Journal of East China Normal University(Natural Science) >

2019 , Vol. 2019 >Issue 3: 164 - 173

DOI: https://doi.org/10.3969/j.issn.1000-5641.2019.03.018

Ecological and Environmental Science

Community structure and gene expression analysis for nitrifier enrichment cultures

  • YU Chen-di ,
  • HOU Li-jun ,
  • ZHENG Yan-ling ,
  • LIU Min ,
  • YIN Guo-yu ,
  • GAO Juan ,
  • LIU Cheng ,
  • CHANG Yong-kai
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  • 1. State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China;
    2. Key Laboratory of Geographic Information Science(Ministry of Education), East China Normal University, Shanghai 200241, China;
    3. School of Geographic Sciences, East China Normal University, Shanghai 200241, China

Received date: 2018-03-02

  Online published: 2019-05-30

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Abstract

Nitrifiers were enriched from the tidal sediments of the Yangtze Estuary. Four kinds of nitrifying groups (accounting for 34.7% of the total reads) were detected based on metagenomics, including the recently discovered complete ammonia oxidizers (comammox), strictly nitrite-oxidizing Nitrospira, β-proteobacterial ammonia-oxidizing bacteria, and ammonia-oxidizing archaea. Comammox accounted for 48% of the detected nitrifiers. In addition, gene expression patterns of the nitrifier group (according to the classification in Evolutionary genealogy of genes:Non-supervised Orthologous Groupsdatabase) were analyzed based on metatranscriptomics. The present study showed the community structure and gene expression characteristics of nitrifiers enriched from the tidal sediments, especially the newly discovered comammox. Results enriched our knowledge about the nitrifying communities of estuarine environment, which have great significance to the further molecular ecology research of the nitrification processes.

Key words： nitrifier; enrichment culture; tidal sediment; community structure; gene expression

Cite this article

YU Chen-di , HOU Li-jun , ZHENG Yan-ling , LIU Min , YIN Guo-yu , GAO Juan , LIU Cheng , CHANG Yong-kai . Community structure and gene expression analysis for nitrifier enrichment cultures[J]. Journal of East China Normal University(Natural Science), 2019 , 2019(3) : 164 -173 . DOI: 10.3969/j.issn.1000-5641.2019.03.018

References

[1] LAM P, LAVIK G, JENSEN M M, et al. Revising the nitrogen cycle in the Peruvian oxygen minimum zone[J]. Proc Natl Acad Sci USA, 2009, 12(106):4752-4757.
[2] KRAFT B, HALINA E T, RITIN S, et al. The environmental controls that govern the end product of bacterial nitrate respiration[J]. Science, 2014, 345(6197):676-679.
[3] VAN KESSEL M A, SPETH D R, ALBERTSEN M, et al. Complete nitrification by a single microorganism[J]. Nature, 2015, 528(7583):555-559.
[4] DAIMS H, LEBEDEVA E V, PJEVAC P, et al. Complete nitrification by Nitrospira bacteria[J]. Nature, 2015, 528(7583):504-509.
[5] LI J, NEDWELL D B, BEDDOW J, et al. AmoA gene abundances and nitrification potential rates suggest that benthic ammonia-oxidizing bacteria and not archaea dominate N cycling in the Colne Estuary, United Kingdom[J]. Appl Environ Microbiol, 2014, 81(1):159-165.
[6] LAGOSTINA L, GOLDHAMMER T, RØY H, et al. Ammonia-oxidizing bacteria of the Nitrosospira cluster 1 dominate over ammonia-oxidizing archaea in oligotrophic surface sediments near the South Atlantic Gyre[J]. Environ Microbiol Reports, 2015, 7(3):404-413.
[7] SHEN J, ZHANG L, DI H J, et al. A review of ammonia-oxidizing bacteria and archaea in Chinese soils[J]. Frontiers in Microbiology, 2012(3):296.
[8] DAIMS H, LÜCKER S, WAGNER M. A new perspective on microbes formerly known as nitrite-oxidizing bacteria[J]. Trends in Microbiology, 2016, 24(9):699-712.
[9] PINTO A J, MARCUS D N, IJAZ U Z, et al. Metagenomic evidence for the presence of comammox Nitrospiralike bacteria in a drinking water system[J]. Msphere, 2015(1):e15-e54.
[10] CHAO Y, MAO Y, YU K, et al. Novel nitrifiers and comammox in a full-scale hybrid biofilm and activated sludge reactor revealed by metagenomic approach[J]. Appl Microbiol Biotechnol, 2016, 100(18):8225-8237.
[11] PALOMO A, JANE FOWLER S, GÜLAY A, et al. Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp.[J]. The ISME Journal, 2016, 10(11):2569-2581.
[12] WANG Y, MA L, MAO Y, et al. Comammox in drinking water systems[J]. Water Research, 2017, 116:332-341.
[13] BARTELME R P, MCLELLAN S L, NEWTON R J. Freshwater recirculating aquaculture system operations drive biofilter bacterial community shifts around a stable nitrifying consortium of ammonia-oxidizing archaea and comammox Nitrospira[J]. Frontiers in Microbiology, 2017(8):101.
[14] WANG J, XIA F, ZELEKE J, et al. An improved protocol with a highly degenerate primer targeting coppercontaining membrane-bound monooxygenase genes for community analysis of methane-and ammonia-oxidizing bacteria[J]. FEMS Microbiol Ecol, 2017, 93(3):w244.
[15] HU H W, HE J Z. Comammox-a newly discovered nitrification process in the terrestrial nitrogen cycle[J]. Journal of Soils & Sediments, 2017, 17(12):1-9.
[16] PJEVAC P, SCHAUBERGER C, POGHOSYAN L, et al. AmoA-targeted polymerase chain reaction primers for the specific detection and quantification of comammox Nitrospira in the environment[J]. Frontiers in Microbiology, 2017(8):1508.
[17] BAKER B J, LAZAR C S, TESKE A P, et al. Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria[J]. Microbiome, 2015, 3(1):3-14.
[18] MURRAY N J, MA Z, FULLER R A. Tidal flats of the Yellow Sea:A review of ecosystem status and anthropogenic threats[J]. Austral Ecology, 2015, 40(4):472-481.
[19] ZHENG Y, HOU L, NEWELL S, et al. Community dynamics and activity of ammonia-oxidizing prokaryotes in intertidal sediments of the Yangtze Estuary[J]. Appl Environ Microbiol, 2013, 80(1):408-419.
[20] STARR M P, STOLP H, TRÜPER H G, et al. The prokaryotes:a handbook on habitats, isolation and identification of bacteria[M].[S.l.]:Springer Science & Business Media, 1981.
[21] HOU L J, LIU M, XU S Y, et al. The effects of semi-lunar spring and neap tidal change on nitrification, denitrification and N2O vertical distribution in the intertidal sediments of the Yangtze estuary, China[J]. Estuarine, Coastal and Shelf Science, 2007, 73(3/4):607-616.
[22] ROTTHAUWE J H, WITZEL K P, LIESACK W. The ammonia monooxygenase structural gene amoa as a functional marker:Molecular fine-scale analysis of natural ammonia-oxidizing populations[J]. Appl Environ Microbiol, 1997, 63(12):4704-4712.
[23] FRANCIS C A, ROBERTS K J, BEMAN J M, et al. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean.[J]. Proc Natl Acad Sci USA, 2005, 102(41):14683-14688.
[24] LI D, LIU C, LUO R, et al. MEGAHIT:An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph[J]. Bioinformatics, 2015, 31(10):1674-1676.
[25] DR M, WALLER A, SUNAGAWA S, et al. Assessment of metagenomic assembly using simulated next generation sequencing data[J]. PLoS ONE, 2012, 7(2):e31386.
[26] NIELSEN H B, ALMEIDA M, JUNCKER A S, et al. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes[J]. Nature Biotechnology, 2014, 32(8):822-828.
[27] KARLSSON F H, FÅK F, NOOKAEW I, et al. Symptomatic atherosclerosis is associated with an altered gut metagenome[J]. Nature Communications, 2012, 3(4):1245.
[28] ZELLER G, TAP J, VOIGT A Y, et al. Potential of fecal microbiota for early-stage detection of colorectal cancer[J]. Mol Syst Biol, 2014, 10(11):766.
[29] LI J, JIA H, CAI X, et al. An integrated catalog of reference genes in the human gut microbiome[J]. Nature Biotechnology, 2014, 32(8):834-841.
[30] GU S, FANG L, XU X. UNIT 11.11 using SOAPaligner for short reads alignment[J]. Current Protocols in Bioinformatics, 2013, 44:11.
[31] FU L, NIU B, ZHU Z, et al. CD-HIT:Accelerated for clustering the next-generation sequencing data[J]. Bioinformatics, 2012, 28(23):3150-3152.
[32] COTILLARD A, KENNEDY S P, KONG L C, et al. Dietary intervention impact on gut microbial gene richness[J]. Nature, 2013, 500(7464):585-588.
[33] BUCHFINK B, XIE C, HUSON D H. Fast and sensitive protein alignment using DIAMOND[J]. Nature Methods, 2014, 12(1):59-60.
[34] QIN J, LI R, RAES J, et al. A human gut microbial gene catalogue established by metagenomic sequencing[J]. Nature, 2010, 464(7285):59-65.
[35] HUSON D H, MITRA S, RUSCHEWEYH H J, et al. Integrative analysis of environmental sequences using MEGAN4[J]. Genome Research, 2011, 21(9):1552-1560.
[36] PRUESSE E, QUAST C, KNITTEL K, et al. SILVA:A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB[J]. Nucleic Acids Research, 2007, 35(21):7188-7196.
[37] GRABHERR M G, HAAS B J, YASSOUR M, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome[J]. Nature Biotechnology, 2011, 29(7):644-652.
[38] TRAPNELL C, WILLIAMS B A, PERTEA G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation[J]. Nature Biotechnology, 2010, 28(5):511-515.
[39] LI B, DEWEY C N. RSEM:Accurate transcript quantification from RNA-Seq data with or without a reference genome[J]. BMC Bioinformatics, 2011, 12(1):323.
[40] PARK B J, PARK S J, YOON D N, et al. Cultivation of autotrophic ammonia-oxidizing archaea from marine sediments in coculture with sulfur-oxidizing bacteria[J]. Appl Environ Microbiol, 2010, 76(22):7575-7587.
[41] 金文标, 李志鑫, 岳洋洋, 等. 一种污水处理系统中氨氧化古细菌富集培养的方法:中国, CN 103451120[P]. 2013-12-18.
[42] GONZALEZ-CABALEIRO R, CURTIS T P O. Study of the competition betw éen complete nitrification by a single organism and ammonia-and nitrite-oxidizing bacteria[C]//Frontiers in Wastewater Treatment and Modelling. Lecture Notes in Civil Engineering, MANNINA G, Cham, 2017:287-291.
[43] KITS K D, SEDLACEK C J, LEBEDEVA E V, et al. Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle[J]. Nature, 2017, 549(7671):269-272.
[44] COSTA E, PÉREZ J, KREFT J. Why is metabolic labour divided in nitrification?[J]. Trends in Microbiology, 2006, 14(5):213-219.
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