长江下游厌氧氨氧化细菌标记基因相对丰度及影响因素
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摘要
为探索河流系统中厌氧氨氧化细菌的分布情况,于2014年春秋两季采集长江下游6个断面的水体和沉积物样品,通过宏基因组测序方法,根据优化序列与自建厌氧氨氧化细菌标记基因hzsA, hzsB, hzsC, hdh数据集的比对结果,计算各基因相对丰度。结果表明,水体溶解氧浓度较高导致厌氧氨氧化细菌标记基因丰度极低,而沉积物中各基因相对丰度较高,平均值分别为4.540×10~(-10), 4.939×10~(-10), 4.333×10~(-10)和2.859×10~(-10)。随着温度升高,秋季沉积物中各基因相对丰度显著高于春季。大通、南京和徐六泾沉积物中各基因相对丰度较高,这与人类活动扰动的增强以及入海口盐度升高有关。物种分类鉴定结果表明,长江下游沉积物中厌氧氨氧化细菌在属水平上以Candidatus Brocadia和Candidatus Jettenia为主。厌氧氨氧化细菌标记基因相对丰度与NO_2~--N,NO_3~--N和NH_4~+-N等理化因子相关,并且,由于NO_2~--N浓度远远低于NH_4~+-N,因此NO_2~--N浓度是长江下游沉积物中厌氧氨氧化细菌生长的限制性因子。
In order to investigate the distribution of anammox bacteria in river ecosystems, water and sediment samples were collected at 6 sites along the lower Yangtze River in spring and autumn in 2014. Clean reads of metagenomic sequencing were BLAST against self-constructed datasets of anammox bacterial marker genes hzsA,hzsB, hzsC and hdh, and valid hits were used to calculate their relative abundances. As results, average relative abundances of hzsA, hzsB, hzsC and hdh genes in water were extremely low due to the excess dissolved oxygen which was not suitable for anammox bacteria. Whereas, the average relative abundances in sediments were much higher, i.e., 4.540×10~(-10), 4.939×10~(-10), 4.333×10~(-10) and 2.859×10~(-10), respectively. Due to the temperature rise,average relative abundances of hzsA, hzsB, hzsC and hdh genes in sediment samples in autumn were higher than those in spring. From the changes alongside the river, average relative abundances of hzsA, hzsB, hzsC and hdh genes at Datong, Nanjing and Xuliujing were relatively higher, which was due to anthropogenic activity and salinity increase in the estuary. Based on the results of taxonomic identification, anammox bacteria in the lower Yangtze River mainly consisted of Candidatus Brocadia and Candidatus Jettenia at genus level. Relative abundances of hzsA, hzsB, hzsC and hdh genes were related to NO_2~--N, NO_3~--N and NH_4~+-N concentration, of which NO_2~--N concentration was the restrictive factor as it was much lower than NH_4~+-N concentration.
In order to investigate the distribution of anammox bacteria in river ecosystems, water and sediment samples were collected at 6 sites along the lower Yangtze River in spring and autumn in 2014. Clean reads of metagenomic sequencing were BLAST against self-constructed datasets of anammox bacterial marker genes hzsA,hzsB, hzsC and hdh, and valid hits were used to calculate their relative abundances. As results, average relative abundances of hzsA, hzsB, hzsC and hdh genes in water were extremely low due to the excess dissolved oxygen which was not suitable for anammox bacteria. Whereas, the average relative abundances in sediments were much higher, i.e., 4.540×10~(-10), 4.939×10~(-10), 4.333×10~(-10) and 2.859×10~(-10), respectively. Due to the temperature rise,average relative abundances of hzsA, hzsB, hzsC and hdh genes in sediment samples in autumn were higher than those in spring. From the changes alongside the river, average relative abundances of hzsA, hzsB, hzsC and hdh genes at Datong, Nanjing and Xuliujing were relatively higher, which was due to anthropogenic activity and salinity increase in the estuary. Based on the results of taxonomic identification, anammox bacteria in the lower Yangtze River mainly consisted of Candidatus Brocadia and Candidatus Jettenia at genus level. Relative abundances of hzsA, hzsB, hzsC and hdh genes were related to NO_2~--N, NO_3~--N and NH_4~+-N concentration, of which NO_2~--N concentration was the restrictive factor as it was much lower than NH_4~+-N concentration.
引文
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[22]Jacomy M,Bastian M,Heymann S.Gephi:an open source software for exploring and manipulating networks//Proceedings of the Third International Conference on Weblogs and Social Media.San Jose,2009:doi:10.13140/2.1.1341.1520
[23]Strous M,Van G E,Kuenen J G,et al.Effects of aerobic and microaerobic conditions on anaerobic ammonium-oxidizing(anammox)sludge.Applied and Environmental Microbiology,1997,63(6):2446-2448
[24]Laureni M,Weissbrodt D G,Szivák I,et al.Activity and growth of anammox biomass on aerobically pretreated municipal wastewater.Water Research,2015,80:325-336
[25]Tomaszewski M,Cema G,Ziembińskabuczyńska A.Influence of temperature and pH on the anammox process:a review and meta-analysis.Chemosphere,2017,182:203-214
[26]Koop-Jakobsen K,Giblin A E.Anammox in tidal marsh sediments:the role of salinity,nitrogen loading,and marsh vegetation.Estuaries and Coasts,2009,32(2):238-245
[27]Speth D R,In’t Zandt M H,Simon G C,et al.Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system.Nature Communications,2016,7:11172
[28]Newman M E.Modularity and community structure in networks//APS March Meeting.Baltimore:American Physical Society,2006:8577-8582
[29]Strous M,Heijnen J J,Kuenen J G,et al.The sequencing batch reactor as a powerful tool for the study of slowly growing anaerobic ammonium-oxidizing microorganisms.Applied Microbiology and Biotechnology,1998,50(5):589-596
[2]Humbert S,Tarnawski S,Fromin N,et al.Molecular detection of anammox bacteria in terrestrial ecosystems:distribution and diversity.The ISME Journal,2010,4(3):450-454
[3]王衫允,祝贵兵,曲冬梅,等.白洋淀富营养化湖泊湿地厌氧氨氧化菌的分布及对氮循环的影响.生态学报,2012,32(21):6591-6598
[4]Dalsgaard T,Thamdrup B,Canfield D E.Anaerobic ammonium oxidation(anammox)in the marine environment.Research in Microbiology,2005,156(4):457-464
[5]Van D U,Jetten M S,van Loosdrecht M C.The SHARON?-Anammox?process for treatment of ammonium rich wastewater.Water Science and Technology,2001,44(1):153-160
[6]Zhang Y,Ruan X H,Hj O D C,et al.Diversity and abundance of aerobic and anaerobic ammoniumoxidizing bacteria in freshwater sediments of the Xinyi River(China).Environmental Microbiology,2007,9(9):2375-2382
[7]Hu Baolan,Shen Lidong,Zheng Ping,et al.Distribution and diversity of anaerobic ammonium-oxidizing bacteria in the sediments of the Qiantang River.Environmental Microbiology Reports,2012,4(5):540-547
[8]Sun Wei,Xu Meiying,Wu Weimin,et al.Molecular diversity and distribution of anammox community in sediments of the Dongjiang River,a drinking water source of Hong Kong.Journal of Applied Microbiology,2014,116(2):464-476
[9]Amano T,Yoshinaga I,Okada K,et al.Detection of anammox activity and diversity of anammox bacteriarelated 16S rRNA genes in coastal marine sediment in Japan.Microbes and Environments,2007,22(3):232-242
[10]Bhattacharjee A S,Wu S,Lawson C E,et al.Wholecommunity metagenomics in two different anammox configurations:process performance and community structure.Environmental Science&Technology,2017,51(8):4317-4327
[11]Harhangi H R,Le Roy M,van Alen T,et al.Hydrazine synthase,a unique phylomarker with which to study the presence and biodiversity of anammox bacteria.Applied and Environmental Microbiology,2012,78(3):752-758
[12]Hou Lijun,Liu Min,Xu Shiyuan,et al.The diffusive fluxes of inorganic nitrogen across the intertidal sediment-water interface of the Changjiang Estuary in China.Acta Oceanologica Sinica,2006,25(3):48-57
[13]Joshi N,Fass J.Sickle:a sliding-window,adaptive,quality-based trimming tool for fastq files(Version1.33)[EB/OL].(2011)[2018-04-01].https://github.com/najoshi/sickle
[14]Patel R K,Jain M.NGS QC toolkit:a toolkit for quality control of next generation sequencing data.Plos One,2012,7(2):e30619
[15]Yu Peng,Leung H C,Yiu S M,et al.IDBA-UD:a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.Bioinformatics,2012,28(11):1420-1428
[16]Zhu W H,Lomsadze A,Borodovsky M.Ab initio gene identification in metagenomic sequences.Nucleic Acids Research,2010,38(12):e132
[17]Edgar R C.Search and clustering orders of magnitude faster than BLAST.Bioinformatics,2010,26(19):2460-2461
[18]Lobo I.Basic local alignment search tool(BLAST).Journal of Molecular Biology,2012,215(3):403-410
[19]Buchfink B,Xie Chao,Huson D H.Fast and sensitive protein alignment using DIAMOND.Nature Methods,2015,12(1):59-60
[20]Katoh K,Standley D M.MAFFT multiple sequence alignment software version 7:improvements in performance and usability.Molecular Biology and Evolution,2013,30(4):772-780
[21]Price M N,Dehal P S,Arkin A P.FastTree 2-approximately maximum-likelihood trees for large alignments.Plos One,2010,5(5):e9490
[22]Jacomy M,Bastian M,Heymann S.Gephi:an open source software for exploring and manipulating networks//Proceedings of the Third International Conference on Weblogs and Social Media.San Jose,2009:doi:10.13140/2.1.1341.1520
[23]Strous M,Van G E,Kuenen J G,et al.Effects of aerobic and microaerobic conditions on anaerobic ammonium-oxidizing(anammox)sludge.Applied and Environmental Microbiology,1997,63(6):2446-2448
[24]Laureni M,Weissbrodt D G,Szivák I,et al.Activity and growth of anammox biomass on aerobically pretreated municipal wastewater.Water Research,2015,80:325-336
[25]Tomaszewski M,Cema G,Ziembińskabuczyńska A.Influence of temperature and pH on the anammox process:a review and meta-analysis.Chemosphere,2017,182:203-214
[26]Koop-Jakobsen K,Giblin A E.Anammox in tidal marsh sediments:the role of salinity,nitrogen loading,and marsh vegetation.Estuaries and Coasts,2009,32(2):238-245
[27]Speth D R,In’t Zandt M H,Simon G C,et al.Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system.Nature Communications,2016,7:11172
[28]Newman M E.Modularity and community structure in networks//APS March Meeting.Baltimore:American Physical Society,2006:8577-8582
[29]Strous M,Heijnen J J,Kuenen J G,et al.The sequencing batch reactor as a powerful tool for the study of slowly growing anaerobic ammonium-oxidizing microorganisms.Applied Microbiology and Biotechnology,1998,50(5):589-596
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