SCIEnTIfIC RePoRts | 7: 16707 | DOI:10.1038/s41598-017-17080-z
Legume crop rotation suppressed
nitrifying microbial community in a
sugarcane cropping soil
, Weijin Wang
, Yun Kit Yeoh
& Neil Halpin
Nitrifying microorganisms play an important role in nitrogen (N) cycling in agricultural soils as
nitrication leads to accumulation of nitrate (NO
) that is readily lost through leaching and
denitrication, particularly in high rainfall regions. Legume crop rotation in sugarcane farming systems
can suppress soil pathogens and improve soil health, but its eects on soil nitrifying microorganisms
are not well understood. Using shotgun metagenomic sequencing, we investigated the impact of
two legume break crops, peanut (Arachis hypogaea) and soybean (Glycine max), on the nitrifying
communities in a sugarcane cropping soil. Cropping with either legume substantially increased
abundances of soil bacteria and archaea and altered the microbial community composition, but did
not signicantly alter species richness and evenness relative to a bare fallow treatment. The ammonia
oxidisers were mostly archaeal rather than bacterial, and were 24–44% less abundant in the legume
cropping soils compared to the bare fallow. Furthermore, abundances of the archaeal amoA gene
encoding ammonia monooxygenase in the soybean and peanut cropping soils were only 30–35% of that
in the bare fallow. These results warrant further investigation into the mechanisms driving responses of
ammonia oxidising communities and their nitrication capacity in soil during legume cropping.
Sugarcane farms are mostly located in high rainfall (>1000 mm per year) tropics and subtropics. Fertiliser nitro-
gen (N) applied in such regions is susceptible to loss through processes such as denitrication and leaching,
leading to nitrous oxide (N
O) emissions into the atmosphere and nitrate (NO
) pollution in waterways, respec-
. In order to achievehigh crop yields, the amount of N fertiliser applied to sugarcane crops are generally
high (120 to 300 kg N ha
. In recent years, legume crop rotation during the fallow period between two
consecutive sugarcane crop cycles has been promoted in Australia to improve soil health and to benet from
xation, thus reducing reliance on synthetic N for the subsequent crop
. Compared to the con-
ventional practice of bare fallow or continuous cane as “plough-out replant”, legume rotation can improve soil
fertility and suppress soil pathogens
. However, few studies have investigated the eects of legume rotation on
soil microbiota and their function in relation to soil N cycling.
Nitrication is the microbe-mediated conversion of ammonium (NH
) to nitrate (NO
) which can be eas-
ily lost through leaching and denitrication, particularly in tropical or subtropical regions with high rainfall.
One of the management strategies to enhance fertiliser N use eciency and reduce its negative impact on the
environment is to add nitrication inhibitors into NH
-based fertilisers (including urea) or directly into soil
Recent studies under controlled conditions found that certain plant species such as peanut, sorghum and grasses
release phytochemicals from roots that inhibit activities of soil nitrifying microorganisms
. We hypothesised
that compared to continuous mono-cropping or bare fallow, legume crop rotation may inuence soil microbial
community composition and the abundance of nitriers by altering soil N status and other bio-physico-chemical
properties in the rhizosphere. Hence in the present study, we investigated possible impacts of two major rotational
legume crops, peanut (Arachis hypogaea) and soybean (Glycine max), on soil nitrifying microbial communities in
a sugarcane cropping soil under eld conditions.
School of Agriculture and Food Sciences, The University of Queensland, St Lucia, QLD 4072, Australia.
Organic Solutions Pty Ltd, Indooroopilly, QLD 4068, Australia.
Department of Science, Information Technology and
Innovation, Brisbane, QLD 4001, Australia.
Environmental Futures Research Institute, Grith University, Nathan,
QLD 4111, Australia.
Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The
University of Queensland, St Lucia, QLD 4072, Australia.
Department of Agriculture and Fisheries, 49 Asheld Rd,
Bundaberg, QLD 4670, Australia. Correspondence and requests for materials should be addressed to W.W. (email:
Received: 27 June 2017
Accepted: 21 November 2017
Published: xx xx xxxx