Microbial diversity of alkane- and plastic-degrading microbiome in offshore sediments of Ross Sea, Southern Ocean
-
摘要: 石油污染以及塑料垃圾对海洋生态安全具有严重威胁，甚至在南大洋的罗斯海地区也发现石油污染和微塑料的存在。本研究为了获得该地区的低温烷烃降解菌和塑料降解菌，通过采集自南大洋罗斯海地区的12个沉积物样品用于富集分离南大洋低温烷烃降解菌株，结果表明十四烷富集菌群优势属主要包括假单胞菌属（Pseudomonas）、食烷菌属（Alcanivorax）、海单胞菌属（Marinomonas）、假交替单胞菌属（Pseudoalteromonas）等。进一步利用分离获得的烃类富集菌对聚对苯二甲酸乙二醇酯（PET）和聚乙烯（PE）进行降解验证，扫描电子显微镜（SEM）以及傅里叶变换红外光谱技术（ATR-FTIR）证明了Pseudomonas pelagia R1-05-CR3、Pseudomonas taeanensis A11-04-CA4、Halomonas titanicae A11-02-7C2和Rhodococcus cerastii R1-05-7C3这4株细菌对PE可进行有效降解。高效液相色谱质谱技术（UPLC-MS）和SEM结果表明R. cerastii R1-05-7C3、Microbacterium maritypicum RA1-00-CA1、H. titanicae A11-02-7C2对PET塑料具有降解能力。研究结果表明南大洋罗斯海近海沉积物中存在多样性的低温烃类及塑料降解菌，在原位环境污染中发挥自净作用，同时也为低温下烃与塑料污染生物降解提供了菌种资源。Abstract: Oil and plastic pollutants are a serious threat to marine ecosystems and have even been found in the Ross Sea of the Southern Ocean. In order to obtain low-temperature alkane degrading bacteria and plastic-degrading bacteria in the region, a total of twelve sediment samples were collected in the Ross Sea area for enrichment and isolation of alkane-degrading bacteria at low-temperature, and the diversity analyses of the tetradecane-enriched communities showed that the most dominant genera were Pseudomonas, Alcanivorax, Marinomonas, Pseudoalteromonas. The polyethylene terephthalate(PET)and polyethylene(PE)was further validated using the dominant alkane-degrading bacteria. Scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (ATR-FTIR) demonstrated that the four pure cultures of Pseudomonas pelagia R1-05-CR3, Pseudomonas taeanensis A11-04-CA4, Halomonas titanicae A11-02-7C2 and Rhodococcus cerastii R1-05-7C3 could degrade PE effectively. The results of UPLC-MS and SEM confirmed the PET degradation by isolates of R. cerastii R1-05-7C3, Microbacterium maritypicum RA1-00-CA1, and H. titanicae A11-02-7C2. In conclusion, this study reports the diversity of the tetradecane-enriched consortia at low-temperature and plastic degrading bacteria in the offshore sediments of the Ross Sea in the Southern Ocean, which play a selfpurifying role in in-situ environmental contamination, and also provided strain resources for the biodegradation of hydrocarbon and plastic contaminants at low temperature.
-
Key words:
- Ross Sea /
- alkanes /
- polyethylene /
- polyethylene terephthalate /
- biodegradation /
- cold-adapted microorganisms
-
图 1 罗斯海沉积物样品采样站位图
左侧图片来自维基百科
https://www.163.com/dy/article/GHUO74P105526RB5.html Fig. 1 Location map of sediment sampling stations from the Ross Sea
Left image from Wikipedia
https://www.163.com/dy/article/GHUO74P105526RB5.html 
图 2 罗斯海烷烃富集菌群细菌Alpha多样性分析
OTU稀释曲线（a）OTU水平Venn图分析（C0/C1/C2）（b）Shannon指数和Chao指数组间差异分析，Student-t检验（C0/C1/C2）（c1, c2）
Fig. 2 Alpha diversity analysis of tetradecane-enriched consortia from Ross Sea sediments
Rarefaction curves for Sobs index on OTU level (a), Venn diagram analysis on OTU level to depict the number of exclusive and shared OTUs (C0/C1/C2) (b), analysis of intergroup differences in Shannon index and Chao index on OTU level, Student-t test (C0/C1/C2) (c1, c2)
图 3 罗斯海十四烷富集菌群C0/C1/C2组门水平（a），科水平（b）和属水平（c）细菌组成柱形图
Fig. 3 Column diagram of bacterial percent of community abundance atphylum level (a), family level (b), and genus level (c) of tetradecane-enriched consortia of C0/C1/C2 groups from Ross Sea
图 4 罗斯海十四烷富集菌群属水平细菌组成柱形图（a: C0；b: C1, C2）
Fig. 4 Column diagram of bacterial percent of community abundance at genus level of tetradecane-enriched consortia (a: C0; b: C1, C2) from Ross Sea
图 5 罗斯海烷烃富集菌群属水平细菌物种组成差异分析（C0/C1/C2），Kruskal-Wallis秩和检验（a）及OTU水平系统进化分析（C1/C2）（b）
左边为系统发生进化树，进化树中每条树枝代表一类物种，树枝长度为两个物种间的进化距离，右边柱状图展示的是物种在不同分组中的的Reads占比
Fig. 5 Analysis of intergroup differences of community abundance on genus level (C0/C1/C2)，Kruskal-Wallis H test (a) and phylogenetic analysis at OTU level of tetradecane-enriched consortia from Ross Sea (C1/C2) (b)
Each branch of the evolutionary tree on the left represents a OTU, and the length of the branch is the evolutionary distance between two OTUs，the right bar chart shows the proportion of Reads of OTUs in different groups
图 6 细菌Hallmonas titanicae A11-02-7C2，Rhodococcus cerastii R1-05-7C3，Pseudomonas pelagia R1-05-CR3和Pseudomonas taeanensis A11-04-CA4解聚PE的表征特性
左侧图片：菌株生物降解后的PE膜和未接种的PE膜（CK）相比有生物膜附着（a, c）和破损（b）形成。右侧图像：细菌降解后塑料和未接种的PE膜（CK）的 FTIR 分析（d）
Fig. 6 Depolymerization characteristics of the biodegraded PE by the isolated bacterium Hallmonas titanicae A11-02-7C2, Rhodococcus cerastii R1-05-7C3, Pseudomonas pelagia R1-05-CR3 and Pseudomonas taeanensis A11-04-CA4
Left image: the inoculated bacterium attached to PE to form the biofilms (a, c) and visible pores (b) compared with the non-inoculated PE (CK). Right image: FTIR analysis of incubated PE by corresponding strains and non-inoculated PE (CK) (d)
图 7 细菌解聚PET的表征特性
左侧图片：菌株Rhodococcus cerastii R1-05-7C3, Microbacterium maritypicum RA1-00-CA1和H. alomonas titanicae A11-02-7C2生物降解后的PET膜和未接种的PET膜（CK）相比出现生物膜和明显的破损（a）。右侧图像：Rcerastii R1-05-7C3和Maritypicum RA1-00-CA1处理PET 30 d和无细菌处理组（CK）的代谢产物（预测为MHET）和MHET标准品的UPLC出峰时间图（b）
Fig. 7 Depolymerization characteristics of the biodegraded PET by the isolated bacterium
Left image: the inoculated bacterium Rhodococcus cerastii R1-05-7C3, Microbacterium maritypicum RA1-00-CA1 and Halomonas titanicae A11-02-7C2 attached to PET to form the biofilms and visible pores compared with the non-inoculated PET (a). Right image: UPLC spectrum (b) of the standard mono-(2-hydroxyethyl) terephthalate (MHET) and no bacteria-treat group (CK) and the metabolic products (prediction as MHET) released from PET films treated by the pure culture R. cerastii R1-05-7C3 and M. maritypicum RA1-00-CA1 after 30 days
表 1 具体采样点站位信息
Tab. 1 Location information of specific sampling stations
站位名称 取样时间 纬度 经度 水深/m R1-02 2020年1月4日 74º59'S 164º59'E 893.4 R1-05 2020年1月4日 74º59'S 170º24'E 330.5 R1-07 2020年1月5日 75º00'S 175º16'E 285.5 RA1-00 2020年1月10日 75º27'S 149º57'W 3241.5 RA2-01A 2020年1月13日 74º23'S 141º34'W 503.3 RA3-02 2020年1月13日 74º28'S 140º18'W 482 RA3-03 2020年1月14日 74º50'S 139º38'W 2560.8 A3-01 2020年1月29日 73º00'S 119º50'W 405.8 A11-04 2020年1月25日 72º10'S 117º50'W 502.1 A11-02 2020年1月26日 72º58'S 115º03'W 659.5 A11-01 2020年1月26日 73º26'S 113º31'W 622.6 A4-03 2020年1月27日 72º42'S 112º24'W 438.2 
下载: 导出CSV
表 2 验证纯菌株对烷烃，PET和PE降解能力
Tab. 2 Verify the degradation ability of pure strains on alkanes, PET and PE
烷烃降解 PET 降解 PE降解 菌株名称 热门分类单元 所属科 w - + A11-04-CA4 Pseudomonas taeanensis MS-3T Pseudomonadaceae + + - RA1-00-CA1 Microbacterium maritypicum DSM 20578 TMicrobacteriaceae + + + A11-02-7C2 Halomonas titanicae BH1T Halomonadaceae + + + R1-05-CR3 Pseudomonas pelagia CL-AP6T Pseudomonadaceae + + w A11-02-CR2 Pseudomonas xanthomarina DSM 18231 TPseudomonadaceae + + + A3-01-CR8 Psychrobacter okhotskensis MD17T Moraxellaceae + + + R1-05-7C3 Rhodococcus cerastii C5T Nocardiaceae - - - A11-02-CA2 Marinomonas rhizomae IVIA-Po-145T Oceanospirillaceae - - - A11-04-CA2 Pseudoalteromonas neustonica PAMC 28425 TPseudoalteromonadaceae - - - A4-03-CR4 Pseudomonas neustonica SSM26T Pseudomonadaceae + - - A3-01-7C5 Rhodococcus erythropolis NBRC 15567 TNocardiaceae - - - A11-02-CA1 Shewanella livingstonensis LMG 19866 TShewanellaceae + + + A11-02-7C4 Alcanivorax borkumensis SK2T Alcanivoracaceae w + w R1-05-7C2 Pseudomonas zhaodongensis NEAU-ST5-21T Pseudomonadaceae 注：-, 不降解；w，降解效果微弱；+，降解效果良好。
下载: 导出CSV
-
[1] Bargagli R, Rota E. Microplastic interactions and possible combined biological effects in antarctic marine ecosystems[J]. Animals, 2022, 13(1): 162. doi: 10.3390/ani13010162 [2] Suaria G, Perold V, Lee J R, et al. Floating macro- and microplastics around the Southern Ocean: results from the Antarctic Circumnavigation Expedition[J]. Environment International, 2020, 136: 105494. doi: 10.1016/j.envint.2020.105494 [3] Cincinelli A, Scopetani C, Chelazzi D, et al. Microplastic in the surface waters of the Ross Sea (Antarctica): occurrence, distribution and characterization by FTIR[J]. Chemosphere, 2017, 175: 391−400. doi: 10.1016/j.chemosphere.2017.02.024 [4] Munari C, Infantini V, Scoponi M, et al. Microplastics in the sediments of Terra Nova Bay (Ross Sea, Antarctica)[J]. Marine Pollution Bulletin, 2017, 122(1/2): 161−165. [5] Cunningham E M, Ehlers S M, Dick J T A, et al. High abundances of microplastic pollution in deep-sea sediments: evidence from antarctica and the Southern Ocean[J]. Environmental Science & Technology, 2020, 54(21): 13661−13671. [6] Vázquez S, Monien P, Pepino Minetti R, et al. Bacterial communities and chemical parameters in soils and coastal sediments in response to diesel spills at Carlini Station, Antarctica[J]. Science of the Total Environment, 2017, 605-606: 26−37. doi: 10.1016/j.scitotenv.2017.06.129 [7] Zakaria N N, Convey P, Gomez-Fuentes C, et al. Oil bioremediation in the marine environment of antarctica: a review and bibliometric keyword cluster analysis[J]. Microorganisms, 2021, 9(2): 419. doi: 10.3390/microorganisms9020419 [8] Curtosi A, Pelletier E, Vodopivez C L, et al. Polycyclic aromatic hydrocarbons in soil and surface marine sediment near Jubany Station (Antarctica). Role of permafrost as a low-permeability barrier[J]. Science of the Total Environment, 2007, 383(1/3): 193−204. [9] Luigi M, Gaetano D M, Vivia B, et al. Biodegradative potential and characterization of psychrotolerant polychlorinated biphenyl-degrading marine bacteria isolated from a coastal station in the Terra Nova Bay (Ross Sea, Antarctica)[J]. Marine Pollution Bulletin, 2007, 54(11): 1754−1761. doi: 10.1016/j.marpolbul.2007.07.011 [10] Yakimov M M, Giuliano L, Bruni V, et al. Characterization of antarctic hydrocarbon-degrading bacteria capable of producing bioemulsifiers[J]. The New Microbiologica, 1999, 22(3): 249−256. [11] Pepi M, Cesàro A, Liut G, et al. An antarctic psychrotrophic bacterium Halomonas sp. ANT-3b, growing on n-hexadecane, produces a new emulsyfying glycolipid[J]. FEMS Microbiology Ecology, 2005, 53(1): 157−166. doi: 10.1016/j.femsec.2004.09.013 [12] Lo Giudice A, Michaud L, De Pascale D, et al. Lipolytic activity of Antarctic cold-adapted marine bacteria (Terra Nova Bay, Ross Sea)[J]. Journal of Applied Microbiology, 2006, 101(5): 1039−1048. doi: 10.1111/j.1365-2672.2006.03006.x [13] Yakimov M M, Gentile G, Bruni V, et al. Crude oil-induced structural shift of coastal bacterial communities of rod bay (Terra Nova Bay, Ross Sea, Antarctica) and characterization of cultured cold-adapted hydrocarbonoclastic bacteria[J]. FEMS Microbiology Ecology, 2004, 49(3): 419−432. doi: 10.1016/j.femsec.2004.04.018 [14] Sfriso A A, Tomio Y, Rosso B, et al. Microplastic accumulation in benthic invertebrates in Terra Nova Bay (Ross Sea, Antarctica)[J]. Environment International, 2020, 137: 105587. doi: 10.1016/j.envint.2020.105587 [15] Zadjelovic V, Erni-Cassola G, Obrador-Viel T, et al. A mechanistic understanding of polyethylene biodegradation by the marine bacterium Alcanivorax[J]. Journal of Hazardous Materials, 2022, 436: 129278. doi: 10.1016/j.jhazmat.2022.129278 [16] Delacuvellerie A, Cyriaque V, Gobert S, et al. The plastisphere in marine ecosystem hosts potential specific microbial degraders including Alcanivorax borkumensis as a key player for the low-density polyethylene degradation[J]. Journal of Hazardous Materials, 2019, 380: 120899. doi: 10.1016/j.jhazmat.2019.120899 [17] Moog D, Schmitt J, Senger J, et al. Using a marine microalga as a chassis for polyethylene terephthalate (PET) degradation[J]. Microbial Cell Factories, 2019, 18(1): 171. doi: 10.1186/s12934-019-1220-z [18] Tournier V, Topham C M, Gilles A, et al. An engineered PET depolymerase to break down and recycle plastic bottles[J]. Nature, 2020, 580(7802): 216−219. doi: 10.1038/s41586-020-2149-4 [19] Yoshida S, Hiraga K, Takehana T, et al. A bacterium that degrades and assimilates poly(ethylene terephthalate)[J]. Science, 2016, 351(6278): 1196−1199. doi: 10.1126/science.aad6359 [20] Blázquez-Sánchez P, Engelberger F, Cifuentes-Anticevic J, et al. Antarctic polyester hydrolases degrade aliphatic and aromatic polyesters at moderate temperatures[J]. Applied and Environmental Microbiology, 2022, 88(1): e0184221. doi: 10.1128/AEM.01842-21 [21] Yakimov M M, Bargiela R, Golyshin P N. Calm and Frenzy: Marine obligate hydrocarbonoclastic bacteria sustain ocean wellness[J]. Current Opinion in Biotechnology, 2022, 73: 337−345. doi: 10.1016/j.copbio.2021.09.015 [22] Denaro R, Aulenta F, Crisafi F, et al. Marine hydrocarbon-degrading bacteria breakdown poly(ethylene terephthalate) (PET)[J]. Science of the Total Environment, 2020, 749: 141608. doi: 10.1016/j.scitotenv.2020.141608 [23] Roberts C, Edwards S, Vague M, et al. Environmental consortium containing Pseudomonas and Bacillus species synergistically degrades polyethylene terephthalate plastic[J]. mSphere, 2020, 5(6): e01151−20. [24] Zhao Sufang, Liu Renju, Wang Juan, et al. Biodegradation of polyethylene terephthalate (PET) by diverse marine bacteria in deep-sea sediments[J]. Environmental Microbiology, 2023, 25(12): 2719−2731. doi: 10.1111/1462-2920.16460 [25] Hassanshahian M, Emtiazi G, Cappello S. Isolation and characterization of crude-oil-degrading bacteria from the Persian Gulf and the Caspian Sea[J]. Marine Pollution Bulletin, 2012, 64(1): 7−12. doi: 10.1016/j.marpolbul.2011.11.006 [26] 叶静, 戴文芳, 刘圣, 等. 熊本牡蛎、葡萄牙牡蛎和长牡蛎组织菌群构成及功能的比较分析[J]. 海洋学报, 2022, 44(8): 66−77.Ye Jing, Dai Wenfang, Liu Sheng, et al. Comparison of the composition and functional potentials of bacterial communities in different tissues from Crassostrea sikamea, Crassostrea angulata and Crassostrea gigas[J]. Haiyang Xuebao, 2022, 44(8): 66−77. [27] Hassanshahian M, Boroujeni N A. Enrichment and identification of naphthalene-degrading bacteria from the Persian Gulf[J]. Marine Pollution Bulletin, 2016, 107(1): 59−65. doi: 10.1016/j.marpolbul.2016.04.020 [28] Gao Rongrong, Sun Chaomin. A marine bacterial community capable of degrading poly(ethylene terephthalate) and polyethylene[J]. Journal of Hazardous Materials, 2021, 416: 125928. doi: 10.1016/j.jhazmat.2021.125928 [29] Cole M, Lindeque P, Halsband C, et al. Microplastics as contaminants in the marine environment: a review[J]. Marine Pollution Bulletin, 2011, 62(12): 2588−2597. doi: 10.1016/j.marpolbul.2011.09.025 [30] Vergeynst L, Wegeberg S, Aamand J, et al. Biodegradation of marine oil spills in the Arctic with a Greenland perspective[J]. Science of the Total Environment, 2018, 626: 1243−1258. doi: 10.1016/j.scitotenv.2018.01.173 [31] Tapilatu Y, Acquaviva M, Guigue C, et al. Isolation of alkane-degrading bacteria from deep-sea Mediterranean sediments[J]. Letters in Applied Microbiology, 2010, 50(2): 234−236. doi: 10.1111/j.1472-765X.2009.02766.x [32] 王世杰, 王翔, 卢桂兰, 等. 低温微生物修复石油烃类污染土壤研究进展[J]. 应用生态学报, 2011, 22(4): 1082−1088.Wang Shijie, Wang Xiang, Lu Guilan, et al. Bioremediation of petroleum hydrocarbon-contaminated soils by cold-adapted microorganisms: research advance[J]. Chinese Journal of Applied Ecology, 2011, 22(4): 1082−1088. [33] Cappello S, Corsi I, Patania S, et al. Characterization of five psychrotolerant Alcanivorax spp. strains isolated from antarctica[J]. Microorganisms, 2022, 11(1): 58. doi: 10.3390/microorganisms11010058 [34] Koh J, Bairoliya S, Salta M, et al. Sediment-driven plastisphere community assembly on plastic debris in tropical coastal and marine environments[J]. Environment International, 2023, 179: 108153. doi: 10.1016/j.envint.2023.108153 [35] Khandare S D, Chaudhary D R, Jha B. Marine bacterial biodegradation of low-density polyethylene (LDPE) plastic[J]. Biodegradation, 2021, 32(2): 127−143. doi: 10.1007/s10532-021-09927-0 [36] Bitalac J M S, Lantican N B, Gomez N C F, et al. Attachment of potential cultivable primo-colonizing bacteria and its implications on the fate of low-density polyethylene (LDPE) plastics in the marine environment[J]. Journal of Hazardous Materials, 2023, 451: 131124. doi: 10.1016/j.jhazmat.2023.131124 [37] Wilkes R A, Aristilde L. Degradation and metabolism of synthetic plastics and associated products by Pseudomonas sp. : Capabilities and challenges[J]. Journal of Applied Microbiology, 2017, 123(3): 582−593. doi: 10.1111/jam.13472 [38] Bacha A U R, Nabi I, Zaheer M, et al. Biodegradation of macro- and micro-plastics in environment: A review on mechanism, toxicity, and future perspectives[J]. Science of the Total Environment, 2023, 858: 160108. doi: 10.1016/j.scitotenv.2022.160108 [39] Lv Shiwei, Cui Kexin, Zhao Sufang, et al. Continuous generation and release of microplastics and nanoplastics from polystyrene by plastic-degrading marine bacteria[J]. Journal of Hazardous Materials, 2024, 465: 133339. doi: 10.1016/j.jhazmat.2023.133339 [40] Liu R, Xu H, Zhao S, et al. Polyethylene terephthalate (PET)-degrading bacteria in the pelagic deep-sea sediments of the Pacific Ocean[J]. Environ Pollut, 2024, 352:124131. [41] Auta H S, Emenike C U, Jayanthi B, et al. Growth kinetics and biodeterioration of polypropylene microplastics by Bacillus sp. and Rhodococcus sp. isolated from mangrove sediment[J]. Marine Pollution Bulletin, 2018, 127: 15−21. [42] Guo Wenbin, Duan Jingjing, Shi Zhengguang, et al. Biodegradation of PET by the membrane-anchored PET esterase from the marine bacterium Rhodococcus pyridinivorans P23[J]. Communications Biology, 2023, 6(1): 1090. [43] Yan Zhengfei, Wang Lei, Xia Wei, et al. Synergistic biodegradation of poly(ethylene terephthalate) using Microbacterium oleivorans and Thermobifida fusca cutinase[J]. Applied Microbiology and Biotechnology, 2021, 105(11): 4551−4560. [44] Habib S, Iruthayam A, Abd Shukor M Y, et al. Biodeterioration of untreated polypropylene microplastic particles by antarctic bacteria[J]. Polymers, 2020, 12(11): 2616. [45] Won S J, Yim J H, Kim H K. Functional production, characterization, and immobilization of a cold-adapted cutinase from Antarctic Rhodococcus sp.[J]. Protein Expression and Purification, 2022, 195−196: 106077. [46] Zhang Ailin, Hou Yanhua, Wang Quanfu, et al. Characteristics and polyethylene biodegradation function of a novel coldadapted bacterial laccase from Antarctic sea ice psychrophile Psychrobacter sp. NJ228[J]. Journal of Hazardous Materials, 2022, 439: 129656. -
计量
- 文章访问数: 109
- HTML全文浏览量: 47
- PDF下载量: 20
- 被引次数: 0
