Nitrification in terrestrial environment: Nitrogen is a key element controlling terrestrial productivity. The nitrogen cycle, mediated by microorganisms, transforms nitrogen among its six redox states. Nitrification converts reduced (ammonia) to oxidized (nitrite and nitrate) forms of nitrogen. Although nitrification has been studied for over a century, it is only recently that ammonia-oxidizing archaea (AOA) were discovered in addition to their counterparts, ammonia-oxidizing bacteria (AOB), which were formerly regarded as the sole contributors to nitrification. Since their discovery, questions regarding the ecology, physiology, and metabolism of AOA are still not well answered. My Ph.D. project endeavored to study the biogeography and function of soil AOA in an effort to better understand AOA distributions and their contribution to nitrification.
Metagenomic data mining: As the cost of shotgun metagenomic is decreasing, the number of environmental metagenomes deposited into public database is increasing exponentially. However, due to the large-size and complexity of metagenomic data (big data), the available data haven't been exploited thoroughly, leaving a room for further discovery. Comparing to 16S rRNA amplicon sequencing, metagenomic sequencing data contain not only phylogenetic information but also functional gene information, making it possible to make functional prediction of a soil microbial community with a higher confidence. My research involves soil metagenomic data mining, targeting functional genes of critical biogeochemical metabolism, elucidating their ecological importance. Function profiling of soil metagenomic data is carried out using MetAnnotate, a hidden Markov model (HMM) based taxonomic profiling tool, developed by Dr. Doxey's lab.
Metagenomic data mining: As the cost of shotgun metagenomic is decreasing, the number of environmental metagenomes deposited into public database is increasing exponentially. However, due to the large-size and complexity of metagenomic data (big data), the available data haven't been exploited thoroughly, leaving a room for further discovery. Comparing to 16S rRNA amplicon sequencing, metagenomic sequencing data contain not only phylogenetic information but also functional gene information, making it possible to make functional prediction of a soil microbial community with a higher confidence. My research involves soil metagenomic data mining, targeting functional genes of critical biogeochemical metabolism, elucidating their ecological importance. Function profiling of soil metagenomic data is carried out using MetAnnotate, a hidden Markov model (HMM) based taxonomic profiling tool, developed by Dr. Doxey's lab.
My research has been supported by Drs. Myrold, Bottomley, Neufeld, Chisholm, and the following institutions:
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For a complete publication list, please see my Google Scholar.
- X. Lu, G. W. Nicol, J. D. Neufeld, 2018. Differential responses of soil ammonia-oxidizing archaea and bacteria to temperature and depth under two different land uses. Soil Biology and Biochemistry 120, 272-282.
- X. Lu, B. Seuradge, J. D. Neufeld, 2016. Biogeography of soil thaumarchaeota in relation to soil depth and land usage. FEMS Microbiology Ecology fiw246.
- X. Lu, P. J. Bottomley, D. D. Myrold, 2015. Contributions of ammonia-oxidizing archaea and bacteria to nitrification in Oregon forest soils. Soil Biology and Biochemistry 85, 54-62.
