Environmental and edaphic drivers of bacterial communities involved in soil N-cycling
M.S. Forbes A B D , K. Broos A C , J.A. Baldock A , A.L. Gregg A and S.A. Wakelin AA CSIRO Land and Water, PMB 2, Glen Osmond, SA 5064, Australia.
B Department of Environment and Conservation, Locked Bag 104, Bentley, WA 6983, Australia.
C Current address: VITO – Flemish Institute for Technological Research, Boeretang 200, 2400 Mol, Belgium.
D Corresponding author. Email: matt.forbes@dec.wa.gov.au
Australian Journal of Soil Research 47(4) 380-388 https://doi.org/10.1071/SR08126
Submitted: 25 May 2008 Accepted: 27 January 2009 Published: 30 June 2009
Abstract
The cycling of N in soil is supported both directly and indirectly by numerous microbial processes. These processes affect ecosystem fertility, but can also generate forms of N which have detrimental environmental impacts, such as N2O. Understanding drivers of biological communities involved in key N-transformations is therefore of much interest. The effects of physicochemical and environmental properties on the relative size (abundance within total DNA pool) of biological communities involved in 3 key N transformations were investigated. Soils from 14 locations spanning a rainfall gradient across 3 agricultural regions (Clare, Mallee, Balaclava) were sampled, with samples taken from the surface and at depth from each site. Based on PCA of physicochemical and environmental properties, the soils fell into 2 distinct groupings: Clare and Mallee + Balaclava ‘types’. The abundance of functional genes involved in N2 fixation (nifH), ammonia oxidation (amoA), and nitrate reduction (narG) was quantified in DNA extracted from the soils using real-time PCR. The abundance of the nifH gene varied significantly with site (P = 0.03) but not depth, and no regional association with nifH gene abundance was found. Multivariate analysis indicated that the abundance of nifH was positively correlated with soil total C (ρ = 0.382; P = 0.006). Similarly, the abundance of narG varied with site (P < 0.001) and not soil depth. The abundance of narG was positively correlated with increasing rainfall (ρ = 0.417; P = 0.002). The abundance of amoA did not significantly vary between soils, but significantly decreased with soil depth (P = 0.006). The abundance of amoA was negatively correlated with soil electrical conductivity and positively with organic C (combined ρ = 0.44; P = 0.003). Whereas there was no relationship between the abundance of nifH and amoA or narG, the abundance of amoA was positively correlated with the abundance of narG (P < 0.001). These results indicate that the abundance of the N cycling genes is independently affected by different physicochemical or environmental properties. The interactions between soil, environment, and the functionally significant biological communities they support are complex. To gain fuller understanding of soil N cycling, the ecology of the various biological components affecting N-transformations must be investigated simultaneously.
Additional keywords: amoA, denitrification, functional genes, N cycling, N2 fixation, narG, nifH, nitrification.
Acknowledgments
This work was funded by the Australian Greenhouse Office. B. Roberts, K. L’Anson, P. Schmaal, R. Graetz, J. Faulkner, D. Wormald, and M. Behn kindly provided access to agricultural sites. Drs Matt Colloff and Don Gomez, CSIRO Entomology, kindly reviewed and commented on the manuscript.
Bolan N,
Saggar S,
Luo J,
Bhandral R, Singh J
(2004) Gaseous emissions of nitrogen from grazed pastures: Processes, measurements and modelling, environmental implications, and mitigation. Advances in Agronomy 84, 37–120.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
Broos K,
Macdonald LM,
Warne MSJ,
Heemsbergen DA,
Barnes MB,
Bell M, McLaughlin MJ
(2007a) Limitations of soil microbial biomass carbon as an indicator of soil pollution in the field. Soil Biology & Biochemistry 39, 2693–2695.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
Broos K,
Warne MSJ,
Heemsbergen DA,
Stevens D,
Barnes MB,
Correll RL, McLaughlin MJ
(2007b) Soil factors controlling the toxicity of Cu and Zn to microbial processes in Australian soils. Environmental Toxicology and Chemistry 26, 583–590.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
PubMed |
Chen XP,
Zhu YG,
Xia Y,
Shen JP, He JZ
(2008) Ammonia-oxidising archaea: important players in paddy rhizosphere soil? Environmental Microbiology 10(8), 1978–1987.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
PubMed |
Clarke KR
(1993) Non-parametric multivariate analysis of changes in community structure. Australian Journal of Ecology 18, 117–143.
| Crossref | GoogleScholarGoogle Scholar |
Clarke KR, Ainsworth M
(1993) A method of linking multivariate community structure to environmental variables. Marine Ecology Progress Series 92, 205–219.
| Crossref | GoogleScholarGoogle Scholar |
Cookson WR,
Müller C,
O’Brien PA,
Murphy DV, Grierson PF
(2006) Nitrogen dynamics in an Australian semiarid grassland soil. Ecology 87, 2047–2057.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
PubMed |
De Boer W, Kowalchuk GA
(2001) Nitrification in acid soils: micro-organisms and mechanisms. Soil Biology & Biochemistry 33, 853–866.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
Gillman GP, Sumpter EA
(1986) Modification to the compulsive exchange method for measuring exchange characteristics of soils. Australian Journal of Soil Research 24, 61–66.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
Gupta VVSR,
Roper MM, Roget DK
(2006) Potential for non-symbiotic N2-fixation in different agroecological zones of southern Australia. Australian Journal of Soil Research 44, 343–354.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
He J,
Shen J,
Zhang L,
Zhu Y,
Zheng Y,
Xu M, Di HJ
(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. Environmental Microbiology 9, 2364–2374.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
PubMed |
Horz HP,
Barbrook A,
Field CB, Bohannan BJM
(2004) Ammonia-oxidizing bacteria respond to multifactorial global change. Proceedings of the National Academy of Sciences of the United States of America 101, 15136–15141.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
PubMed |
Inubushi K,
Barahona MA, Yamakawa K
(1999) Effects of salts and moisture content on N2O emission and nitrogen dynamics in Yellow soil and Andosol in model experiments. Biology and Fertility of Soils 29, 401–407.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
Janik LJ,
Skjemstad JO, Raven MD
(1995) Characterisation and analysis of soils using mid-infra red partial least squares. I. Correlations with XRF-determined major element composition. Australian Journal of Soil Research 33, 621–636.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
Kloos K,
Mergel A,
Rösch C, Bothe H
(2001) Denitrification within the genus Azospirillum and other associative bacteria. Australian Journal of Plant Physiology 28, 991–998.
Kowalchuk GA, Stephen JR
(2001) Ammonia-oxidising bacteria: A model for molecular microbial ecology. Annual Review of Microbiology 55, 485–529.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
PubMed |
Kumar V, Wagenet RJ
(1985) Salt effects on urea hydrolysis and nitrification during leaching through laboratory soil columns. Plant and Soil 85, 219–227.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
Kumar V,
Yadav DS, Singh M
(1988) Effects of urea rates, farmyard manure, CaCO3, salinity and alkalinity levels on urea hydrolysis and nitrification in soils. Australian Journal of Soil Research 26, 367–374.
| Crossref | GoogleScholarGoogle Scholar |
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.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
PubMed |
López-Gutiérrez JC,
Henry S,
Hallet S,
Martin-Laurent F,
Catroux G, Philippot L
(2004) Quantification of a novel group of nitrate-reducing bacteria in the environment by real-time PCR. Journal of Microbiological Methods 57, 399–407.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Mergel A,
Schmitz O,
Mallmann T, Bothe H
(2001) Relative abundance of denitrifying and dinitrogen-fixing bacteria in layers of a forest soil. FEMS Microbiology Ecology 36, 33–42.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
PubMed |
Merry RH, Spouncer LR
(1988) The measurement of carbon in soils using a microprocessor-controlled resistance furnace. Communications in Soil Science and Plant Analysis 19, 707–720.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
Murphy DV,
Recous S,
Stockdale EA,
Fillery IRP,
Jensen LS,
Hatch DJ, Goulding KWT
(2003) Gross nitrogen fluxes in soil: theory, measurement and application of 15N pool dilution techniques. Advances in Agronomy 79, 69–118.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
Philippot L, Hallin S
(2005) Finding the missing link between diversity and activity using denitrifying bacteria as a model functional community. Current Opinion in Microbiology 8, 234–239.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
PubMed |
Philippot L,
Piutti S,
Martin-Laurent F,
Hallet S, Germon JC
(2002) Molecular analysis of the nitrate-reducing community from unplanted and maize-planted soils. Applied and Environmental Microbiology 68, 6121–6128.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
PubMed |
Rhoades JD
(1993) Electrical conductivity methods for measuring and mapping soil salinity. Advances in Agronomy 49, 201–251.
| Crossref | GoogleScholarGoogle Scholar |
Roper MM
(1983) Field measurements of nitrogenase activity in soils amended with wheat straw. Australian Journal of Agricultural Research 34, 725–739.
| Crossref | GoogleScholarGoogle Scholar |
Rösch C,
Mergel A, Bothe H
(2002) Biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil. Applied and Environmental Microbiology 68, 3818–3829.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Rotthauwe J,
Witzel KP, Liesack W
(1997) The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Applied and Environmental Microbiology 63, 4704–4712.
|
CAS |
PubMed |
Sadras VO
(2002) Interaction between rainfall and nitrogen fertilisation of wheat in environments prone to terminal drought. Economic and environmental risk analysis. Field Crops Research 77, 201–215.
| Crossref | GoogleScholarGoogle Scholar |
Sadras VO, Roget DK
(2004) Production and environmental aspects of cropping intensification in a semiarid environment of southeastern Australia. Agronomy Journal 96, 236–264.
Shen J,
Zhang L,
Zhu Y,
Zhang J, He J
(2008) Abundance and composition of ammonia-oxidising bacteria and ammonia-oxidising archaea communities of an alkaline sandy loam. Environmental Microbiology 10(6), 1601–1611.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
PubMed |
Stevens RJ,
Laughlin RJ, Malone JP
(1998) Soil pH affects the processes reducing nitrate to nitrous oxide and di-nitrogen. Soil Biology & Biochemistry 30, 1119–1126.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
Taroncher-Oldenburg G,
Griner EM,
Francis CA, Ward BB
(2003) Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Applied and Environmental Microbiology 69, 1159–1171.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
PubMed |
Vitousek P,
Hättenschwiler S,
Olander L, Allison S
(2002) Nitrogen and nature. Ambio 31, 97–101.
| PubMed |
Wakelin SA,
Colloff MJ,
Harvey PR,
Marschner P,
Gregg AL, Rogers SL
(2007) The effects of stubble retention and nitrogen application on soil microbial community structure and functional gene abundance under irrigated maize. FEMS Microbiology Ecology 59, 661–670.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
PubMed |
Wallenstein MD,
Myrold DD,
Firestone M, Voytek M
(2006) Environmental controls on denitrifying communities and denitrification rates: Insights from molecular methods. Ecological Applications 16, 2143–2152.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Wallenstein MD, Vilgalys RJ
(2005) Quantitative analyses of nitrogen cycling genes in soils. Pedobiologia 49, 665–672.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
Whelan JA,
Russell NB, Whelan MA
(2003) A method for the absolute quantification of cDNA using real-time PCR. Journal of Immunological Methods 278, 261–269.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
PubMed |
White RE
(1969) On the measurement of soil pH. Journal of the Australian Institute of Agricultural Science 35, 3–14.
|
CAS |
Yeager CM,
Northup DE,
Grow CC,
Barns SM, Kuske CR
(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.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
PubMed |
Zehr JP,
Jenkins BD,
Short SM, Steward GF
(2003) Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environmental Microbiology 5, 539–554.
| Crossref | GoogleScholarGoogle Scholar |
CAS |
PubMed |
