Bacterial Community Shift and Coexisting/Coexcluding Patterns Revealed by Network Analysis in A Bioreduced Uranium Contaminated Site after Reoxidation

Bing Li, Wei-Min Wu, David B. Watson, Erick Cardenas, Yuanqing Chao, Debra Phillips, Tonya Mehlhorn, Ken Lowe, Shelly D. Kelly, Pingsong Li, Huchun Tao, James M. Tiedje, Craig S. Criddle, Tong Zhang

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A site in Oak Ridge, Tennessee, USA, has sediments that contain >3% iron oxides and is contaminated with uranium (U). The U(VI) was bioreduced to U(IV) and immobilized in situ through intermittent injections of ethanol. Then it was allowed to reoxidize via the invasion of low-pH (3.6–4.0), high-nitrate (up to 200 mM) groundwater back into the reduced zone for 1,383 days. To examine the biogeochemical response, high-throughput sequencing and network analysis were applied to characterize bacterial population shifts, as well as co-occurrence and co-exclusion patterns among microbial communities. Paired t-test indicated no significant changes of α-diversity for the bioactive wells. However, both nonmetric multidimensional scaling and analysis of similarity confirmed a significant distinction in the overall composition of the bacterial communities between the bioreduced and the reoxidized sediments. The top 20 major genera accounted for >70% of the cumulative contribution to the dissimilarity in the bacterial communities before and after the groundwater invasion. Castellaniella had the largest dissimilarity contribution (17.7%). For the bioactive wells, the abundance of the U(VI)-reducing genera Geothrix, Desulfovibrio, Ferribacterium, and Geobacter decreased significantly, whereas the denitrifying Acidovorax abundance increased significantly after groundwater invasion. Additionally, seven genera, i.e., Castellaniella, Ignavibacterium, Simplicispira, Rhizomicrobium, Acidobacteria Gp1, Acidobacteria Gp14 and Acidobacteria Gp23 were significant indicators of bioactive wells under reoxidation stage. Canonical correspondence 57 analysis indicated that nitrate, manganese and pH affected mostly the U(VI)-reducing genera and indicator genera. Co-occurrence patterns among microbial taxa suggested the presence of taxa sharing similar ecological niches or mutualism/commensalism/synergism interactions.
Original languageEnglish
JournalApplied and Environmental Microbiology
Early online date16 Feb 2018
Publication statusEarly online date - 16 Feb 2018


Cite this

Li, B., Wu, W-M., Watson, D. B., Cardenas, E., Chao, Y., Phillips, D., Mehlhorn, T., Lowe, K., Kelly, S. D., Li, P., Tao, H., Tiedje, J. M., Criddle, C. S., & Zhang, T. (2018). Bacterial Community Shift and Coexisting/Coexcluding Patterns Revealed by Network Analysis in A Bioreduced Uranium Contaminated Site after Reoxidation. Applied and Environmental Microbiology.