Habitat Specialization Along a Wetland Moisture Gradient Differs Between Ammonia-oxidizing and Denitrifying Microorganisms

Microbial Ecology

Volumn 68, Issue 2, 2014, Pages 339-350

  Peralta, Ariane L ^a,c   Matthews, Jeffrey W ^a,b   Kent, Angela D ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b UNIVERSITY OF ILLINOIS   (United States)

^c EAST CAROLINA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEA;

AMMONIA; WATER;

ARCHAEAL GENE; ARCHAEON; CLASSIFICATION; DENITRIFICATION; DNA SEQUENCE; GENETICS; HYDROLOGY; METABOLISM; MICROBIAL CONSORTIUM; MICROBIOLOGY; OXIDATION REDUCTION REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; UNITED STATES; WETLAND;

AMMONIA; ARCHAEA; DENITRIFICATION; GENES, ARCHAEAL; HYDROLOGY; ILLINOIS; MICROBIAL CONSORTIA; OXIDATION-REDUCTION; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; WATER; WETLANDS;

EID: 84904580164     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-014-0407-4     Document Type: Article

References (58)

1. Dumbrell AJ, Nelson M, Helgason T, Dytham C, Fitter AH (2010) Relative roles of niche and neutral processes in structuring a soil microbial community. ISME J 4: 337-345. doi: 10. 1038/ismej. 2009. 122.
2. Gutknecht JLM, Goodman RM, Balser TC (2006) Linking soil process and microbial ecology in freshwater wetland ecosystems. Plant Soil 289: 17-34. doi: 10. 1007/s11104-006-9105-4.
3. Ikenaga M, Guevara R, Dean AL, Pisani C, Boyer JN (2010) Changes in community structure of sediment bacteria along the Florida Coastal Everglades marsh-mangrove-seagrass salinity gradient. Microb Ecol 59: 284-295. doi: 10. 1007/s00248-009-9572-2.
4. Pett-Ridge J, Firestone MK (2005) Redox fluctuation structures microbial communities in a wet tropical soil. Appl Environ Microbiol 71: 6998-7007. doi: 10. 1128/aem. 71. 11. 6998-7007. 2005.
5. Rousk J, Baath E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG, Knight R, Fierer N (2010) Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J 4: 1340-1351. doi: 10. 1038/ismej. 2010. 58.
6. Swan BK, Ehrhardt CJ, Reifel KM, Moreno LI, Valentine DL (2010) Archaeal and bacterial communities respond differently to environmental gradients in anoxic sediments of a California hypersaline lake, the Salton Sea. Appl Environ Microbiol 76: 757-768. doi: 10. 1128/aem. 02409-09.
7. Shelford VE (1913) Animal communities in a Temperate America. University of Chicago Press, Chicago, IL.
8. Grinnell J (1917) The niche relationship of the California Thrasher. Auk 34: 427-433.
9. Hughes JB (2000) The scale of resource specialization and the distribution and abundance of lycaenid butterflies. Oecologia 123: 375-383. doi: 10. 1007/s004420051024.
10. Silvertown J, Dodd M, Gowing D, Lawson C, McConway K (2006) Phylogeny and the hierarchical organization of plant diversity. Ecology 87: S39-S49, doi: 10. 1890/0012-9658(2006)87[39: PATHOO]2. 0. CO;2.
11. Soberon J (2007) Grinnellian and Eltonian niches and geographic distributions of species. Ecol Lett 10: 1115-1123. doi: 10. 1111/j. 1461-0248. 2007. 01107. x.
12. Giri B, Giang P, Kumari R, Prasad R, Varma A (2005) Microbial diversity in soils. In: Buscot F, Varma A (eds) Microorganisms in soils: roles in genesis and functions. Springer, Berlin, pp 19-55.
13. Strickland MS, Lauber C, Fierer N, Bradford MA (2009) Testing the functional significance of microbial community composition. Ecology 90: 441-451. doi: 10. 1111/j. 1574-6941. 2007. 00386. x.
14. DeAngelis KM, Silver WL, Thompson AW, Firestone MK (2010) Microbial communities acclimate to recurring changes in soil redox potential status. Environ Microbiol 12: 3137-3149. doi: 10. 1111/j. 1462-2920. 2010. 02286. x.
15. Picek T, Šimek M, Santruckova H (2000) Microbial responses to fluctuation of soil aeration status and redox conditions. Biol Fertil Soils 31: 315-322. doi: 10. 1007/s003740050662.
16. Keddy PA (2000) Wetland ecology: principles and conservation. Cambridge University Press, Cambridge.
17. 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. doi: 10. 1038/ismej. 2007. 8.
18. Wallenstein MD, Myrold DD, Firestone M, Voytek M (2006) Environmental controls on denitrifying communities and denitrification rates: insights from molecular methods. Ecol Appl 16: 2143-2152, doi: 10. 1890/1051-0761(2006)016[2143: ECODCA]2. 0. CO;2.
19. Bodelier PLE, Libochant JA, Blom C, Laanbroek HJ (1996) Dynamics of nitrification and denitrification in root-oxygenated sediments and adaptation of ammonia-oxidizing bacteria to low-oxygen or anoxic habitats. Appl Environ Microbiol 62: 4100-4107. doi: 10. 1364/AO. 35. 002649.
20. Jayakumar A, O'Mullan GD, Naqvi SWA, Ward BB (2009) Denitrifying bacterial community composition changes associated with stages of denitrification in oxygen minimum zones. Microb Ecol 58: 350-362. doi: 10. 1007/s00248-009-9487-y.
21. Nogales B, Timmis KN, Nedwell DB, Osborn AM (2002) Detection and diversity of expressed denitrification genes in estuarine sediments after reverse transcription-PCR amplification from mRNA. Appl Environ Microbiol 68: 5017-5025. doi: 10. 1128/aem. 68. 10. 5017-5025. 2002.
22. Rich JJ, Heichen RS, Bottomley PJ, Cromack K, Myrold DD (2003) Community composition and functioning of denitrifying bacteria from adjacent meadow and forest soils. Appl Environ Microbiol 69: 5974-5982. doi: 10. 1128/aem. 69. 10. 5974-5982. 2003.
23. Rich JJ, Myrold DD (2004) Community composition and activities of denitrifying bacteria from adjacent agricultural soil, riparian soil, and creek sediment in Oregon, USA. Soil Biol Biochem 36: 1431-1441. doi: 10. 1016/j. soilbio. 2004. 03. 008.
24. Peralta AL, Matthews JW, Kent AD (2010) Microbial community structure and denitrification in a wetland mitigation bank. Appl Environ Microbiol 76: 4207-4215. doi: 10. 1128/aem. 02977-09.
25. Cavigelli MA, Robertson GP (2000) The functional significance of denitrifier community composition in a terrestrial ecosystem. Ecology 81: 1402-1414, doi: 10. 1890/0012-9658(2000)081[1402: TFSODC]2. 0. CO;2.
26. Kowalchuk GA, Stephen JR (2001) Ammonia-oxidizing bacteria: a model for molecular microbial ecology. Ann Rev Microbiol 55: 485-529. doi: 10. 1146/annurev. micro. 55. 1. 485.
27. 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. doi: 10. 1073/pnas. 0506625102.
28. Erguder TH, Boon N, Wittebolle L, Marzorati M, Verstraete W (2009) Environmental factors shaping the ecological niches of ammonia-oxidizing archaea. FEMS Microbiol Rev 33: 855-869. doi: 10. 1111/j. 1574-6976. 2009. 00179. x.
29. Prosser JI, Nicol GW (2008) Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. Environ Microbiol 10: 2931-2941. doi: 10. 1111/j. 1462-2920. 2008. 01775. x.
30. Caffrey JM, Bano N, Kalanetra K, Hollibaugh JT (2007) Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with differing histories of hypoxia. ISME J 1: 660-662. doi: 10. 1038/ismej. 2007. 79.
31. Martens-Habbena W, Berube PM, Urakawa H, de la Torre JR, Stahl DA (2009) Ammonia oxidation kinetics determine niche separation of nitrifying archaea and bacteria. Nature 461: 976-981. doi: 10. 1038/nature08465.
32. Moin NS, Nelson KA, Bush A, Bernhard AE (2009) Distribution and diversity of archaeal and bacterial ammonia oxidizers in salt marsh sediments. Appl Environ Microbiol 75: 7461-7468, doi: 10. 1128/aem. 01001-09.
33. Lennon JT, Aanderud ZT, Lehmkuhl BK, Schoolmaster DR (2012) Mapping the niche space of soil microorganisms using taxonomy and traits. Ecology 93: 1867-1879.
34. Gee GW, Bauder JW (1979) Particle-size analysis by hydrometer-simplified method for routine textural analysis and a sensitivity test of measurement parameters. Soil Sci Soc Am J 43: 1004-1007.
35. Wang DL, Anderson DW (1998) Direct measurement of organic carbon content in soils by the leco CR-12 carbon analyzer. Commun Soil Sci Plan 29: 15-21. doi: 10. 1080/00103629809369925.
36. Kent AD, Yannarell AC, Rusak JA, Triplett EW, McMahon KD (2007) Synchrony in aquatic microbial community dynamics. ISME J 1: 38-47. doi: 10. 1038/ismej. 2007. 6.
37. Rees GN, Baldwin DS, Watson GO, Perryman S, Nielsen DL (2004) Ordination and significance testing of microbial community composition derived from terminal restriction fragment length polymorphisms: application of multivariate statistics. Anton Leeuw Int J G 86: 339-347. doi: 10. 1007/s10482-004-0498-x.
38. Yannarell AC, Triplett EW (2005) Geographic and environmental sources of variation in lake bacterial community composition. Appl Environ Microbiol 71: 227-239. doi: 10. 1128/aem. 71. 1. 227-239. 2005.
39. Fierer N, Schimel JP (2003) A proposed mechanism for the pulse in carbon dioxide production commonly observed following the rapid rewetting of a dry soil. Soil Sci Soc Am J 67: 798-805. doi: 10. 2307/3546335.
40. Legendre P, Legendre L (1998) Numerical ecology. Elsevier, Amsterdam.
41. Decaens T (2010) Macroecological patterns in soil communities. Global Ecol Biogeogr 19: 287-302. doi: 10. 1111/j. 1466-8238. 2009. 00517. x.
42. Smith J, Wagner-Riddle C, Dunfield K (2010) Season and management related changes in the diversity of nitrifying and denitrifying bacteria over winter and spring. Appl Soil Ecol 44: 138-146. doi: 10. 1016/j. apsoil. 2009. 11. 004.
43. Šimek M, Cooper JE (2002) The influence of soil pH on denitrification: progress towards the understanding of this interaction over the last 50 years. Eur J Soil Sci 53: 345-354. doi: 10. 1046/j. 1365-2389. 2002. 00461. x.
44. Henderson SL, Dandie CE, Patten CL, Zebarth BJ, Burton DL, Trevors JT, Goyer C (2010) Changes in denitrifier abundance, denitrification gene mRNA levels, nitrous oxide emissions, and denitrification in anoxic soil microcosms amended with glucose and plant residues. Appl Environ Microbiol 76: 2155-2164. doi: 10. 1128/aem. 02993-09.
45. 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. doi: 10. 1111/j. 1462-2920. 2008. 01701. x.
46. Bernhard AE, Landry ZC, Blevins A, de laTorre JR, Giblin AE, Stahl DA (2010) Abundance of ammonia-oxidizing archaea and bacteria along an estuarine salinity gradient in relation to potential nitrification rates. Appl Environ Microbiol 76: 1285-1289. doi: 10. 1128/aem. 02018-09.
47. Philippot L (2002) Denitrifying genes in bacterial and archaeal genomes. BBA-Gene Struct Expr 1577: 355-376. doi: 10. 1016/S0167-4781(02)00420-7.
48. Zumft WG (1997) Cell biology and molecular basis of denitrification. Microbiol Mol Biol R 61: 533-616, 10. 1. 1. 110. 7225.
49. Blom C (1999) Adaptations to flooding stress: from plant community to molecule. Plant Biol 1: 261-273. doi: 10. 1111/j. 1438-8677. 1999. tb00252. x.
50. Bodelier PLE, Wijlhuizen AG, Blom C, Laanbroek HJ (1997) Effects of photoperiod on growth of and denitrification by Pseudomonas chlororaphis in the root zone of Glyceria maxima, studied in a gnotobiotic microcosm. Plant Soil 190: 91-103. doi: 10. 1023/A: 1004212814097.
51. Prosser JI (2007) The ecology of nitrifying bacteria. In: Bothe H, Ferguson SJ, Newton WE (eds) Biology of the nitrogen cycle. Elsevier, Oxford, pp 223-244.
52. Worthen WB (1996) Community composition and nested-subset analyses: basic descriptors for community ecology. Oikos 76: 417-426.
53. Naeem S, Wright JP (2003) Disentangling biodiversity effects on ecosystem functioning: deriving solutions to a seemingly insurmountable problem. Ecol Lett 6: 567-579. doi: 10. 1046/j. 1461-0248. 2003. 00471. x.
54. Petchey OL, Gaston KJ (2006) Functional diversity: back to basics and looking forward. Ecol Lett 9: 741-758. doi: 10. 1111/j. 1461-0248. 2006. 00924. x.
55. Botton S, van Heusden M, Parsons JR, Smidt H, van Straalen N (2006) Resilience of microbial systems towards disturbances. Crit Rev Microbiol 32: 101-112. doi: 10. 1080/10408410600709933.
56. Folke C, Holling CS, Perrings C (1996) Biological diversity, ecosystems, and the human scale. Ecol Appl 6: 1018-1024. doi: 10. 2307/2269584.
57. Loreau M, Mouquet N, Gonzalez A (2003) Biodiversity as spatial insurance in heterogeneous landscapes. Proc Natl Acad Sci USA 100: 12765-12770. doi: 10. 1073/pnas. 2235465100.
58. Naeem S, Li SB (1997) Biodiversity enhances ecosystem reliability. Nature 390: 507-509. doi: 10. 1038/37348.