Effects of pH and polycyclic aromatic hydrocarbon pollution on thaumarchaeotal community in agricultural soils

Journal of Soils and Sediments

Volumn 16, Issue 7, 2016, Pages 1960-1969

  Wu, Yucheng ^a   Zhu, Qinghe ^a   Zeng, Jun ^a   Ding, Qingmin ^a   Gong, Yi ^b   Xing, Peng ^b   Lin, Xiangui ^a  

^a HONG KONG BAPTIST UNIVERSITY   (Hong Kong)

^b NANJING INSTITUTE OF GEOGRAPHY AND LIMNOLOGY   (China)

Author keywords

Abundance; Community composition; Polycyclic aromatic hydrocarbons; Soil acidification; Soil pollution; Thaumarchaeota

Indexed keywords

AGRICULTURAL LAND; AGRICULTURAL SOIL; AROMATIC HYDROCARBON; BIOAVAILABILITY; COMMUNITY COMPOSITION; CONCENTRATION (COMPOSITION); CORRESPONDENCE ANALYSIS; ENVIRONMENTAL FACTOR; EUKARYOTE; MICROCOSM; NITROGEN CYCLE; PAH; PH; POLLUTION EFFECT; SOIL POLLUTION;

ARCHAEA;

EID: 84960366218     PISSN: 14390108     EISSN: 16147480     Source Type: Journal    
DOI: 10.1007/s11368-016-1390-9     Document Type: Article

References (45)

1. Alexander M (2000) Aging, bioavailability, and overestimation of risk from environmental pollutants. Environ Sci Technol 34:4259–4265
2. Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P (2008) Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol 6:245–252
3. Chang S, Hyman M, Williamson K (2002) Cooxidation of naphthalene and other polycyclic aromatic hydrocarbons by the nitrifying bacterium, Nitrosomonas europaea. Biodegradation 13:373–381
4. de Menezes A, Clipson N, Doyle E (2012) Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil. Environ Microbiol 14:2577–2588
5. Großkopf R, Janssen PH, Liesack W (1998) Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl Environ Microbiol 64:960–969
6. Gubry-Rangin C, Hai B, Quince C, Engel M, Thomson BC, James P, Schloter M, Griffiths RI, Prosser JI, Nicol GW (2011) Niche specialization of terrestrial archaeal ammonia oxidizers. Proc Natl Acad Sci 108:21206–21211
7. Guo JH, Liu XJ, Zhang Y, Shen JL, Han WX, Zhang WF, Christie P, Goulding KWT, Vitousek PM, Zhang FS (2010) Significant acidification in major Chinese croplands. Science 327:1008–1010
8. Harvey RG (1991) Polycyclic aromatic hydrocarbons: chemistry and carcinogenicity. Cambridge University Press, Cambridge
9. He J-Z, Hu H-W, Zhang L-M (2012) Current insights into the autotrophic thaumarchaeal ammonia oxidation in acidic soils. Soil Biol Biochem 55:146–154
10. Huber T, Faulkner G, Hugenholtz P (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20:2317–2319
11. Juhasz AL, Naidu R (2000) Bioremediation of high molecular weight polycyclic aromatic hydrocarbons: a review of the microbial degradation of benzo[a]pyrene. Int Biodeter Biodegrad 45:57–88
12. Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437:543–546
13. Lehtovirta-Morley LE, Stoecker K, Vilcinskas A, Prosser JI, Nicol GW (2011) Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil. Proc Natl Acad Sci 108:15892–15897
14. Liu Y-R, Zheng Y-M, Shen J-P, Zhang L-M, He J-Z (2010) Effects of mercury on the activity and community composition of soil ammonia oxidizers. Environ Sci Pollut Res 17:1237–1244
15. Lu R (2000) Analytical methods for soil and agrochemistry. China Agricultural Science and Technology Press, Beijing
16. Mertens J, Broos K, Wakelin SA, Kowalchuk GA, Springael D, Smolders E (2009) Bacteria, not archaea, restore nitrification in a zinc-contaminated soil. ISME J 3:916–923
17. Mertens J, Wakelin SA, Broos K, McLaughlin MJ, Smolders E (2010) Extent of copper tolerance and consequences for functional stability of the ammonia-oxidizing community in long-term copper-contaminated soils. Environ Toxicol Chem 29:27–37
18. Nicol GW, Leininger S, Schleper C, Prosser JI (2008) The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environ Microbiol 10:2966–2978
19. Ochsenreiter T, Selezi D, Quaiser A, Bonch-Osmolovskaya L, Schleper C (2003) Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR. Environ Microbiol 5:787–797
20. Oton EV, Quince C, Nicol GW, Prosser JI, Gubry-Rangin C (2016) Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota. ISME J 10:85–96
21. Pester M, Schleper C, Wagner M (2011) The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology. Curr Opin Microbiol 14:300–306
22. Pester M, Rattei T, Flechl S, Gröngröft A, Richter A, Overmann J, Reinhold-Hurek B, Loy A, Wagner M (2012) amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions. Environ Microbiol 14:525–539
23. Ping LF, Luo YM, Zhang HB, Li QB, Wu LH (2007) Distribution of polycyclic aromatic hydrocarbons in thirty typical soil profiles in the Yangtze River Delta region, east China. Environ Pollut 147:358–365
24. Prosser JI, Nicol GW (2008) Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. Environ Microbiol 10:2931–2941
25. Prosser JI, Nicol GW (2012) Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation. Trends Microbiol 20:523–531
26. Rotthauwe J, Witzel K, Liesack W (1997) 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
27. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541
28. Shen J-P, Xu Z, He J-Z (2014) Frontiers in the microbial processes of ammonia oxidation in soils and sediments. J Soils Sediments 14:1023–1029
29. Sipos AJ, Urakawa H (2016) Differential responses of nitrifying archaea and bacteria to methylene blue toxicity. Lett Appl Microbiol 62:199–206
30. Subrahmanyam G, Hu H-W, Zheng Y-M, Gattupalli A, He J-Z, Liu Y-R (2014a) Response of ammonia oxidizing microbes to the stresses of arsenic and copper in two acidic alfisols. Appl Soil Ecol 77:59–67
31. Subrahmanyam G, Shen J-P, Liu Y-R, Archana G, He J-Z (2014b) Response of ammonia-oxidizing archaea and bacteria to long-term industrial effluent-polluted soils, Gujarat, Western India. Environ Monit Assess 186:4037–4050
32. Sverdrup LE, Hagen SB, Krogh PH, van Gestel CAM (2007) Benzo(a)pyrene shows low toxicity to three species of terrestrial plants, two soil invertebrates, and soil-nitrifying bacteria. Ecotoxicol Environ Saf 66:362–368
33. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599
34. ter Braak CJF, Šmilauer P (2002) CANOCO reference manual and CanoDraw for Windows user’s guide. Wageningen, Biometris
35. Tourna M, Stieglmeier M, Spang A, Könneke M, Schintlmeister A, Urich T, Engel M, Schloter M, Wagner M, Richter A, Schleper C (2011) Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proc Natl Acad Sci 108:8420–8425
36. Urakawa H, Garcia JC, Barreto PD, Molina GA, Barreto JC (2012) A sensitive crude oil bioassay indicates that oil spills potentially induce a change of major nitrifying prokaryotes from the Archaea to the bacteria. Environ Pollut 164:42–45
37. Weber EB, Lehtovirta-Morley LE, Prosser JI, Gubry-Rangin C (2015) Ammonia oxidation is not required for growth of group 1.1c soil Thaumarchaeota. FEMS Microbiol Ecol. doi:10.1093/femsec/fiv001
38. Wu Y, Conrad R (2014) Ammonia oxidation-dependent growth of group I.1b Thaumarchaeota in acidic red soil microcosms. FEMS Microbiol Ecol 89:127–134
39. Wu Y, Luo Y, Zou D, Ni J, Liu W, Teng Y, Li Z (2008) Bioremediation of polycyclic aromatic hydrocarbons contaminated soil with Monilinia sp.: degradation and microbial community analysis. Biodegradation 19:247–257
40. Wu Y, Lu L, Wang B, Lin X, Zhu J, Cai Z, Yan X, Jia Z (2011) Long-term field fertilization significantly alters community structure of ammonia-oxidizing bacteria rather than archaea in a paddy soil. Soil Sci Soc Am J 75:1431–1439
41. Xu SS, Liu WX, Tao S (2006) Emission of polycyclic aromatic hydrocarbons in China. Environ Sci Technol 40:702–708
42. Yao H, Gao Y, Nicol GW, Campbell CD, Prosser JI, Zhang L, Han W, Singh BK (2011) Links between ammonia oxidizer community structure, abundance, and nitrification potential in acidic soils. Appl Environ Microbiol 77:4618–4625
43. Zeng J, Lin X, Zhang J, Zhu H, Chen H, Wong M (2013) Successive transformation of benzo[a]pyrene by laccase of Trametes versicolor and pyrene-degrading Mycobacterium strains. Appl Microbiol Biotechnol 97:3183–3194
44. Zhalnina K, de Quadros PD, Gano KA, Davis-Richardson A, Fagen JR, Brown CT, Giongo A, Drew JC, Sayavedra-Soto LA, Arp DJ, Camargo FAO, Daroub SH, Clark IM, McGrath SP, Hirsch PR, Triplett EW (2013) Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments. Front Microbiol 4:104
45. Zhang L-M, Hu H-W, Shen J-P, He J-Z (2012) Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils. ISME J 6:1032–1045