Citation: | Quanrui Chen, Jingfeng Fan, Jie Su, Hongxia Ming, Zhihao Sun, Mengfei Li, Xiaohui Zhao, Yantao Wang, Yingxue Zhang, Huizhen Zhang, Yuan Jin, Xiaowan Ma, Bin Wang. Spatial distribution characteristics of bacterial community structure and gene abundance in sediments of the Bohai Sea[J]. Acta Oceanologica Sinica, 2020, 39(2): 69-78. doi: 10.1007/s13131-020-1554-8 |
[1] |
Alain K, Intertaglia L, Catala P, et al. 2008. Eudoraea adriatica gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae. International Journal of Systematic and Evolutionary Microbiology, 58(10): 2275–2281. doi: 10.1099/ijs.0.65446-0
|
[2] |
Alauzet C, Jumas-Bilak E. 2014. The phylum deferribacteres and the genus Caldithrix. In: Rosenberg E, DeLong E F, Lory S, et al., eds. The Prokaryotes. Berlin, Heidelberg: Springer, 595–611
|
[3] |
Brown M V, Philip G K, Bunge J A, et al. 2009. Microbial community structure in the North Pacific Ocean. The ISME Journal, 3(12): 1374–1386. doi: 10.1038/ismej.2009.86
|
[4] |
Cabrera G, Pérez R, Gómez J M, et al. 2006. Toxic effects of dissolved heavy metals on Desulfovibrio vulgaris and Desulfovibrio sp. strains. Journal of Hazardous Materials, 135(1–3): 40–46. doi: 10.1016/j.jhazmat.2005.11.058
|
[5] |
Dai Tianjiao, Zhang Yan, Tang Yushi, et al. 2016. Identifying the key taxonomic categories that characterize microbial community diversity using full-scale classification: a case study of microbial communities in the sediments of Hangzhou Bay. FEMS Microbiology Ecology, 92(10): fiw150. doi: 10.1093/femsec/fiw150
|
[6] |
Fan Jingfeng, Chen jiaying, Chen Liguang, et al. 2011. Research on denitrifying bacteria quantification and diversity in Liaohe Estuary sediments. Haiyang Xuebao (in Chinese), 33(3): 94–102
|
[7] |
Feng Biwei, Li Xiaoran, Wang Jinhui, et al. 2009. Bacterial diversity of water and sediment in the Changjiang estuary and coastal area of the East China Sea. FEMS Microbiology Ecology, 70(2): 236–248. doi: 10.1111/j.1574-6941.2009.00772.x
|
[8] |
General Administration of Quality Supervision, Inspection and Quarantine of the People’s Republic of China, Standardization Administration of China. 2008. GB 17378.5-2007 The specification for marine monitoring—Part 5: sediment analysis (in Chinese). Beijing: Standards Press of China, 1–104
|
[9] |
Gomez-Alvarez V, Teal T K, Schmidt T M. 2009. Systematic artifacts in metagenomes from complex microbial communities. The ISME Journal, 3(11): 1314–1317. doi: 10.1038/ismej.2009.72
|
[10] |
Guan Xiangyu, Zhu Lingling, Li Youxun, et al. 2014. Composition and variation of sediment bacterial and nirS-harboring bacterial communities at representative sites of the Bohai Gulf coastal zone, China. World Journal of Microbiology and Biotechnology, 30(4): 1291–1300. doi: 10.1007/s11274-013-1553-4
|
[11] |
Guo Xingpan, Lu Dapei, Niu Zuoshun, et al. 2018. Bacterial community structure in response to environmental impacts in the intertidal sediments along the Yangtze Estuary, China. Marine Pollution Bulletin, 126: 141–149. doi: 10.1016/j.marpolbul.2017.11.003
|
[12] |
Gutierrez T. 2017 Aerobic Hydrocarbon-degrading Gammaproteobacteria: Xanthomonadales. In: McGenity T, ed. Taxonomy, Genomics and Ecophysiology of Hydrocarbon-Degrading Microbes. Cham: Springer, 1–15
|
[13] |
Jing Xiaoyan, Gou Honglei, Gong Yanhai, et al. 2018. Raman-activated cell sorting and metagenomic sequencing revealing carbon-fixing bacteria in the ocean. Environmental Microbiology, 20(6): 2241–2255. doi: 10.1111/1462-2920.14268
|
[14] |
Kim Y O, Park S, Nam B H, et al. 2014. Description of Lutimonas halocynthiae sp. nov., isolated from a golden sea squirt (Halocynthia aurantium), reclassification of Aestuariicola saemankumensis as Lutimonas saemankumensis comb. nov. and emended description of the genus Lutimonas. International Journal of Systematic and Evolutionary Microbiology, 64(6): 1984–1990
|
[15] |
Könneke M, Kuever J, Galushko A, et al. 2013. Desulfoconvexum algidum gen. nov., sp. nov., a psychrophilic sulfate-reducing bacterium isolated from a permanently cold marine sediment. International Journal of Systematic and Evolutionary Microbiology, 63(3): 959–964
|
[16] |
Köster M, Meyer-Reil L A. 2001. Characterization of carbon and microbial biomass pools in shallow water coastal sediments of the southern Baltic Sea (Nordrügensche Bodden). Marine Ecology Progress Series, 214: 25–41. doi: 10.3354/meps214025
|
[17] |
Kuever J, Rainey F A, Widdel F. 2015. Desulfobulbus. In: Whitman W B, DeVos P, Chun J, et al., eds. Bergey’s Manual of Systematics of Archaea and Bacteria. Hoboken: John Wiley & Sons, Inc, 1–6
|
[18] |
Li Hongjun, Ye Sheng, Ye Jinqing, et al. 2017. Baseline survey of sediments and marine organisms in Liaohe Estuary: heavy metals, polychlorinated biphenyls and organochlorine pesticides. Marine Pollution Bulletin, 114(1): 555–563. doi: 10.1016/j.marpolbul.2016.09.002
|
[19] |
Liu Zongzhi, DeSantis T Z, Andersen G L, et al. 2008. Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Research, 36(18): e120. doi: 10.1093/nar/gkn491
|
[20] |
Liu Jiwen, Liu Xiaoshou, Wang Min, et al. 2015. Bacterial and archaeal communities in sediments of the north Chinese marginal seas. Microbial Ecology, 70(1): 105–117. doi: 10.1007/s00248-014-0553-8
|
[21] |
Lofrano G, Libralato G, Minetto D, et al. 2017. In situ remediation of contaminated marinesediment: an overview. Environmental Science and Pollution Research, 24(6): 5189–5206. doi: 10.1007/s11356-016-8281-x
|
[22] |
Lv Xiaofei, Ma Bin, Yu Junbao, et al. 2016. Bacterial community structure and function shift along a successional series of tidal flats in the Yellow River Delta. Scientific Reports, 6: 36550. doi: 10.1038/srep36550
|
[23] |
Marshall I P G, Karst S M, Nielsen P H, et al. 2018. Metagenomes from deep Baltic Sea sediments reveal how past and present environmental conditions determine microbial community composition. Marine Genomics, 37: 58–68. doi: 10.1016/j.margen.2017.08.004
|
[24] |
Martiny J B H, Eisen J A, Penn K, et al. 2011. Drivers of bacterial β-diversity depend on spatial scale. Proceedings of the National Academy of Sciences of the United States of America, 108(19): 7850–7854. doi: 10.1073/pnas.1016308108
|
[25] |
Ministry of Environmental Protection of the People’s Republic of China. 2012. HJ 634-2012 Soil-determination of ammonium, nitrite and nitrate by extraction with potassium chloride solution-spectrophotometric methods (in Chinese). Beijing: China Environmental Press, 1–18
|
[26] |
Miroshnichenko M L, Kostrikina N A, Chernyh N A, et al. 2003. Caldithrix abyssi gen. nov., sp. nov., a nitrate-reducing, thermophilic, anaerobic bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent, represents a novel bacterial lineage. International Journal of Systematic and Evolutionary Microbiology, 53(1): 323–329. doi: 10.1099/ijs.0.02390-0
|
[27] |
Muller G. 1969. Index of geoaccumulation in sediments of the Rhine River. Geojournal, 2(3): 108–118
|
[28] |
Müller G, Förstner U. 1976. Schwermetalle in den Sedimenten der Elbe bei Stade: veränderungen seit 1973. Naturwissenschaften, 63(5): 242–243. doi: 10.1007/BF00610914
|
[29] |
Park S, Yoshizawa S, Inomata K, et al. 2012. Halioglobus japonicus gen. nov., sp. nov. and Halioglobus pacificus sp. nov., members of the class Gammaproteobacteria isolated from seawater. International Journal of Systematic and Evolutionary Microbiology, 62(8): 1784–1789
|
[30] |
Quince C, Lanzén A, Curtis T P, et al. 2009. Accurate determination of microbial diversity from 454 pyrosequencing data. Nature Methods, 6(9): 639–641. doi: 10.1038/nmeth.1361
|
[31] |
Shade A. 2018. Understanding microbiome stability in a changing world. Msystems, 3(2): e00157-17. doi: 10.1128/mSystems.00157-17
|
[32] |
Sinkko H, Lukkari K, Sihvonen L M, et al. 2013. Bacteria contribute to sediment nutrient release and reflect progressed eutrophication-driven hypoxia in an organic-rich continental sea. PLoS One, 8(6): e67061. doi: 10.1371/journal.pone.0067061
|
[33] |
Su Zhiguo, Dai Tianjiao, Tang Yushi, et al. 2018. Sediment bacterial community structures and their predicted functions implied the impacts from natural processes and anthropogenic activities in coastal area. Marine Pollution Bulletin, 131: 481–495. doi: 10.1016/j.marpolbul.2018.04.052
|
[34] |
Tian Qi, Wang Jia, Fan Xiaolei, et al. 2014. Methanogenic activity and methanogen diversity in marine gas field sediments. Environmental Science (in Chinese), 35(6): 2322–2327
|
[35] |
Vandieken V, Pester M, Finke N, et al. 2012. Three manganese oxide-rich marine sediments harbor similar communities of acetate-oxidizing manganese-reducing bacteria. The ISME Journal, 6(11): 2078–2090. doi: 10.1038/ismej.2012.41
|
[36] |
Wada M, Suzuki S, Nara T, et al. 2012. Microbial community respiration and structure of dead zone sediments of Omura Bay, Japan. Journal of Oceanography, 68(6): 857–867. doi: 10.1007/s10872-012-0136-6
|
[37] |
Wang Haitao, Gilbert J A, Zhu Yongguan, et al. 2018. Salinity is a key factor driving the nitrogen cycling in the mangrove sediment. Science of the Total Environment, 631–632: 1342–1349. doi: 10.1016/j.scitotenv.2018.03.102
|
[38] |
Wang Yafen, Tam N F Y. 2012. Natural attenuation of contaminated marine sediments from an old floating dock Part II: changes of sediment microbial community structure and its relationship with environmental variables. Science of the Total Environment, 423: 95–103. doi: 10.1016/j.scitotenv.2012.01.066
|
[39] |
Woese C R. 1987. Bacterial evolution. Microbiological Reviews, 51(2): 221–271
|
[40] |
Yang Yonghua, Yao Jian, Hua Xiaomei. 2000. Effect of pesticide pollution against functional microbial diversity in soil. Journal of Microbiology (in Chinese), 20(2): 23–25, 27
|
[41] |
Zhang Huizhen, Chang Yongkai, Chen Quanrui, et al. 2018. Community structure analysis of Archaea and bacteria in sediments of Liaohe Estuary. Haiyang Xuebao (in Chinese), 40(6): 113–130
|
[42] |
Zhang Yao, Zhao Zihao, Dai Minhan, et al. 2014. Drivers shaping the diversity and biogeography of total and active bacterial communities in the South China Sea. Molecular Ecology, 23(9): 2260–2274. doi: 10.1111/mec.12739
|
[43] |
Zhao Yangguo, Feng Gong, Bai Jie, et al. 2014. Effect of copper exposure on bacterial community structure and function in the sediments of Jiaozhou Bay, China. World Journal of Microbiology and Biotechnology, 30(7): 2033–2043. doi: 10.1007/s11274-014-1628-x
|
[44] |
Zheng Binghui, Wang Liping, Liu Lusan. 2014. Bacterial community structure and its regulating factors in the intertidal sediment along the Liaodong Bay of Bohai Sea, China. Microbiological Research, 169(7–8): 585–592. doi: 10.1016/j.micres.2013.09.019
|
[45] |
Zhou Kan, Fan Jie, Liu Hanchu. 2017. Spatiotemporal patterns and driving forces of water pollutant discharge in the Bohai Rim Region. Progress in Geography (in Chinese), 36(2): 171–181. doi: 10.18306/dlkxjz.2017.02.004
|
[46] |
Zinger L, Amaral-Zettler L A, Fuhrman J A, et al. 2011. Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems. PLoS One, 6(9): e24570. doi: 10.1371/journal.pone.0024570
|