Soil-Plant Microbiomes
The Soil-Plant Microbiomes group explores the diversity, composition and functions of microbiota in soil-plant ecosystems, and uses the microbes to improve the agricultural productivity and environmental health.
Research in the Soil-Plant Microbiomes group focuses on the assembly and ecology of soil microbiota (bacteria, fungi, archaea, protist and virus) and soil fauna (eg: nematode and collembola) in soil ecosystems, and:
- Their interactions with plant-associated microbiome
- How these are influenced by biotic and abiotic factors and agricultural management practices
- The development of microbiome-based technologies to improve nutrients using efficiency and agricultural productivity, while to mitigate the negative effects of agricultural practices to the environment.
News and events
Contact the team
Soil microbial testing services have strong capabilities in advanced bio-molecular and physicochemical analyses of functional microbes-mediated carbon (C), nitrogen (N), phosphorus (P), sulphur (S) and other elemental information in order to understand the distribution and diversity of functional microbial genes in soils.
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High-throughput quantitative PCR
The Wafergen SmartChip Real-time PCR system is a complete, high-throughput solution that enables an unrivalled level of assay and sample format flexibility.
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DNA extraction
QIAGEN QIAcube Connect is designed to perform fully automated purification of nucleic acids and proteins in molecular biology applications.
Our researchers and graduate research (PhD/MPhil) students.
Professor Jim (Jizheng) He
Professor (Molecular Soil Ecology)
Jim He’s research employs advanced bio-molecular and physicochemical approaches to understand the distribution and diversity of microbial communities in soils, and the processes and mechanisms of microbes-mediated C, N and other elemental cycling.
Dr Hang-Wei Hu
Lecturer in Soil Biology and Health
Hang-Wei Hu is a soil molecular microbial ecologist with research interests broadly defined within the areas of soil biology and health, plant-microbe interactions, and environmental microbiology.
Dr Qinglin Chen
Research Fellow in Antibiotic Resistance
Qinglin Chen’s research is focused on the plant and soil microbiome, and their relationship with antibiotic resistome in the context of human interruptions.
Qing Xie
Research Assistant
Qing Xie is a research assistant in soil molecular ecology, and is also responsible for management of key research facilities and instruments in Soil Molecular Ecology Labs.
Eric Ireland
PhD candidate
Eric Ireland’s PhD project is focused on the microbial communities regulating the dissimilatory nitrate reduction to ammonium process in various terrestrial ecosystems.
Chaoyu Li
PhD candidate
Chaoyu Li’s PhD project is focused on the newly-discovered complete ammonia oxidizers (comammox Nitrospira) and their contribution to soil nitrification.
Zhenzhen Yan
PhD candidate
Zhenzhen Yan’s PhD project is focused on the biogeographic distribution patterns of antibiotic resistance genes in urban and natural ecosystems.
Bao Anh Nguyen
PhD candidate
Bao Anh Nguyen’s PhD project is focused on the interactions of protists and bacteria and its consequence for evolution of antibiotic resistance in soils.
Group members
Graduate researchers
The Soil-Plant Microbiomes Group has taken advantage of rapidly improving high-throughput sequencing approaches to answer important ecological questions regarding soil/plant microbiome composition and diversity, soil biogeochemical N cycling processes and transmission of antibiotic resistance genes in soil-plant systems.
Current projects
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Contribution of comammox bacteria to nitrification in terrestrial ecosystems
This project aims to understand the diversity, activity and environmental relevance of comammox bacteria, the newly-discovered complete nitrifiers, in Australian soils, and to evaluate their relative contributions to nitrification processes compared to other canonical nitrifying prokaryotes.
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How is antibiotic resistance transferred from animal manure to vegetable?
This project will investigate all the major classes of ARGs in typical animal manure and vegetable farm, and to explore possible routes for transmission of ARGs from manure to soil and further to vegetable surfaces and endophytic bacterial communities.
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Synthetic microbiome: improving crop nitrogen acquisition and productivity
Challenges to food security under conditions of global climate change are forcing us to increase crop production to feed the growing population.
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Completed projects
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Soil microbial indicators for efficient use of nitrification inhibitors
Nitrification inhibitors (NIs) are one tool widely used to improve nitrogen fertiliser efficiency and reduce greenhouse gas nitrous oxide emissions. However, their effectiveness is variable across soil types and one possible reason is the different microbial communities that exist in these soils.
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Unravelling the microbial mechanisms of soil nitrous oxide emissions
Soil ecosystems are believed to be the most dominant sources of global nitrous oxide emissions. However, mitigations of nitrous oxide are strongly hindered by lack of knowledge on microbial mechanisms underpinning its production.
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Reserving nitrogen in soils through microbial nitrate reduction to ammonium
This project aims to gain insights into the roles of abiotic factors controlling the occurrence of dissimilatory nitrate reduction to ammonium (DNRA), the microbial groups involved in the DNRA process, and the contribution of DNRA to nitrogen (N) conservation in soil ecosystems.
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