Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses

ISME Journal

Volumn 8, Issue 3, 2014, Pages 650-659

  Meng, Jun ^a,c   Xu, Jun ^a   Qin, Dan ^a   He, Ying ^a   Xiao, Xiang ^a   Wang, Fengping ^a,b  

^a Shanghai Jiao Tong University   (China)

^b SHANGHAI JIAO TONG UNIVERSITY   (China)

^c UNIVERSITY OF GEORGIA   (United States)

Author keywords

aromatic compound; biogeochemical cycle; gene expression; MCG; metagenome

Indexed keywords

4 CARBOXYMUCONOLACTONE DECARBOXYLASE; 4-CARBOXYMUCONOLACTONE DECARBOXYLASE; ARCHAEAL RNA; CARBOXYLYASE; DNA TOPOISOMERASE; RIBOSOME PROTEIN; RNA 16S;

ARCHAEON; ARTICLE; CLASSIFICATION; ESTUARY; GENETICS; METABOLISM; METAGENOME; MICROBIOLOGY; MOLECULAR GENETICS; PHYLOGENY; SEDIMENT;

ARCHAEA; CARBOXY-LYASES; DNA TOPOISOMERASES, TYPE I; ESTUARIES; GEOLOGIC SEDIMENTS; METAGENOME; MOLECULAR SEQUENCE DATA; PHYLOGENY; RIBOSOMAL PROTEINS; RNA, ARCHAEAL; RNA, RIBOSOMAL, 16S;

EID: 84894363922     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2013.174     Document Type: Article

References (31)

1. Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W et al. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402. (Pubitemid 27359211)
2. Biddle J, Lipp J, Lever M, Lloyd K, Sorensen K, Anderson R et al. (2006). Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. Proc Natl Acad Sci USA 103: 3846-3851. (Pubitemid 43376643)
3. Brochier-Armanet C, Gribaldo S, Forterre P. (2008). A DNA topoisomerase IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya. Biol Direct 3: 54.
4. DeLong E. (1992). Archaea in coastal marine environments. Proc Natl Acad Sci USA 89: 5685-5689.
5. Forterre P, Gribaldo S, Gadelle D, Serre M. (2007). Origin and evolution of DNA topoisomerases. Biochimie 89: 427-446. (Pubitemid 46656307)
6. Fry J, Parkes R, Cragg B, Weightman A, Webster G. (2008). Prokaryotic biodiversity and activity in the deep subseafloor biosphere. FEMS Microbiol Ecol 66: 181-196.
7. Inagaki F, Nunoura T, Nakagawa S, Teske A, Lever M, Lauer A et al. (2006). Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. Proc Natl Acad Sci USA 103: 2815-2820.
8. Inagaki F, Suzuki M, Takai K, Oida H, Sakamoto T, Aoki K et al. (2003). Microbial communities associated with geological horizons in coastal subseafloor sediments from the sea of okhotsk. Appl Environ Microbiol 69: 7224-7235. (Pubitemid 38585373)
9. Jiang L, Zheng Y, Chen J, Xiao X, Wang F. (2011). Stratification of Archaeal communities in shallow sediments of the Pearl River Estuary, Southern China. Antonie Van Leeuwenhoek 99: 739-751.
10. Katoh K, Misawa K, Kuma K, Miyata T. (2002). MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30: 3059-3066. (Pubitemid 34851225)
11. Kubo K, Lloyd K, Biddle J, Amann R, Teske A, Knittel K. (2012). Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments. ISME J 6: 1949-1965.
12. Le SQ, Gascuel O. (2008). An improved general amino acid replacement matrix. Mol Biol Evol 25: 1307-1320. (Pubitemid 351882003)
13. Li PY, Xie BB, Zhang XY, Qin QL, Dang HY, Wang XM et al. (2012a). Genetic structure of three fosmid-fragments encoding 16S rRNA genes of the Miscellaneous Crenarchaeotic Group (MCG): implications for physiology and evolution of marine sedimentary archaea. Environ Microbiol 14: 467-479.
14. Li Q, Wang F, Chen Z, Yin X, Xiao X. (2012b). Stratified active archaeal communites in the sediments of Jiulong River estuary, China. Front Microbiol 3: 311.
15. Lloyd KG, Schreiber L, Petersen DG, Kjeldsen KU, Lever MA, Steen AD et al. (2013). Predominant archaea in marine sediments degrade detrital proteins. Nature 496: 215-218.
16. Lowe TM, Eddy SR. (1997). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964. (Pubitemid 27298263)
17. Lukashin AV, Borodovsky M. (1998). GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res 26: 1107-1115. (Pubitemid 28291669)
18. Meng J, Wang F, Zheng Y, Peng X, Zhou H, Xiao X. (2009). An uncultivated crenarchaeota contains functional bacteriochlorophyll a synthase. ISME J 3: 106-116.
19. Nunoura T, Takaki Y, Kakuta J, Nishi S, Sugahara J, Kazama H et al. (2011). Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res 39: 3204-3223.
20. Parkes RJ, Webster G, Cragg BA, Weightman AJ, Newberry CJ, Ferdelman TG et al. (2005). Deep sub-seafloor prokar-yotes stimulated at interfaces over geological time. Nature 436: 390-394. (Pubitemid 41059048)
21. Pester M, Schleper C, Wagner M. (2011). The Thaumarch-aeota: an emerging view of their phylogeny and ecophysiology. Curr Opin Microbiol 14: 300-306.
22. Petersen TN, Brunak S, von Heijne G, Nielsen H. (2011). SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 8: 785-786.
23. Sørensen KB, Teske A. (2006). Stratified communities of active Archaea in deep marine subsurface sediments. Appl Environ Microbiol 72: 4596-4603. (Pubitemid 44078783)
24. Sonnhammer EL, Eddy SR, Durbin R. (1997). Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 28: 405-420. (Pubitemid 27280344)
25. Stanier R, Ornston L. (1973). The beta-ketoadipate pathway. Adv Microb Physiol 9: 89-151.
26. Szurmant H, Ordal W. (2004). Diversity in chemotaxis mechanisms among the bacteria and archaea. Micro-biol Mol Biol Rev 68: 301-319. (Pubitemid 38756867)
27. Teske A. (2006). Microbial communities of deep marine subsurface sediments: molecular and cultivation surveys. Geomicrobiol J 23: 357-368. (Pubitemid 44446542)
28. Teske A, Sørensen K. (2008). Uncultured archaea in deep marine subsurface sediments: have we caught them all? ISME J 2: 3-18. (Pubitemid 351612350)
29. Zdobnov EM, Apweiler R. (2001). InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17: 847-848. (Pubitemid 32970486)
30. Zhang X, Xu J, Xiao J, Xu J. (2009). Archaeal lineages detected in mangrove sediment in Zhangjiang estuary Fujian province. J Shandong University (Natural Science) 44: 1-7. In Chinese.
31. Zhou J, Bruns M, Tiedje JM. (1996). DNA recovery from soils of diverse composition. Appl Environ Microbiol 62: 316-322. (Pubitemid 26047397)