我们于2016年3月在scientific reports 发表了一株来源于污水处理系统的氨氧化古菌（AOA）——Nitrosotenuis cloacae SAT1（污泥细小亚硝化菌）， 下面展示一下文章的补充材料，相信大家对该菌会有更多的认识： Nitrosotenuis cloacae SAT1 -Supporting information original article ： A novel ammonia-oxidizing archaeon from wastewater treatment plant: Its enrichment, physiological and genomic characteristics http://www.nature.com/articles/srep23747 Yuyang Li 1 , Kun Ding 1 , Xianghua Wen 1* , Bing Zhang 1 , Bo Shen 1 , Yunfeng Yang 1 1 Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, 100084, Beijing, P.R. China *corresponding author The supporting information includes: Supplementary Table S1 to Table S5 (This file) Supplementary Figure Legends (This file) Supplementary Fig. S1 to Fig. S10 (This file) Supplementary reference (This file) Supplementary Data S1 (a separated MS EXCEL file) Tables: Table S 1 Primers used in this study. Name Sequence(5’-3’) Target gene Application Reference 20F TTCCGGTTGATCCYGCCRG Archaeal 16S rRNA Detection and phylogeny 1,2 1492R GGYTACCTTGTTACGACTT 519F CAGCMGCCGCGGTAA Archaeal 16S rRNA qPCR 1,3 727R GCTTTCRTCCCTCACCGT 23F ATGGTCTGGCTWAGACG Archaeal amo A Detection, phylogeny and qPCR 4,5 616R GCCATCCATCTGTATGTCCA 27F AGAGTTTGATCMTGGCTCAG Bacterial 16S rRNA Phylogeny 1 1492R GGYTACCTTGTTACGACTT bac518F CCAGCAGCCGCGGTAAT Bacterial 16S rRNA qPCR 6,7 bac786R CTACCAGGGTATCTAATC amo A1F GGGGTTTCTACTGGTGGT Bacterial amo A Detection 8 amo A2R CCCCTCKGSAAAGCCTTCTTC Table S 2 Genomic features of Nitrosotenuis cloacae strain SAT1 compared with other ammonia oxidizers. Genome Nitrosotenuis cloacae Nitrosopumilus maritimus Ca. Nitrosotenuis uzonensis “Ca. Nitrosotenuis chungbukensis” “ Ca. Nitrososphaera evergladensis” Nitrosococcus oceani ATCC 19707 Affiliation Group I.1a Group I.1a Group I.1a Group I.1a Group I.1b AOB Scaffold 1 1 14 24 1 1 Contigs 1 1 14 24 1 1 Size （ Mb ） 1.62 1.65 1.65 1.76 2.95 3.48 GC content 41.0% 34.2% 42.2% 41.7% 50.1% 50.30% ORFs 1855 1847 1999 2166 3555 3186 ORF density (ORF/kb) 1.15 1.12 1.21 1.23 1.21 1.28 5S rRNA 1 1 1 1 1 1 16S-23S rRNA 1 1 1 1 1 2 tRNA 41 44 41 43 39 45 Plasmid 0 0 0 0 0 1 Table S 3 Important physiological and genomic properties of Nitrosotenuis cloacae stain SAT1 and other ammonia oxidizers. Strain Nitrosotenuis cloacae Nitrosopumilus maritimus Ca. Nitrosotenuis uzonensis “Ca. Nitrosotenui chungbukensis” “ Ca. Nitrososphaera evergladensis” Nitrosococcus oceani ATCC 19707 Affiliation Group I.1a Group I.1a Group I.1a Group I.1a Group I.1b AOB Genome accession Number CP011097.2 CP000866.1 CBTY000000000 AVSQ00000000 CP007174.1 CP000127.1 Salinity range 0.005%-0.03% 3.5% 0.005%-0.1% \ * \ \ Cell shape spherically rod rod rod spherically Spherically/ ellipsoidal urea utilization genes Incomplete × × × Complete Complete Flagella related genes √ × √ √ √ √ Ectoine synthesis gene × √ × × √ √ Mannosylglycerate synthesis gene × × × × √ × DIP synthesis gene × × × × √ √ * “ \ ” means not mentioned in reference paper, “ √ ” means presence, and “ × ” means absence. Table S 4 Genomic traits of Nitrosotenuis cloacae strain SAT1 and other AOA strains. Reference genome ANI AAI 16S rRNA identity amoA gene identity AMO subunit α identity Nitrosotenuis chungbukensis MY2 75.49% 68.88% 96% 86% 97% Nitrosotenuis uzonensis N4 75.11% 73.76% 96% 86% 96% Nitrosoarchaeum limnia 75.46% 63.24% 92% 83% 98% Nitrosopumilus sp. AR2 74.20% 63.08% 92% 84% 96% Nitrosopumilus maritimus 73.96% 63.43% 92% 84% 96% Cenarchaeum symbiosum — 58.30% 92% 78% 95% Nitrososphaera gargensis — 50.38% 85% 73% 83% Table S 5 Summary of the wastewater treatment plants in which wastewater cluster B AOA were found. Study Country/Region Process Representative sequence 9 USA aerated-anoxic Orbal with SRT=20d,HRT=61h DQ278514.1 Merbt et al. unpublished Spain unknown HG938088.1 10 Taiwan conventional activated sludge with SRT=10d, HRT=8h HM589836.1 11 UK Trickling filter HQ317035.2 Wu et al, unpublished Taiwan bioreactor with HRT/SRT10 d HQ677700.1 12 China A/O MBR, BAF, MBR JN813557.1 13 China, Australia A/A/O, Anammox JQ865446.1 Gao et al. unpublished China unknown KC967706.1 Gao et al. unpublished China unknown KJ497592.1 Ma et al. unpublished China Modified bio-contact oxidation process KM110721.1 Gao et al. unpublished China nitritation-ANAMMOX systems KM402141.1 Figures: Fig. S1 The ammonia consumption of Nitrosotenuis cloacae SAT1 of each cultivation cycle from the initial enrichment. Each line represent one cultivation cycle. The ammonia concentrations were monitored every two or three weeks using a salicylic acid assay. Fig. S2 The changes of Denaturing Gradient Gel Electrophoresis (DGGE) profile for archaeal 16S rRNA gene during the enrichment of Nitrosotenuis cloacae SAT1. Lane 0 stand for enrichment sample from Day 0 (original sludge), lane 1 from Day 70, lane 2 from Day 104, lane 3 from Day 310, lane 4 from Day 331. The band with an arrow pointing to was sequenced and confirmed to be the 16S rRNA sequence of the Nitrosotenuis cloacae strain SAT1. Fig. S3 Phylogenetic tree showing the relationships of 16S rRNA gene sequence of Nitrosotenuis cloacae strain SAT1 to reference sequences from the GenBank database. The tree was constructed with the neighbor-joining method using about 1400 nucleotide positions. Bootstrap values shown at nodes where the value was greater than 50, are based on 1000 trials. Fig. S4 Circular representation of the genome of Nitrosotenuis cloacae strain SAT1 . The outermost two circles were forward (circle 1) and reverse (circle 2) gene components shown in arcs, including CDS (blue), tRNA (light red) and rRNA (light purple). Circle 3 showed the blast results in comparison with N.maritimus , using program tblastx, with an alignment cutoff 15, an identity cutoff 40, and an e-value 10 -5 . Circle 4 showed the GC content and circle 5 showed the GC skew, values greater or smaller than the average percentage in the overall chromosome are shown in green and purple respectively. The circular plots were drawn by using CGView server ( http://stothard.afns.ualberta.ca/cgview_server/ , Grant and Stothard, 2008). Fig. S5 Dot plot representation of the pairwise alignments of the genome of Nitrosotenuis cloacae strain SAT1 against (A) Nitrosopumilus maritimus and (B) “Ca. Nitrososphaera gargensis ” . Alignments were performed on the six-frame amino acid translation of the genome sequences using the Promer program in the MUMmer 3.0 package. In all plots, a dot indicates a match (of at least six AA) between the two genome sequences being compared, with forward matches colored in red and reverse matches colored in blue. Fig. S6 Whole-genome based phylogenomic tree of Nitrosotenuis cloacae by using composition vector (CV) approach. This tree was constructed by using composition vector, an alignment-free method, on CVTree3 web server 14,15 ( http://tlife.fudan.edu.cn/archaea/cvtree/cvtree3/ ), with the K-tuple length = 9, the reference genomes were all download from GenBank database. Fig. S7 The gene order of ammonia monooxygenase (AMO) of Nitrosotenuis cloacae strain SAT1 compared with Nitrosopumilus .maritimus , “ Ca. Nitrosotenuis uzonensis ” , AOB, “ Ca. Nitrososphaera gargensis”. Double slash between genes means intervals. Fig. S8 Phylogenetic tree showing the relationships of cephalosporin hydroxylase amino acid sequence of Nitrosotenuis cloacae strain SAT1 to reference sequences from the GenBank database. The tree was constructed with the neighbor-joining method using about 250 amino acid positions. Bootstrap values shown at nodes where the value was greater than 50, are based on 1000 trials. Fig. S9 Pathway for the synthesis of (A) ectoine and hydroxyectoine, (B) mannosylglycerate, and (C) di-myo-inositol-1, 3’-phosphate of Nitrosotenuis cloacae . EctB, L-2,4-diaminobutyrate transaminase; EctA, L-2,4-diaminobutyrate acetyltransferase; EctC, ectoine synthase; EctD, ectoine hydroxylase; MPGS, mannosyl-3-phosphoglycerate synthase; MPGP, mannosyl-3-phosphoglycerate phosphatase; MIPS, myo-inositol-1-phosphate synthase; IPCT, inositol-1-phosphate cytidylyltransferase; DIPPS, di-myo-inositol-1,3-phosphate-1-phosphate synthase; DIPPP, di-myo-inositol-1,3-phosphate-1-phosphate phosphatase. Below enzymes, a red letter “a” inside parenthesis meant that the gene coding for this enzyme was present in high-salinity group I.1a AOA genomes like Nitrosopumilus maritimus , while a letter “b” meant the corresponding gene was present in group I.1b AOA genomes like “Ca. Nitrososphaera gargensis ” , “Ca. Nitrososphaera evergladensis ” and Nitrososphaera viennensis . The green cycle on the arrows meant that the gene was identified in the genome of Nitrosotenuis cloacae SAT1, while the red cross meant not. Fig. S10 The GC-depth plot of primary assembled sequence data. Region 1 showed the sequences of Nitrosotenuis cloacae strain SAT1 and region 2 showed the contaminated bacteria sequences, which were removed from the assembled contigs. References: 1. WEISBURG, W. G., BARNS, S. M., PELLETIER, D. A. LANE, D. J. 16S ribosomal dna amplification for phylogenetic study. J Bacteriol . 173 , 697-703 (1991). 2. DELONG, E. F. Archaea in coastal marine environments. P Natl Acad Sci USA . 89 , 5685-5689 (1992). 3. Park, S. J., Park, B. J. Rhee, S. K. Comparative analysis of archaeal 16S rRNA and amoA genes to estimate the abundance and diversity of ammonia-oxidizing archaea in marine sediments. Extremophiles . 12 , 605-615 (2008). 4. Tourna, M. et al. Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. P Natl Acad Sci USA . 108 , 8420-8425 (2011). 5. Tourna, M., Freitag, T. E., Nicol, G. W. Prosser, J. I. Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms E-4902-2011 F-5280-2010. Environ Microbiol . 10 , 1357-1364 (2008). 6. MUYZER, G., DEWAAL, E. C. UITTERLINDEN, A. G. Profiling of complex microbial-populations by denaturing gradient gel-electrophoresis analysis of polymerase chain reaction-amplified genes-coding for 16s ribosomal-rna. Appl Environ Microb . 59 , 695-700 (1993). 7. Baker, G. C., Smith, J. J. Cowan, D. A. Review and re-analysis of domain-specific 16S primers. J Microbiol Meth . 55 , 541-555 (2003). 8. 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. Appl Environ Microbiol . 63 , 4704-4712 (1997). 9. Park, H. D., Wells, G. F., Bae, H., Criddle, C. S. Francis, C. A. Occurrence of ammonia-oxidizing archaea in wastewater treatment plant bioreactors. Appl Environ Microb . 72 , 5643-5647 (2006). 10. Wu, Y., Whang, L., Fukushima, T. Chang, S. Responses of ammonia-oxidizing archaeal and betaproteobacterial populations to wastewater salinity in a full-scale municipal wastewater treatment plant. J Biosci Bioeng . 115 , 424-432 (2013). 11. Mussmann, M. et al. Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers. P Natl Acad Sci USA . 108 , 16771-16776 (2011). 12. Bai, Y., Sun, Q., Wen, D. Tang, X. Abundance of ammonia-oxidizing bacteria and archaea in industrial and domestic wastewater treatment systems. Fems Microbiol Ecol . 80 , 323-330 (2012). 13. Gao, J. F., Luo, X., Wu, G. X., Li, T. Peng, Y. Z. Abundance and diversity based on amoA genes of ammonia-oxidizing archaea and bacteria in ten wastewater treatment systems. Appl Microbiol Biot . 98 , 3339-3354 (2014). 14. Qi, J., Wang, B. Hao, B. I. Whole proteome prokaryote phylogeny without sequence alignment: A K-string composition approach. J Mol Evol . 58 , 1-11 (2004). 15. Zuo, G. Hao, B. CVTree3 web server for whole-genome-based and alignment-free prokaryotic phylogeny and taxonomy. Genomics Proteomics Bioinformatics . 13 , 321-331 (2015).
分享 QQ 日志：推荐歌曲《忧愁河上的金桥》 2012-05-11 11:05 今天去莱阳农学院溜了一圈，校园果然漂亮，我仍然觉得大学校园是最好的去处。 然后发现他们实在大胆，尽然敢在校园门口建金水桥，好在正冲着是图书馆，而不是行政大楼，以书为尊还是可以接受的。可惜桥下无水，据说有也是污水，忽然感到了桥的悲哀，深深的悲哀。 人有时总是很难避免心凉心寒心痛，特别是在燥热白日褪去后的清凉春夜，会忽然无端生出一种无处无法无能诉说的悲凉，好在有那么多美文好歌可以陪伴……在这个世界上，到底谁在等待谁，谁在指引谁，永远是个问题。 《圣经》中有说 “ 已有之事，后必再有，已行之事后必再行。日光之下并无新事 ” ，又说 “ 我见日光之下所作的一切事，都是虚空，都是捕风 …… 因为我们成了一台戏，给世人和天使观看 ” 。 《忧愁河上的金桥》 Bridge over troubled water When you' re weary feeling small When tears are in your eyes I'll dry them all I'm on your side oh when times get rough And friends just can't be found Like a bridge over troubled water I will lay me down Like a bridge over troubled water I will lay me down When you are down and out When you are on the street When evening falls so hard I will comfort you ooh I'll take your part oh when darkness comes And pain is all around Like a bridge over troubled water I will lay me down Like a bridge over troubled water I will lay me down Sail on silver girl Sail on by Your time has come to shine All your dreams are on their way See how they shine Oh if you need a friend I'm sailing right behind Like a bridge over troubled water I will ease your mind Like a bridge over troubled water I will ease your mind 歌曲创作背景 Paul Simon 听到一首福音歌曲 ， 里面有句歌词打动了他： “如果你相信上帝 ， 呼唤他的名字 ， 他会在深不见底的河流上为你建造一座大桥 。” 由此产生灵感 ， Paul Simon 写下了 《 Bridge Over Troubled Water 》 这首经典歌曲 ， 此歌一举成为上个世纪七十年代最畅销的专辑之一 。
标签: 污水
