Impacts of Spartina alterniflora invasion on abundance and composition of ammonia oxidizers in estuarine sediment

Journal of Soils and Sediments

Volumn 11, Issue 6, 2011, Pages 1020-1031

  Zhang, Qiu Fang ^a,b   Peng, Jing Jing ^a   Chen, Qian ^a   Li, Xiao Fang ^a   Xu, Chun Yan ^a   Yin, Hong Bing ^c   Yu, Shen ^a  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b NINGBO UNIVERSITY   (China)

^c RESEARCH CENTER FOR ECO ENVIRONMENTAL SCIENCES   (China)

Author keywords

Ammonia oxidizer; amoA gene; Coastal wetland; Invasion; Spartina alterniflora

Indexed keywords

ABUNDANCE; AMMONIA; BACTERIUM; BIOLOGICAL INVASION; COASTAL WETLAND; ECOLOGICAL IMPACT; ELECTROKINESIS; ESTUARINE SEDIMENT; GRASS; MANGROVE; MICROBIAL ACTIVITY; NITRIFICATION; OXIDATION; POLYMERASE CHAIN REACTION; POPULATION SIZE; SPECIES DIVERSITY;

ARCHAEA; BACTERIA (MICROORGANISMS); NITROSOMONADALES; SPARTINA ALTERNIFLORA;

EID: 84860402783     PISSN: 14390108     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11368-011-0369-9     Document Type: Article

References (60)

1. Abell GC, Revill AT, Smith C, Bissett AP, Volkman JK, Robert SS (2010) Archaeal ammonia oxidizers and nirS-type denitrifiers dominate sediment nitrifying and denitrifying populations in a subtropical macrotidal estuary. ISME J 4: 286-300.
2. Angeloni NL, Jankowsk KJ, Tuchman NC, Kelly JJ (2006) Effects of an invasive cattail species (Typha x glauca) on sediment nitrogen and microbial community composition in a freshwater wetland. FEMS Microbiol Lett 263: 86-92.
3. Avrahami S, Conrad R (2003) Patterns of community change among ammonia oxidizers in meadow soils upon long-term incubation at different temperatures. Appl Environ Microbiol 69: 6152-6164.
4. Beman JM, Francis CA (2006) Diversity of ammonia-oxidizing archaea and bacteria in the sediments of a hypernutrified subtropical estuary: Bahia del Tobari, Mexico. Appl Environ Microbiol 72: 7767-7777.
5. Berg G, Smalla K (2009) Plant species and soil type cooperatively shape the structure a function of microbial communities in the rhizosphere. FEMS Microbiol Ecol 68: 1-13.
6. Burke DJ, Hamerlynck EP, Hahn D (2002) Interactions among plant species and microorganisms in salt marsh sediments. Appl Environ Microbiol 68: 1157-1164.
7. Caffrey JM, Bano N, Kalanetra K, Hollibaugh JT (2007) Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with differing histories of hypoxia. ISMEJ 1: 660-662.
8. Callaway RM, Aschehoug ET (2000) Invasive plants versus their new and old neighbors: a mechanism for exotic invasion. Science 290: 521-523.
9. Callaway RM, Ridenour WM (2004) Novel weapons: invasive success and the evolution of increased competitive ability. Front Ecol Environ 2: 436-443.
10. Callaway RM, Thelen GC, Barth S, Ramsey PW, Gannon JE (2004) Soil fungi alter interactions between the invader Centaurea maculosa and North American natives. Ecology 85: 1062-1071.
11. Chen XP, Zhu YG, Xia Y, Shen JP, He JZ (2008) Ammonia-oxidizing archaea: important players in paddy rhizosphere soil? Environ Microbiol 10: 1978-1987.
12. Chen X, Zhang LM, Shen JP, Xu Z, He JZ (2010) Soil type determines the abundance and community structure of ammonia-oxidizing bacteria and archaea in flooded paddy soils. J Soils Sediments 10(8): 1510-1516.
13. Clark IM, Hirsch PR (2008) Survival of bacterial DNA and culturable bacteria in archived soils from the Rothamsted Broadbalk experiment. Soil Biol Biochem 40: 1090-1102.
14. Dang H, Li J, Chen R, Wang L, Guo L, Zhang Z, Klotz MG (2010) Diversity, abundance, and spatial distribution of sediment ammonia-oxidizing Betaproteobacteria in response to environmental gradients and coastal eutrophication in Jiaozhou Bay, China. Appl Environ Microbiol 76: 4691-4702.
15. Di HJ, Cameron KC, Shen JP, Winefield CS, O'Callaghan M, Bowatte S, He JZ (2009) Nitrification driven by bacteria and not archaea in nitrogen-rich grassland soils. Nat Geosci 2: 621-624.
16. Di HJ, Cameron KC, Sherlock RR, Shen JP, He JZ, Winefield CS (2010) Nitrous oxide emissions from grazed grassland as affected by a nitrification inhibitor, dicyandiamide, and relationships with ammonia-oxidizing bacteria and archaea. J Soils Sediments 10: 943-954.
17. Dollhopf SL, Hyun JH, Smith AC, Adams HJ, Brien SO, Kostka JE (2005) Quantification of ammonia-oxidizing bacteria and factors controlling nitrification in salt marsh sediments. Appl Environ Microbiol 71: 240-246.
18. Dumonceaux TJ, Hill JE, Briggs SA, Amoako KK, Hemmingsen SM, Kessel AGV (2006) Enumeration of specific bacterial populations in complex intestinal communities using quantitative PCR based on the chaperonin-60 target. J Microbiol Meth 64: 46-62.
19. Ehrenfeld JG (2003) Effects of exotic plant invasions on soil nutrient cycling processes. Ecosystems 6: 503-523.
20. Francis CA, O'Mullan GD, Ward BB (2003) Diversity of ammonia monooxygenase (amoA) genes across environmental gradients in Chesapeake Bay sediments. Geobiology 1: 129-140.
21. Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB (2005) Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc Natl Acad Sci USA 102: 14683-14688.
22. Francis CA, Beman JM, Kuypers MMM (2007) New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. ISME J 1: 19-27.
23. Haichar FZ, Christine M, Berge O, Rangel-Castro JI, Prosser JI, Balesdent J, Heulin T, Achoua W (2008) Plant host habitat and root exudates shape soil bacterial community structure. ISME J 2: 1221-1230.
24. Hawkes CV, Wren IF, Herman DJ, Firestone MK (2005) Plant invasion alters nitrogen cycling by modifying the soil nitrifying community. Ecol Lett 8: 976-985.
25. He JZ, Shen JP, Zhang LM, Zhu YG, Zheng YM, Xu MG, Di H (2007) 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 9: 2364-2374.
26. Hunter EM, Mills HJ, Kostka JE (2006) Microbial community diversity associated with carbon and nitrogen cycling in permeable shelf sediments. Appl Environ Microbiol 72: 5689-5701.
27. Jia Z, Conrad R (2009) Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil. Environ Microbiol 11: 1658-1671.
28. Klironomos JN (2002) Feedback with soil biota contributes to plant rarity and invasiveness in communities. Nature 417: 67-70.
29. 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.
30. Kourtev PS, Ehrenfeld JG, Häggblom M (2002) Exotic plant species alter the microbial community structure and function in the soil. Ecol Lett 83: 3152-3166.
31. Kowalchuk GA, Stephen JR (2001) Ammonia-oxidizing bacteria: a model for molecular microbial ecology. Annu Rev Microbiol 55: 485-529.
32. Kowalchuk GA, Naoumenko ZS, Derikx PJ, Felske A, Stephen JR, Arkhipchenko IA (1999) Molecular analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in compost and composted materials. Appl Environ Microbiol 65: 396-403.
33. Kowalchuk GA, Buma DS, de Boer W, Klinkhamer PGL, van Veen JA (2002) Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms. Anton Leeuwint J G 81: 509-520.
34. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic Acid Techniques in Bacterial Systematics. John Wiley & Sons, New York, pp 115-175.
35. Laverman AM, Speksnijder A, Braster M, Kowalchuk GA, Verhoef HA, van Verseveld HW (2001) Spatiotemporal stability of an ammonia-oxidizing community in a nitrogen-saturated forest soil. Microb Ecol 42: 35-45.
36. Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442: 806-809.
37. Liao CZ, Luo YQ, Fang CM, Chen JK, Li B (2008a) Litter pool sizes, decomposition, and nitrogen dynamics in Spartina alterniflora-invaded and native coastal marshlands of the Yangtze Estuary. Oecologia 156: 589-600.
38. Liao CZ, Peng R, Luo Y, Zhou X, Wu X, Fang C, Chen J, Li B (2008b) Altered ecosystem carbon and nitrogen cycles by plant invasion: a meta-analysis. New Phytol 177: 706-714.
39. Mohamed NM, Saito K, Tal Y, Hill RT (2010) Diversity of aerobic and anaerobic ammonia-oxidizing bacteria in marine sponges. ISMEJ 4: 38-48.
40. Mosier AC, Francis CA (2008) Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary. Environ Microbiol 10: 3002-3016.
41. Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59: 695-700.
42. 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.
43. Okano Y, Hristova KR, Leutenegger CM, Jackson LE, Denison RF, Gebreyesus B, Lebauer D, Scow KM (2004) Application of real-time PCR to study effects of ammonium on population size of ammonia-oxidizing bacteria in soil. Appl Environ Microbiol 70: 1008-1016.
44. Peng JJ, Cai C, Qiao M, Li H, Zhu YG (2010) Dynamic changes in functional gene copy numbers and microbial communities during degradation of pyrene in soils. Environ Pollut 158: 2872-2879.
45. Prosser JI, Embley MT (2002) Cultivation-based and molecular approaches to characterisation of terrestrial and aquatic nitrifiers. Anton van Leeuwenhoek 81: 165-179.
46. Rotthauwe JH, Witzel KP, 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.
47. Ruiz-Rueda O, Hallin S, Bañeras L (2009) Structure and function of denitrifying and nitrifying bacterial communities in relation to the plant species in a constructed wetland. FEMS Microbiol Ecol 67: 308-319.
48. Seitzinger SP (1988) Denitrification in freshwater and coastal marine ecosystems: Ecological and geochemical significance. Limnol Oceanogr 33: 702-724.
49. Shen JP, Zhang LM, Zhu YG, Zhang JB, He JZ (2008) Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam. Environ Microbiol 10: 1601-1611.
50. Speksnijder AG, Kowalchuk GA, Roest K, Laanbroek HJ (1998) Recovery of a Nitrosomonas-like 16S rDNA sequence group from freshwater habitats. Syst Appl Microbiol 21: 321-330.
51. Stribling JM (1997) The relative importance of sulfate availability in the growth of Spartina alterniflora and Spartina cynosuroides. Aquat Bot 56: 131-143.
52. Suzuki MT, Taylor LT, DeLong EF (2000) Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5′-nuclease assays. Appl Environ Microbiol 66: 4605-4614.
53. Theoharides KA, Dukes JS (2007) Plant invasion across space and time: factors affecting nonindigenous species success during four stages of invasion. New Phytol 176: 256-273.
54. Tourna M, Freitag TE, Nicol GW, Prosser J I (2008) Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms. Environ Microbiol 10: 1357-1364.
55. Urakawa H, Tajima Y, Numata Y, Tsuneda S (2008) Low temperature decreases the phylogenetic diversity of ammonia-oxidizing archaea and bacteria in aquarium biofiltration systems. Appl Environ Microbiol 74: 894-900.
56. van der Krift TAJ, Kuikman PJ, Mller F, Berendse F (2001) Plant species and nutritional-mediated control over rhizodeposition and root decomposition. Plant Soil 278: 191-200.
57. Xia Y, Zhu YG, Gu Q, He JZ (2007) Does long-term fertilization treatment affect the response of soil ammonia-oxidizing bacterial communities to Zn contamination? Plant Soil 301: 245-254.
58. Ying JY, Zhang LM, He JZ (2010) Putative ammonia-oxidizing bacteria and archaea in an acidic red soil with different land utilization patterns. Environ Microbiol Rep 2: 304-312.
59. Zhang LM, Offre PR, He JZ, Verhammea DT, Nicola GW, Prosser JI (2010) Autotrophic ammonia oxidation by soil thaumarchaea. Natl Acad Sci USA 107: 17240-17245.
60. Zhou CF, An SQ, Deng ZF, Yin DQ, Zhi YB, Sun ZY, Zhao H, Zhou LX, Fang C, Qian C (2009) Sulfur storage changed by exotic Spartina alterniflora in coastal saltmarshes of China. Ecol Eng 35: 536-543.