Differential response of archaeal groups to land use change in an acidic red soil

Science of the Total Environment

Volumn 461-462, Issue , 2013, Pages 742-749

  Shen, Ju Pei ^a,b   Cao, Peng ^a   Hu, Hang Wei ^a   He, Ji Zheng ^a,b  

^a RESEARCH CENTER FOR ECO ENVIRONMENTAL SCIENCES   (China)

^b GRIFFITH UNIVERSITY   (Australia)

Author keywords

AmoA gene; Archaea; Degradation land; Group1.1c; Land use management

Indexed keywords

AMMONIA-OXIDIZING ARCHAEA; ANTHROPOGENIC DISTURBANCE; ARCHAEA; DENATURING GRADIENT GEL ELECTROPHORESES (DGGE); GROUP1.1C; LAND-USE MANAGEMENT; QUANTITATIVE POLYMERASE CHAIN REACTION; TERRESTRIAL ENVIRONMENTS;

BACTERIA; CONSERVATION; ELECTROPHORESIS; FORESTRY; GENE EXPRESSION; POLYMERASE CHAIN REACTION; RESTORATION; RNA; SOILS;

LAND USE;

CARBON; NITRATE; NITROGEN; RNA 16S;

ABUNDANCE; AMMONIA; ELECTROKINESIS; ENVIRONMENTAL DISTURBANCE; GENE EXPRESSION; LAND DEGRADATION; LAND USE CHANGE; NITRATE; PH; POLYMERASE CHAIN REACTION; PROKARYOTE; RED SOIL; RNA; SOIL MICROORGANISM; TERRESTRIAL ECOSYSTEM;

AMMONIA OXIDIZING ARCHAEON; AMOA GENE; ARCHAEON; ARTICLE; BACTERIUM; COMMUNITY STRUCTURE; CONTROLLED STUDY; CORRELATION ANALYSIS; CROPLAND; DEGRADATION LAND; DENATURING GRADIENT GEL ELECTROPHORESIS; ECOSYSTEM RESTORATION; FOREST; GENE; GENE DOSAGE; GENE EXPRESSION; GENE SEQUENCE; LAND USE; NONHUMAN; NUCLEOTIDE SEQUENCE; PH; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROKARYOTE; SOIL ACIDITY; SOIL ANALYSIS;

AMOA GENE; ARCHAEA; DEGRADATION LAND; GROUP1.1C; LAND USE MANAGEMENT;

ANALYSIS OF VARIANCE; ARCHAEA; BASE SEQUENCE; CHINA; CLUSTER ANALYSIS; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA PRIMERS; ECOSYSTEM; GENE DOSAGE; GENES, ARCHAEAL; HYDROGEN-ION CONCENTRATION; MOLECULAR SEQUENCE DATA; NITRATES; PHYLOGENY; POLYMERASE CHAIN REACTION; POPULATION DENSITY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL; SOIL MICROBIOLOGY; SPECIES SPECIFICITY;

BACTERIA; CONSERVATION; DEGRADATION; ELECTROPHORESIS; FORESTRY; GENES; LAND USE; NUCLEIC ACIDS;

ARCHAEA; BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 84879149155     PISSN: 00489697     EISSN: 18791026     Source Type: Journal    
DOI: 10.1016/j.scitotenv.2013.05.070     Document Type: Article

References (70)

1. Agogue H., Brink M., Dinasquet J., Herndl G.J. Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic. Nature 2008, 456(7223):788-791.
2. Attard E., Poly F., Commeaux C., Laurent F., Terada A., Smets B.F., et al. Shifts between Nitrospira- and Nitrobacter-like nitrite oxidizers underlie the response of soil potential nitrite oxidation to changes in tillage practices. Environ Microbiol 2010, 12(2):315-326.
3. Auguet J.C., Barberan A., Casamayor E.O. Global ecological patterns in uncultured Archaea. ISME J 2010, 4(2):182-190.
4. Baker G.C., Smith J.J., Cowan D.A. Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 2003, 55(3):541-555.
5. Bates S.T., Berg-Lyons D., Caporaso J.G., Walters W.A., Knight R., Fierer N. Examining the global distribution of dominant archaeal populations in soil. ISME J 2011, 5(5):908-917.
6. Berg I.A., Kockelkorn D., Buckel W., Fuchs G. A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in archaea. Science 2007, 318(5857):1782-1786.
7. Bomberg M., Jurgens G., Saano A., Sen R., Timonen S. Nested PCR detection of archaea in defined compartments of pine mycorrhizo spheres developed in boreal forest humus microcosms. FEMS Microbiol Ecol 2003, 43(2):163-171.
8. Bomberg M., Timonen S. Distribution of cren- and euryarchaeota in scots pine mycorrhizospheres and boreal forest humus. Microb Ecol 2007, 54(3):406-416.
9. Brochier-Armanet C., Boussau B., Gribaldo S., Forterre P. Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol 2008, 6(3):245-252.
10. Cao P., Zhang L.M., Shen J.P., Zheng Y.M., Di H.J., He J.Z. Distribution and diversity of archaeal communities in selected Chinese soils. FEMS Microbiol Ecol 2012, 80(1):146-158.
11. Carney K.M., Matson P.A., Bohannan B.J.M. Diversity and composition of tropical soil nitrifiers across a plant diversity gradient and among land-use types. Ecol Lett 2004, 7(8):684-694.
12. Chen J. Rapid urbanization in China: a real challenge to soil protection and food security. Catena 2007, 69(1):1-15.
13. Chen Y.Q., Li X.B., Tian Y.J., Tan M.H. Structural change of agricultural land use intensity and its regional disparity in China. J Geogr Sci 2009, 19(5):545-556.
14. Chen Z., Luo X.Q., Hu R.G., Wu M.N., Wu J.S., Wei W.X. Impact of long-term fertilization on the composition of denitrifier communities based on nitrite reductase analyses in a paddy soil. Microb Ecol 2010, 60(4):850-861.
15. Delong E.F. Archaea in coastal marine environments. Proc Natl Acad Sci U S A 1992, 89(12):5685-5689.
16. Fierer N., Breitbart M., Nulton J., Salamon P., Lozupone C., Jones R., et al. Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol 2007, 73(21):7059-7066.
17. Fierer N., Jackson R.B. The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci U S A 2006, 103(3):626-631.
18. Francis C.A., Roberts K.J., Beman J.M., Santoro A.E., Oakley B.B. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc Natl Acad Sci U S A 2005, 102(41):14683-14688.
19. Gubry-Rangin C., Hai B., Quince C., Engel M., Thomson B.C., James P., et al. Niche specialization of terrestrial archaeal ammonia oxidizers. Proc Natl Acad Sci U S A 2011, 108(52):21206-21211.
20. Hansel C.M., Fendorf S., Jardine P.M., Francis C.A. Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile. Appl Environ Microbiol 2008, 74(5):1620-1633.
21. Hartman W.H., Richardson C.J., Vilgalys R., Bruland G.L. Environmental and anthropogenic controls over bacterial communities in wetland soils. Proc Natl Acad Sci U S A 2008, 105(46):17842-17847.
22. He J.Z., Shen J.P., Zhang L.M., Zhu Y.M., Zheng Y.G., Xu M.G., et al. Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environ Microbiol 2007, 9(9):2364-23674.
23. He J.Z., Hu H.W., Zhang L.M. Current insights into the autotrophic Thaumarchaeal ammonia oxidation in acidic soils. Soil Biol Biochem 2012, 55:146-154.
24. Jesus E.D., Marsh T.L., Tiedje J.M., Moreira F.M.D. Changes in land use alter the structure of bacterial communities in Western Amazon soils. ISME J 2009, 3(9):1004-1011.
25. Jurgens G., Saano A. Diversity of soil Archaea in boreal forest before, and after clear-cutting and prescribed burning. FEMS Microbiol Ecol 1999, 29(2):205-213.
26. Keller M., Varner R., Dias J.D., Silva H., Crill P., de Oliveira R.C., et al. Soil-atmosphere exchange of nitrous oxide, nitric oxide, methane, and carbon dioxide in logged and undisturbed forest in the Tapajos National Forest, Brazil. Earth Interact 2005, 9(23):1-28.
27. Kemnitz D., Kolb S., Conrad R. Phenotypic characterization of Rice Cluster III archaea without prior isolation by applying quantitative polymerase chain reaction to an enrichment culture. Environ Microbiol 2005, 7(4):553-565.
28. Kemnitz D., Kolb S., Conrad R. High abundance of Crenarchaeota in a temperate acidic forest soil. FEMS Microbiol Ecol 2007, 60(3):442-448.
29. Kuramae E.E., Yergeau E., Wong L.C., Pijl A.S., van Veen J.A., Kowalchuk G.A. Soil characteristics more strongly influence soil bacterial communities than land-use type. FEMS Microbiol Ecol 2012, 79(1):12-24.
30. Lauber C.L., Strickland M.S., Bradford M.A., Fierer N. The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biol Biochem 2008, 40(9):2407-2415.
31. Lehtovirta L.E., Prosser J.I., Nicol G.W. Soil pH regulates the abundance and diversity of Group 1.1c Crenarchaeota. FEMS Microbiol Ecol 2009, 70(3):367-376.
32. Lehtovirta-Morley L.E., Stoecker K., Vilcinskas A., Prosser J.I., Nicol G.W. Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil. Proc Natl Acad Sci U S A 2011, 108(38):15892-15897.
33. Leininger S., Urich T., Schloter M., Schwark L., Qi J., Nicol G.W., et al. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 2006, 442(7104):806-809.
34. Lipp J.S., Morono Y., Inagaki F., Hinrichs K.U. Significant contribution of Archaea to extant biomass in marine subsurface sediments. Nature 2008, 454(7207):991-994.
35. Muller F., Brissac T., Le Bris N., Felbeck H., Gros O. First description of giant Archaea (Thaumarchaeota) associated with putative bacterial ectosymbionts in a sulfidic marine habitat. Environ Microbiol 2010, 12(8):2371-2383.
36. Nicol G.W., Glover L.A., Prosser J.I. The impact of grassland management on archaeal community structure in upland pasture rhizosphere soil. Environ Microbiol 2003, 5(3):152-162.
37. Nicol G.W., Schleper C. Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle?. Trends Microbiol 2006, 14(5):207-212.
38. Nicol G.W., Tscherko D., Embley T.M., Prosser J.I. Primary succession of soil Crenarchaeota across a receding glacier foreland. Environ Microbiol 2005, 7(3):337-347.
39. Ochsenreiter T., Selezi D., Quaiser A., Bonch-Osmolovskaya L., Schleper C. Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S rRNA surveys and real time PCR. Environ Microbiol 2003, 5(9):787-797.
40. Pesaro M., Widmer F. Identification of novel Crenarchaeota and Euryarchaeota clusters associated with different depth layers of a forest soil. FEMS Microbiol Ecol 2002, 42(1):89-98.
41. Pester M., Rattei T., Flechl S., Grongroft A., Richter A., Overmann J., et al. amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions. Environ Microbiol 2012, 14(2):525-539.
42. Pester M., Schleper C., Wagner M. The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology. Curr Opin Microbiol 2011, 14(3):300-306.
43. 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 1997, 63(12):4704-4712.
44. Rousk J., Baath E., Brookes P.C., Lauber C.L., Lozupone C., Caporaso J.G., et al. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J 2010, 4(10):1340-1351.
45. Sauder L.A., Engel K., Stearns J.C., Masella A.P., Pawliszyn R., Neufeld J.D. Aquarium nitrification revisited: Thaumarchaeota are the dominant ammonia oxidizers in freshwater aquarium biofilters. PLOS One 2011, 6(8):e23281.
46. Schimel J., Bennett J. Nitrogen mineralization: challenges of a changing paradigm. Ecology 2004, 85:591-602.
47. Shen J.P., Zhang L.M., Guo J.F., Ray J.L., He J.Z. Impact of long-term fertilization practices on the abundance and composition of soil bacterial communities in Northeast China. Appl Soil Ecol 2010, 46:119-124.
48. Sliwinski M.K., Goodman R.M. Spatial heterogeneity of Crenarchaeal assemblages within mesophilic soil ecosystems as revealed by PCR-single-stranded conformation polymorphism profiling. Appl Environ Microbiol 2004, 70(3):1811-1820.
49. Spang A., Hatzenpichler R., Brochier-Armanet C., Rattei T., Tischler P., Spieck E., et al. Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends Microbiol 2010, 18(8):331-340.
50. Stopnisek N., Gubry-Rangin C., Hofferle S., Nicol G.W., Mandic-Mulec I., Prosser J.I. Thaumarchaeal ammonia oxidation in an acidic forest peat soil is not influenced by ammonium amendment. Appl Environ Microbiol 2010, 76(22):7626-7634.
51. Suzuki M.T., Taylor L.T., DeLong E.F. Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5'-nuclease assays. Appl Environ Microbiol 2000, 66(11):4605-4614.
52. Taketani R.G., Tsai S.M. The influence of different land uses on the structure of archaeal communities in Amazonian anthrosols based on 16S rRNA and amoA genes. Microb Ecol 2010, 59(4):734-743.
53. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011, 28(10):2731-2739.
54. Teske A., Sorensen K.B. Uncultured archaea in deep marine subsurface sediments: have we caught them all?. ISME J 2008, 2(1):3-18.
55. Timonen S., Bomberg M. Archaea in dry soil environments. Phytochem Rev 2009, 8(3):505-518.
56. Torsvik V., Ovreas L. Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 2002, 5(3):240-245.
57. Valentine D.L. Adaptations to energy stress dictate the ecology and evolution of the Archaea. Nat Rev Microbiol 2007, 5(4):316-323.
58. Walker C.B., de la Torre J.R., Klotz M.G., Urakawa H., Pinel N., Arp D.J., et al. Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine Crenarchaea. Proc Natl Acad Sci U S A 2010, 107(19):8818-8823.
59. Wallenius K., Rita H., Mikkonen A., Lappi K., Lindstrom K., Hartikainen H., et al. Effects of land use on the level, variation and spatial structure of soil enzyme activities and bacterial communities. Soil Biol Biochem 2011, 43(7):1464-1473.
60. Wessen E., Hallin S. Abundance of archaeal and bacterial ammonia oxidizers - possible bioindicator for soil monitoring. Ecol Indic 2011, 11(6):1696-1698.
61. Wessén E., Nyberg K., Jansson J.K., Hallin S. Responses of bacterial and archaeal ammonia oxidizers to soil organic and fertilizer amendments under long-term management. Appl Soil Ecol 2010, 45(3):193-200.
62. Woese C.R., Kandler O., Wheelis M.L. Towards a natural system of organisms - proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A 1990, 87(12):4576-4579.
63. Xu Q.F., Jiang P.K., Wang H.L. Improvement of biochemical and biological properties of eroded red soil by artificial revegetation. J Soils Sediment 2010, 10(2):255-262.
64. Xu Y.B., Cai Z.C. Denitrification characteristics of subtropical soils in China affected by soil parent material and land use. Eur J Soil Sci 2007, 58(6):1293-1303.
65. Yao H., Gao Y., Nicol G.W., Campbell C.D., Prosser J.I., Zhang L., et al. Links between ammonia oxidizer community structure, abundance, and nitrification potential in acidic soils. Appl Environ Microbiol 2011, 77(13):4618-4625.
66. Yao H., He Z., Wilson M.J., Campbell C.D. Microbial biomass and community structure in a sequence of soils with increasing fertility and changing land use. Microb Ecol 2000, 40(3):223-237.
67. Ying J.Y., Zhang L.M., He J.Z. Putative ammonia-oxidizing bacteria and archaea in an acidic red soil with different land utilization patterns. Environ Microbiol Rep 2010, 2(2):304-312.
68. Zhang L.M., Hu H.W., Shen J.P., He J.Z. Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils. ISME J 2012, 6(5):1032-1045.
69. Zhang T., Wang X., Zhang B., Zhao Q. Soil degradation in relation to land use and its countermeasures in the red and yellow soil region of Southern China. Integrated watershed management in the global ecosystem 1999, 51-64. CRC Press. R. Lal (Ed.).
70. Zheng Y., Liu X.Z., Zhang L.M., Zhou Z.F., He J.Z. Do land utilization patterns affect methanotrophic communities in a Chinese upland red soil?. J Environ Sci (China) 2010, 22(12):1936-1943.