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Soil, land care and environmental research
RESEARCH ARTICLE

Bacterial community structure and denitrifier (nir-gene) abundance in soil water and groundwater beneath agricultural land in tropical North Queensland, Australia

Steven A. Wakelin A B F , Paul N. Nelson C D , John D. Armour D , Velupillai Rasiah D and Matthew J. Colloff E

A CSIRO Land and Water, Environmental Biogeochemistry Theme, PMB 2, Glen Osmond, SA 5064, Australia.

B AgResearch Ltd, Lincoln Research Centre, Private Bag 4749, Christchurch 8140, New Zealand.

C James Cook University, School of Earth and Environmental Sciences, PO Box 6811, Cairns, Qld 4870, Australia.

D Department of Environment and Resource Management, PO Box 156, Mareeba, Qld 4880, Australia.

E CSIRO Entomology, GPO Box 1700, Canberra, ACT 2601, Australia.

F Corresponding author. Email: steve.wakelin@agresearch.co.nz

Soil Research 49(1) 65-76 http://dx.doi.org/10.1071/SR10055
Submitted: 5 March 2010  Accepted: 2 August 2010   Published: 4 February 2011

Abstract

We explored the microbial ecology of water draining through the soil (lysimeter samples) and in the shallow aquifers (bore samples) underlying sugarcane and banana fields near the Great Barrier Reef (GBR), Australia. Lysimeter and bore water samples were collected and analysed chemically and with DNA fingerprinting methods (PCR-DGGE and clone library sequencing) to characterise the structure of the bacterial community. Bacterial communities in soil water and bore water were distinct (P < 0.05), and a primary factor linked with bacterial community structure was water pH (P < 0.05), particularly in water sampled from lysimeters. Irrespective of treatment, >80% of all rRNA gene sequences originated from proteobacteria. However, groundwater communities differed from those in soil water by greater occurrence of Neisseriales and Comamonadaceae (P < 0.01). qPCR was used to measure copy numbers of the nirK and nirS genes encoding NO-forming nitrite reductases. Copy numbers of both genes were greater in soil water samples than groundwater (P = 0.05), with the difference in nirK being greater under sugarcane than banana. These differences in nirK-gene abundance show that there is greater potential for denitrification in soil water under sugarcane, leading to low concentrations of nitrate in the underlying groundwater. This knowledge can be used towards development of soil and land-use management practices promoting bacterial denitrification in groundwater to lessen the undesirable ecological consequences where groundwater discharges lower in the GBR catchment zones.


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