the substrate positioning mechanism of a new PL7 subfamily alginate lyase from the Arctic. J Biol Chem 295(48) 16380–16392. 

  • 72. AT Kengmo, RA Jones, A Kuroki, MT Alam, S Perrier, Y Chen, M Unnikrishnan (2020) The type VII secretion system protects Staphylococcus aureus against antimicrobial host fatty acids. Scientific Reports 10, https://www.nature.com/articles/s41598-020-71653-z 

  • 71. Wang Y, Li PY, Zhang Y, Cao HY, Wang YJ, Li CY, Wang P, Su HN, Chen Y, Chen XL, Zhang YZ. (2020) 3,6-anhydro-L-galactose dehydrogenase VvAHGD is a member of a new aldehyde dehydrogenase family and catalyzes by a novel mechanism with conformational switch of two catalytic residues cysteine 282 and glutamate 248. J Mol Biol, 432:2186-2203 

  • 70. Tang BL, Yang J, Chen XL, Wang P, Zhao HL, Su HN, Li CY, Yu Y, Zhong S, Wang L, Lidbury I, Ding H, Wang M, McMinn A, Zhang XY, Y Chen, Zhang YZ (2019) A predator-prey interaction between a marine Pseudoalteromonas sp. and Gram-positive bacteria. Nature Communications 11,285 (2020) doi:10.1038/s41467-019-14133-x 

 

2019

  • 69. F Dong, F Xu, XL Chen, PY Li, CY Li, Y Chen, P Wang, YZ Zhang (2019) Alginate lyase Aly36B is a new bacterial member of the polysaccharide lyase family 36 and catalyzes by a novel mechanism with lysine as both the catalytic base and catalytic acid. Journal of Molecular Biology. 431, 4897-4909. 

  • 68. HJ Jones, E Krober, J Stephenson, M Mausz, E Jameson, A Millard, KJ Purdy, Y Chen (2019) A new family of uncultivated bacteria involved in methanogenesis from the ubiquitous osmolyte glycine betaine in coastal saltmarsh sediments. Microbiome, http://doi.org/10.1186/s40168-019-0732-4.

  • 67 Taubert M, Grob C, Crombie A, Howat AM, Burns OJ, Weber M, Lott C, Kaster AK, Vollmers J, Jehmlich N, von Bergen M, Chen Y, Murrell JC (2019) Aerobic communal metabolism of methane by Methylococcaceae and Methylophilaceae at a shallow seep near Elba, Italy. Environmental Microbiology, 10:3780-3795 

  • 66. Y Chen, H Schäfer (2019) Towards a systematic understanding of structure-function relationship of dimethylsulfoniopropionate-catabolizing enzymes. Molecular Microbiology (micro-commentary). 111(6), 1399–1403.

  • 65. M Mausz, Y Chen (2019) Microbiology and ecology of methylamine metabolism in the marine environment. In Methylotrophs and Methylotroph Communities. Caister Academic Press 33:133-148.

  • 64. J Sun, MA Mausz, Y Chen, S Giovannoni (2019) Microbial Trimethylamine Metabolism in Marine Environments. Environmental Microbiology. 21(2):513-520. 

  • 63. E Jameson, J Stephenson, H Jones, A Millard, AK Kaster, KJ Purdy, R Airs, JC Murrell, Y Chen*. (2019) Deltaproteobacteria (Pelobacter) and Methanococcides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment. ISME Journal, 13(2):277–289 

  • 62. AF Smith, B Rihtman, R Stirrup, E Silvano, M Mausz, DJ Scanlan, Y Chen* (2019) Elucidation of glutamine lipid biosynthesis in marine bacteria reveals its importance under phosphorus deplete growth in Rhodobacteraceae. ISME Journal. 13(1):39-49 

 

2018

  • 61. T Wei, M Quareshy, Y-Z Zhang, DJ Scanlan, Y Chen* (2018) Manganese is essential for PlcP metallophosphoesterase activity involved in lipid remodelling in abundant marine heterotrophic bacteria. Applied and Environmental Microbiology,84(15):e01109-18 

  • 60. AM Howat, J Vollmers, M Taubert, C Grob, JL Dixon, JD Todd, Y Chen, A-K Kaster, JC Murrell (2018) Comparative genomics and mutational analysis reveals a novel XoxF-utilising methylotroph in the Roseobacter group isolated from the marine environment. Frontiers in Microbiology doi: 10.3389/fmicb.2018.00766

  • 59. Jameson E, Quareshy M, Chen Y (2018) Methodological considerations for the identification of choline and carnitine-degrading bacteria in the gut. Methods. 149:42-48. 

 

2017

  • 58. Lidbury I1, Mausz M1, Scanlan DJ, Chen Y*. (2017) Identification of dimethylamine monooxygenase in marine bacteria reveals a metabolic bottleneck in the marine methylated amine degradation pathway.(1equal contribution). The ISME Journal, 11: 1592-1601 

  • 57. M Taubert, C Grob, AM Howat, OJ Burns, J Pratscher, N Jehmlich, M von Bergen, HH Richnow, Y Chen*, JC Murrell *(2017) Methylamine as a Nitrogen Source for Microorganisms from a Coastal Marine Environment Environmental Microbiology, 19(6): 2246–2257. see highlight by L Stein 

  • 56. CY Li, XL Chen, D Zhang, P Wang, Q Sheng, M Peng, BB Xie, QL Qin, PY Li, XY Zhang, HN Su, XY Song, M Shi, BC Zhou, LY Xun, Y Chen, YZ Zhang (2017) Structural mechanisms for bacterial oxidation of oceanic trimethylamine into trimethylamine N-oxide. Molecular Microbiology 103:992–1003 

  • 55. Jameson E, Taubert M, Coyotzi S, Chen Y, Eyice Ö, Schäfer H, Murrell JC, Neufeld JD, Dumont MG. (2017) DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms. Methods Mol Biol. 1539:57-74 

 

2016

  • 54. Zhu Y, Ksibe AZ, Schäfer H, Blindauer CA, Bugg TDH, Chen Y*. (2016) O2-independent demethylation of trimethylamine N-oxide by Tdm of Methylocella silvestris. The FEBS Journal. 283: 3979–3993.

  • 53. Jameson E, Doxey AC, Airs R, Purdy KJ, Murrell JC, Chen Y*. (2016) Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems. Microbial Geonmics, 2(9): doi:10.1099/mgen.0.000080 

  • 52. Lidbury I, Kröber E, Zhang Z, Zhu Y, Murrell JC, Chen Y*, Schäfer H* (2016) A mechanism for bacterial transformations of DMS to DMSO: a missing link in the marine organic sulfur cycle. Environmental Microbiology18(8), 2754–2766. See highlight  by P Carini.

  • 51. Jameson E1, Fu T1, Brown IR,Paszkiewicz K, Purdy KJ, Frank S*, Chen Y*. (2016) Anaerobic choline metabolism in microcompartments promotes growth and swarming of Proteus mirabilis. (1equal contribution). Environmental Microbiology, 18(9) 2886-2898. 

  • 50. Sibastian M, Smith AF, Gonzalez JM, Fredricks HF, Van Mooy B, Koblizek M, Brandsma J, Koster G, Mestre M, Mostajir B, Pitta P, Postle AD, Sanchez P, Gasol JM, Scanlan DJ, Chen Y. (2016) Lipid remodelling is a widespread strategy in marine heterotrophic bacteria upon phosphorus deficiency. The ISME Journal, 10: 968-978. 

  • 49. Taubert, M., Grob, C., Howat, A.M., Burns, O.J., Chen, Y. Neufeld JD, and Murrell, J.C. (2016) Analysis of Active Methylotrophic Communities: When DNA-SIP Meets High-Throughput Technologies. Methods Mol Biol.  2016;1399:235-55.

  • 48. D. Kumaresan, A.M. Hillebrand-Voiculescu, D. Wisher, J. Stephenson, Y. Chen, J.C. Murrell (2016) Microbial life in unusual cave ecosystems sustained by chemosynthetic primary production. In Microbial Life of Cave Systems Ed. AS Engel P 215-230.

  • 47. Grob, C., Taubert, M., Howat, A.M., Burns, O.J., Chen, Y. and Murrell, J.C. (2016) Chapter: Generating enriched metagenomes from active microorganisms with DNA stable isotope probing. Hydrocarbon and Lipid Microbiology Protocols 163-180.

 

2015

  • 46. Lidbury, I., Kimberley, G., Scanlan, D.J., Murrell, J.C. Chen, Y. (2015) Comparative genomics and mutagenesis analyses of choline metabolism in the marine Roseobacter clade. Environmental Microbiology  17(12):5048–5062. See highlight  by L Bodrossy.

  • 45. Grob, C., Taubert, M., Howat, A.M., Burns, O.J., Dixon, J.L., Richnow H.H., Jehmlich N., von Bergen M., Chen, Y. and Murrell, J.C. (2015)Combining metagenomics with metaproteomics and stable isotope probing reveals metabolic pathways used by a naturally occurring marine methylotroph. Environmental Microbiology 17(10):4007-4018.

  • 44. Taubert, M., Grob, C., Howat, A.M., Burns, O.J., Dixon, J.L., Chen, Y. and Murrell, J.C. (2015) XoxF encoding an alternative methanol dehydrogenase is widespread in coastal marine environments. Environmental Microbiology  17(10):3937-3948.

  • 43. Eyice, O., Namura, M., Chen, Y., Mead, A., Samavedam, S., Schäfer, H. (2015) SIP metagenomics identifies uncultivated Methylophilaceae as dimethylsulphide degrading bacteria in soil and lake sediment. The ISME Journal  9(11): 2336–2348.

  • 42. Zhang, D., Berry, J., Zhu, D., Wang, Y., Chen, Y., Jiang, Bo., Huang, S., Langford, H., Li, G., Davision, P.A., Xu, J., Aries, E., Huang, W.E. (2015) Magnetic nanoparticle mediated isolation of functional bacteria in a complex microbial community. The ISME Journal 9 (3):603-614.

  • 41. Lidbury, I. Murrell, J.C., Chen, Y.* (2015) 'Trimethylamine and trimethylamine N-oxide are supplementary energy sources for a marine heterotrophic bacterium: implications for marine carbon and nitrogen cycling', The ISME Journal  9 (3):610-619. (*corresponding author).

  • 40. Wischer, D., Kumaresan, D., Johnston, A., Khawand M. EI., Stephenson, J., Hillebrand-Voiculescu, A.M., Chen, Y., Murrell, J.C. (2015) Bacterial metabolism of methylated amines and identification of novel methylotrophs in Movile Cave. The ISME Journal , 9(1):195–206.

 

2014

 

2013

  • 36. Z Huang, F Ye, C Zhang, S Chen, Y Chen J Wu, M Togo, XH Xing (2013) Rational design of a tripartite fusion protein of heparinase I enables one-step affinity purification and real-time activity detection. J Biotech, 163:30¨C 37. 

  • 35. S Chen, Z Huang, J Wu, Y Chen, F Ye, C Zhang, R Yatsunami, S Nakamura, X Xing (2013) Combination of site-directed mutagenesis and calcium ion addition for enhanced production of thermostable MBP-fused heparinase I in recombinant Escherichia coli. Appl. Microbiol. Biotechnol. 97(7):2907-16. 

 

2012

  • 34. Y Wang, Y Chen, Q Zhou, S Huang, K Ning, J Xu, RM Kalin, S Rolfe, WE Huang (2012) A culture-independent approach to unravel uncultured bacteria and functional genes in a complex microbial community. PLoS ONE, 7(10): e47530. 

  • 33. Y. Chen* (2012) Comparative genomics of methylated amine utilization by marine Roseobacter clade bacteria and development of functional gene markers (tmm, gmaS). Environmental Microbiology. 14(9)2308-2322.  (*corresponding author).

  • 32. W-L Hung, W.G. Wade, Y. Chen, D.P. Kelly, A.P. Wood (2012) Design and evaluation of novel primers for the detection of genes encoding diverse enzymes of methylotrophy and autotrophy. Pol. J Microbiol. 61(1):11-22. 

 

2011

  • 31. Chen, Y*. Patel, N.A., Crombie, A. Scrivens, J.H. & Murrell, J.C.* (2011) Bacterial flavin-containing monooxygenase is trimethylamine monooxygenase. Proceedings of the National Academy of Science, 108:17791-17796 (*corresponding author).

  • 30. Md.T Rahman, A Crombie, H Moussard, Y Chen and J C Murrell (2011) 'Acetate represses methane oxidation by Methylocella silvestris in a peat soil microcosm', Applied and Environmental Microbiology, 77:4234-4236 

  • 29. Y Chen*, D Kumaresan, JC Murrell (2011) Stable-isotope probing and its application in soil microbiology. Handbook of Soil Science (2nd Edition). Vol. I 28(3):30-38, Ed. PM Huang, Y Li and ME Sumner. Taylor & Francis Group. (*corresponding author).

  • 28. Md T Rahman, A Crombie, Y Chen, N Stralis-Pavese, L Bodrossy, N P McNamara, J C Murrell. (2011) The distribution and abundance of facultative methanotroph Methylocella. ISME J 5, 1061-1066 

  • 27. Y Chen, MG Dumont, JD Neufeld, JC Murrell (2011) 'Towards 'focused metagenomics': A case study combining DNA stable-isotope probing, multiple displacement amplification and metagenomics', in Handbook of Molecular Microbial Ecology, 491- 496, Editors: F J de Bruijn, John Wiley & Sons, Inc.

  • 26. A Cebron, B Louvel, P Faure, C France-Lanord, Y Chen, J C Murrell, C Leyval.(2011) Root exudates modify the diversity of active phenanthrene-degraders in an aged PAH-contaminated soil as revealed by stable isotope probing. Environmental Microbiology 13(3)722-736 

  • 25. Y Chen*, J C Murrell (2011) DNA-stable isotope probing. In Stable Isotope Probing and Related Technologies. 3-24.   Edited by JC Murrell & A Whiteley, ASM press (*corresponding author).

 

2010

  • 24. Y Chen*, JC Murrell. (2010) Methanotrophs in moss. Nature Geoscience 3:(9)595-596. (*corresponding author).

  • 23. Y Chen, A Crombie, Md T Rahman, S N Dedysh, W Liesack, M B Stott, M Alam, A R Theisen, J C Murrell and P F Dunfield. (2010) Complete genome sequence of the aerobic methanotroph Methylocella silvestris BL2. Journal of Bacteriology, 192 (14)3840-3841.

  • 22. Y Chen, J Scanlan, L Song, A Crombie, Md T Rahman, H Schafer, J C Murrell (2010). Gamma-glutamylmethylamide is an essential intermediate for monomethylamine metabolism by Methylocella silvestris. Applied and Environmental Microbiology, 76:4530-4537.

  • 21. Y Chen, K L McAleer, J C Murrell. (2010) Monomethylamine as a nitrogen source for a non-methylotrophic bacterium Agrobacterium tumefaciens. Applied and Environmental Microbiology, 76:4012-4014.

  • 20. Y Chen, J C Murrell. (2010) When metagenomics meets stable isotope probing : recent progresses and future perspectives. Trends in Microbiology, 18 : 157-163.

  • 19. H Jiang, Y Chen, P Jiang, C Zhang, T J Smith, J C Murrell, X-H Xing. (2010) Methanotrophs: multifunctional bacteria with promising applications in environmental engineering. Biochemical Engineering Journal, 49: 277-288.

  • 18. Y Chen, J D Neufeld, M G. Dumont, M W. Friedrich, J. C Murrell (2010) Metagenomic analysis of isotopically enriched DNA. Methods Mol Biol. 668: 67-75.

  • 17. Y Chen, J. C Murrell (2010) Ecology of aerobic methanotrophs and their role in methane cycling. In Handbook of Hydrocarbon and Lipid Microbiology. 28: 3067-3076. Edited by KN Timmis. Springer.

  • 16. Y Chen, J Vohra and J. C Murrell (2010) Application of DNA Stable-isotope probing for bioremediation. Methods Mol Biol. 599:129-139.

 

2009

  • 15. B Han, Y Chen, G Abell, H Jiang, L Bodrossy, J Zhao, J. C Murrell, X-H Xing. (2009) Molecular ecology study of methanotroph community of an alkaline coal mine soil. FEMS Microbiology Ecology, 70: 196-207.

  • 14. Y Chen, L Wu, R Boden, A Hillebrand, D Kumaresan, H Moussard, M Baciu, Y Lu, J C Murrell (2009) Life without light: Microbial diversity and evidence of sulfur- and ammonium-based chemolithotrophy in Movile Cave. The ISME Journal, 3 (9): 1093-1104.

  • 13. F Ye, Y Kuang, S Chen, C Zhang, Y Chen, X-H Xing (2009) Characteristics of low molecular weight heparin production by an ultrafiltration membrane bioreactor using maltose binding protein fused heparinase I. Biochemical Engineering Journal, 46:193-198.

  • 12. B Han, T Su, H Wu, Z Gou, X-H Xing, H Jiang, Y Chen, X Li, J C Murrell. (2009) Paraffin oil as a methane vector for rapid and high cell density cultivation of Methylosinus trichosporium OB3b. Applied Microbiology Biotechnology, 83: 669-677.

 

2008

  • 11. Y Chen, M G. Dumont, J D. Neufeld, L Bodrossy, N Stralis-Pavese, N P. McNamara, N Ostle, M J.I. Briones, and J. C Murrell (2008) Revealing the uncultivated majority: Combining stable isotope probing, multiple displacement amplification and metagenomic analysis of uncultivated Methylocystis in acidic peatlands. Environmental Microbiology, 10 (10): 2609-2622.

  • 10. Y Chen, M G. Dumont, N P. McNamara, P M. Chamberlain, L Bodrossy, N Stralis-Pavese, J. C Murrell. (2008). Diversity of active methanotrophic community in acidic peatland as assessed by mRNA and SIP-PLFA analyses. Environmental Microbiology, 10 (2): 446- 459.

  • 9. Y Chen, N P. McNamara, M G. Dumont, L Bodrossy, N Stralis-Pavese, J. C Murrell. (2008) The impact of Calluna burning and removal on methanotrophs diversity and activity. Applied Soil Ecology, 40 (2): 291-298.

  • 8. J D. Neufeld, Y Chen, M G. Dumont, J. C Murrell. (2008) Marine methylotrophs revealed by stable-isotope probing, multiple displacement amplification and metagenomics. Environmental Microbiology, 10 (6): 1526- 1535.

  • 7. I R. McDonald, L Bodrossy, Y Chen, J. C Murrell. (2008) Molecular ecology techniques for the study of aerobic methanotrophs. Applied and Environmental Microbiology, 74 (5): 1305-1315.

 

2007

  • 6. Y Chen, M G. Dumont, A Cebron, J. C Murrell. (2007) Detection of active methanotrophs in a landfill cover soil through detection of expression of 16S rRNA and functional genes. Environmental Microbiology, 9 (11): 2855- 2869.

  • 5. Y Chen, X-H Xing, F Ye, Y Kuang, M Luo. (2007) Production of MBP-HepA fusion protein in recombinant Escherichia coli by optimization of culture medium. Biochemical Engineering Journal, 34: 114-121.

  • 4. A Cebron, L Bodrossy, Y Chen, A C. Singer, I P. Thompson, J I. Prosser, J. C Murrell. (2007) Identity of active methanotrophs in landfill cover soil as revealed by DNA-stable isotope probing. FEMS Microbiology Ecology, 62: 12-23.

  • 3. Y Chen, X-H Xing, F Ye, Y Kuang. (2007) Soluble expression and rapid quantification of GFP-hepA fusion protein in recombinant Escherichia coli. Chinese Journal of Chemical Engineering. 15(1): 122-126.

 

2006

  • 2. Y Kuang, X-H Xing, Y Chen, F Ye, Y Chen, Y Yan, Z Liu, R Bi. (2006) Production of heparin oligosaccharides by fusion protein of MBP-Heparinase I and the enzyme thermostability. Journal of Molecular Catalysis B: Enzymatic. 43: 90-95.

 

2005

  • 1. Y Chen, X-H Xing, K Lou. (2005) Construction of recombinant E. coli for over-production of soluble heparinase I by fusion to maltose-binding protein. Biochemical Engineering Journal. 23: 155-159.

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