|
|
|
Variation of Potential Nitrification and Ammonia-Oxidizing Bacterial Community with Plant-Growing Period in Apple Orchard Soil |
LIU Ling-zhi, QIN Si-jun, LÜ De-guo, WANG Bing-ying , YANG Ze-yuan |
1.Key Laboratory for Northern Fruit Cultivation and Physio-Ecology of Shenyang City/College of Horticulture, Shenyang Agricultural University, Shenyang 110866, P.R.China
2.College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, P.R.China
3.Foreign Language Department, Shenyang Agricultural University, Shenyang 110866, P.R.China |
|
|
摘要 In this study, we investigated the potential nitrification and community structure of soil-based ammonia-oxidizing bacteria (AOB) in apple orchard soil during different growth periods and explored the effects of environmental factors on nitrification activity and AOB community composition in the soil of a Hanfu apple orchard, using a culture-dependent technique and denaturing gradient gel electrophoresis (DGGE). We observed that nitrification activity and AOB abundance were the highest in November, lower in May, and the lowest in July. The results of statistical analysis indicated that total nitrogen (N) content, NH4 +-N content, NO3 --N content, and pH showed significant correlations with AOB abundance and nitrification activity in soil. The Shannon-Winner diversity, as well as species richness and evenness indices (determined by PCR-DGGE banding patterns) in soil samples were the highest in September, but the lowest in July, when compared to additional sampled dates. The DGGE fingerprints of soil-based 16S rRNA genes in November were apparently distinct from those observed in May, July, and September, possessing the lowest species richness indices and the highest dominance indices among all four growth periods. Fourteen DGGE bands were excised for sequencing. The resulting analysis indicated that all AOB communities belonged to the β-Proteobacteria phylum, with the dominant AOB showing high similarity to the Nitrosospira genus. Therefore, soil-based environmental factors, such as pH variation and content of NH4 +-N and NO3 --N, can substantially influence the abundance of AOB communities in soil, and play a critical role in soil-based nitrification kinetics.
Abstract In this study, we investigated the potential nitrification and community structure of soil-based ammonia-oxidizing bacteria (AOB) in apple orchard soil during different growth periods and explored the effects of environmental factors on nitrification activity and AOB community composition in the soil of a Hanfu apple orchard, using a culture-dependent technique and denaturing gradient gel electrophoresis (DGGE). We observed that nitrification activity and AOB abundance were the highest in November, lower in May, and the lowest in July. The results of statistical analysis indicated that total nitrogen (N) content, NH4 +-N content, NO3 --N content, and pH showed significant correlations with AOB abundance and nitrification activity in soil. The Shannon-Winner diversity, as well as species richness and evenness indices (determined by PCR-DGGE banding patterns) in soil samples were the highest in September, but the lowest in July, when compared to additional sampled dates. The DGGE fingerprints of soil-based 16S rRNA genes in November were apparently distinct from those observed in May, July, and September, possessing the lowest species richness indices and the highest dominance indices among all four growth periods. Fourteen DGGE bands were excised for sequencing. The resulting analysis indicated that all AOB communities belonged to the β-Proteobacteria phylum, with the dominant AOB showing high similarity to the Nitrosospira genus. Therefore, soil-based environmental factors, such as pH variation and content of NH4 +-N and NO3 --N, can substantially influence the abundance of AOB communities in soil, and play a critical role in soil-based nitrification kinetics.
|
Received: 31 October 2012
Accepted:
|
Corresponding Authors:
QIN Si-jun, E-mail: qinsijun1975@163.com; Lü De-guo, Tel/Fax: +86-24-88487219, E-mail: shynydxgshzp@163.com
E-mail: qinsijun1975@163.com
|
About author: LIU Ling-zhi, Mobile: 13238832696, E-mail: liulingzhi74@163.com |
Cite this article:
LIU Ling-zhi, QIN Si-jun, Lü De-guo, WANG Bing-ying , YANG Ze-yuan.
2014.
Variation of Potential Nitrification and Ammonia-Oxidizing Bacterial Community with Plant-Growing Period in Apple Orchard Soil. Journal of Integrative Agriculture, 13(2): 415-425.
|
Allison S M, Prosser J I. 1991. Survival of ammonia oxidizing bacteria in air-dried soil. FEMS Microbiology Letters, 79, 65-68 Allison S M, Prosser J I. 1993. Ammonia oxidation at low pH by attached populations of nitrifying bacteria. Soil Biology and Biochemistry, 25, 935-941 Avrahami S, Conrad R. 2005. Cold-temperature climate: a factor for selection of ammonia oxidizers in upland soil? Canadian Journal of Microbiology, 51, 709-714 Bäckman J S K, Hermansson A, Tebbe C C. 2003. Liming induces growth of a diverse flora of ammonia-oxidizing bacteria in acid spruce forest soil as determined by SSCP and DGGE. Soil Biology and Biochemistry, 35, 1337- 1347. Bäckman J S K, Klemedtsson A K, Klemedtsson L, Lindgren P. 2004. Clear-cutting affects the ammonia- oxidizing community differently in limed and non-limed coniferous forest soils. Biology and Fertility of Soils, 40, 260-267 de Boer W, Kowalchuk G A. 2001. Nitrification on acid soils: micro-organisms and mechanisms. Soil Biology and Biochemisty, 33, 853-866 de Boer W, Laanbroek H J. 1989. Ureolytic nitrification at low pH by Nitrosospira spec. Archives of Microbiology, 152, 178-181 Boyle-Yarwood S A, Bottomley P J, Myrold D D. 2008. Community composition of ammonia-oxidizing bacteria and archaea in soils under stands of red alder and Douglas fir in Oregon. Environmental Microbiology, 10, 2956-2965 Cebron A, Coci M, Garnier J, Laanbroek H J. 2004. Denaturing gradient gel electrophoretic analysis of ammonia-oxidizing bacterial community structure in the lower Seine River: Impact of Paris wastewater effluents. Applied Environmental Microbiology, 70, 6726-6737 Chanasyk D S, Whitson I R, Mapfumo E, Burke J M, Prepas E E. 2003. The impacts of forest harvest and wildfire on soils and hydrology in temperate forests: A baseline to develop hypotheses for the Boreal Plain. Journal of Environmental Engineering and Science, 2, 51-62 Di H J, Cameron K C, Shen J P, Winefield C S, Callaghan M, Bowatte S, He J Z. 2009. Nitrification driven by bacteria and not archaea in nitrogen-rich grass-land soils. National Geoscience, 2, 621-624 F i e r e r N, Jackson R B. 2006. The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences of the United States of America, 103, 626-631 Frijlink M J, Abee T, Laanbroek H J, de Boer W, Konings W N. 1992. The bioenergetics of ammonia and hydroxylamine oxidation in Nitrosomonas europaea at acid and alkaline pH. Archives of Microbiology, 157, 194-199 Freitag T E, Chang L, Prosser J I. 2006. Changes in the community structure and activity of betaproteobacterial ammonia-oxidizing sediment bacteria along a freshwater marine gradient. Environmental Microbiology, 8, 684- 696. Grigal D F. 2000. Effects of extensive forest management on soil productivity. Forest Ecology and Management, 138, 167-185 Hart S C, Stark J M, Davidson E A, Firestone M K. 1994. Soil Science Society of America Book Series #5. Madison, WI. pp. 985-1018 Hastings R C, Ceccherini M T, Miclaus N, Saunders J R, Bazzicalupo M, McCarthy A J. 1997. Direct molecular biological analysis of ammonia oxidizing bacteria populations in cultivated soil plots treated with swine manure. FEMS Microbiology Ecology, 23, 45-54 He J Z, Hu H W, Zhang L M. 2012. Current insights into the autotrophic thaumarchaeal ammonia oxidation in acidic soils. Soil Biology and Biochemistry, 55, 146-154 Helgason B L Walley F L, Gemida J J. 2009. Fungal and bacterial abundance in long-term no-till and intensive- till soils of the northern Great Plains. Soil Biology and Biochemistry, 73, 120-127 Hermansson A, Backman J S K, Svensson B H. 2004, Quantification of ammonia-oxidizing bacteria in limed and non-limed acidic coniferous forest soil using real- time PCR. Soil Biology and Biochemistry, 34, 1935- 1941. Holly M H, James J, Germida. 2012. Relationship between ammonia oxidizing bacteria and bioavailable nitrogen in harvested forest soils of central Alberta. Soil Biology and Biochemistry, 46, 18-25 Jiang Q Q, Bakken L R. 1999. Comparison of Nitrosospira strains isolated from terrestrial environments. FEMS Microbiology Ecology, 30, 171-186 Kemmitt S J, Wright D, Goulding K W T, Jones D L. 2006. pH regulation of carbon and nitrogen dynamics in two agricultural soils. Soil Biology and Biochemistry, 38, 898-911 Killham K. 1990. Nitrification in coniferous forest soils. Plant and Soil, 128, 31-44 Kong A Y Y, Hristova K, Scow K M, Six J. 2010. Impacts of different N management regimes on nitrifier and denitrifier communities and N cycling in soil microenvironments. Soil Biology and Biochemistry, 42, 1523-1533 Koops H P, Pommerening-Röser A. 2001. Distribution and ecophysiology of the nitrifying bacteria emphasizing cultured species. FEMS Microbiology Ecology, 37, 1-9 Kowalchuk G A, Stephen J R. 2001. Ammonia-oxidizing bacteria: a model for molecular microbial ecology. Annual Review of Microbiology, 55, 485-529 Kowalchuk G A, Stephen J R, de Boer W, Prosser J I, Embley T M, Woldendorp J W. 1997. Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments. Applied and Environmental Microbiology, 63, 1489- 1497. Li H, Qiu J J, Wang L G, Xu M Y, Liu Z Q, Wang W. 2012. Estimates of N2O emissions and mitigation potential from a spring maize field based on DNDC model. Journal of Integrative Agriculture, 11, 2067-2078 Li Y L, Wang L, Zhang W Q, Wang H L, Fu X H, Le Y Q. The variability of soil microbial community composition of different types of tidal wetland in Chongming Dongtan and its effect on soil microbial respiration. Ecological Engineering, 37, 1276-1282 Li Z D, Wang Y H, Li L Y. 2009. Orchard soil acidification status in Jiaodong peninsula of Shandong Province and control techniques. Phosphate and Compound Fertilizer, 24, 80-81 (in Chinese) Lueders T, Friedrich M W. 2003. Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Applied Environmental Microbiology, 69, 320-326 Mathieu-Daude F, Welsh J, Vogt T, McClelland M. 1996. DNA rehybridization during PCR: the ‘Cot effect’ and its consequences. Nucleic Acids Research, 24, 2080- 2086. Mahmood S, Freitag T E, Prosser J I. 2006. Comparison of PCR primer-based strategies for characterization of ammonia oxidizer communities in environmental samples. FEMS Microbiology Ecology, 56, 482-493 Malchair S, de Boeck H J, Lemmens C M H M, Merckx R, Nijs I, Ceulemans R, Carnol M. 2010. Do climate warming and plant species richness affect potential nitrification, basal respiration and ammonia-oxidizing bacteria in experimental grasslands? Soil Biology and Biochemistry, 42, 1944-1951 Meng H Q, Xu M G, Lü J L, He X H Li J W, Shi X J, Peng C, Wang B R, Zhang H M. 2013. Soil pH dynamics and nitrogen transformations under long-term chemical fertilization in four typical Chinese croplands. Journal of Integrative Agriculture, 12, 2092-2102. Miao Y X, Bobby A S, Zhang F S. 2011. Long-term experiments for sustainable nutrient management in China. A Review. Agronomy for Sustainable Development, 31, 397-414 Mintie A T, Heichen R S, Cromack K, Myrold D D, Bottomley P J. 2003. Ammonia-oxidizing bacteria along meadow-to-forest transects in the Oregon cascade mountains. Applied and Environmental Microbiology, 69, 3129-3136 Muyzer G, de Waal E C, Uitterlinden A G. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology, 59, 695-700 Nicol G W, Leininger S, Schleper C, Prosser J I. 2008. The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environmental Microbiology, 10, 2966- 2978. Nicolaisen M H, Ramsing N B. 2002. Denaturing gradient gel electrophoresis (DGGE) approaches to study the diversity of ammonia-oxidizing bacteria. Journal of Microbiological Methods, 50, 189-203 Nugroho R A, Röling W F M, Laverman A M, Zoomer H R, Verhoef H A. 2005. Presence of Nitrosospira cluster 2 bacteria corresponds to N transformation rates in nine acid Scots pine forest soils. FEMS Microbiology Ecology, 53, 473-481 Prosser J I. 1989. Autotrophic nitrification in bacteria. Advances in Microbial Physiology, 30, 125-181 Rennenberg H, Dannenmann M, Gessler A, Kreuzwiesser J, Simon J, Papen H. 2009. Nitrogen balance in forest soils: nutritional limitation of plants under climate change stresses. Plant Biology, 11, 4-23 Rowe R, Todd R, Waide J. 1977. Microtechnique for most- probable-number analysis. Applied and Environmental Microbiology, 33, 675-680 Purkhold U, Pommerening-Röser A, Juretschko S, Schmid MC, Koops H P, Wagner M. 2000. Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys. Applied Environmental Microbiology, 66, 5368-5382 dos Santos A C F, Marques E L S, Gross E, Souza S S, Dias J C T, Brendel M, Rezende R P. 2012. Detection by denaturing gradient gel electrophoresis of ammonia- oxidizing bacteria in microcosms of crude oil- contaminated mangrove sediments. Genetics and Molecular Research, 11, 190-201 Shen J P, Zhang L M, Di H J, He J Z. 2012. A review of ammonia-oxidizing bacteria and archaea in Chinese soils. Frontiers in Microbiology, 3, 1-7 Shen X Y, Zhang L M, Shen J P, Li L H, Yuan C L, He J Z. 2011. Nitrogen loading levels affect abundance and composition of soil ammonia oxidizing prokaryotes in semi-arid temperate grassland. Journal of Soil Sediment, 11, 1243-1252 Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 24, 1596-1599 Tong D, Xu R. 2012. Effects of urea and (NH4)2SO4 on nitrification and acidification of Ultisols from southern China. Journal of Environmental Science (in China), 24, 682-689 Wrage N, Velthof G L, van Beusichem M L, Oenema O. 2001. Role of nitrifier denitrification in the production of nitrous oxide. Soil Biology and Biochemistry, 33, 1723- 1732. Xia W W, Zhang C X, Zeng X W, Feng Y Z, Weng J H, Lin X G, Zhu J G, Xiong Z Q, Xu J, Cai Z C, et al. 2011. Autotrophic growth of nitrifying community in an agricultural soil. The ISME Journal, 5, 1226-1236 Xiao L, Liu G B, Xue S, Zhang C. 2013. Soil microbial community composition during natural recovery in the Loess Plateau, China. Journal of Integrative Agriculture, 12, 1872-1883 Yeager C M, Northup D E, Grow C C, Barns S M, Kuske C R. 2005. Changes in nitrogen-fixing and ammonia- oxidizing bacterial communities in soil of a mixed conifer forest after wildfire. Applied and Environmental Microbiology, 71, 2713-2722 |
No Suggested Reading articles found! |
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
|
Shared |
|
|
|
|
|
Discussed |
|
|
|
|