Differential structure and functional gene response to geochemistry associated with the suspended and attached shallow aquifer microbiomes from the Illinois Basin, IL

Dong, Yiran; Sanford, Robert A.; Connor, Lynn; Chee-Sanford, Joanne; Wimmer, Bracken T.; Iranmanesh, Abbas; Shi, Liang; Krapac, Ivan G.; Locke, II, Randall A.; Shao, Hongbo

doi:10.1016/j.watres.2021.117431

Title: Differential structure and functional gene response to geochemistry associated with the suspended and attached shallow aquifer microbiomes from the Illinois Basin, IL

Journal Article · 14 July 2021 · Water Research

DOI: https://doi.org/10.1016/j.watres.2021.117431 · OSTI ID:1810109

^[1];

^[2]; Connor, Lynn ^[3]; Chee-Sanford, Joanne ^[3]; Wimmer, Bracken T. ^[4]; Iranmanesh, Abbas ^[4]; Shi, Liang ^[5]; Krapac, Ivan G. ^[4];

^[4];

^[4]

China Univ. of Geosciences, Wuhan (China); 547002
Univ. of Illinois at Urbana-Champaign, IL (United States)
USDA-ARS, Urbana, IL (United States)
Illinois State Geological Survey, Champaign, IL (United States)
China Univ. of Geosciences, Wuhan (China)

Despite the clear ecological significance of the microbiomes inhabiting groundwater and connected ecosystems, our current understanding of their habitats, functionality, and the ecological processes controlling their assembly have been limited. In this study, an efficient pipeline combining geochemistry, high-throughput Fluidigm^TM functional gene amplification and sequencing was developed to analyze the suspended and attached microbial communities inhabiting five groundwater monitoring wells in the Illinois Basin, USA. The dominant taxa in the suspended and the attached microbial communities exhibited significantly different spatial and temporal changes in both alpha- and beta-diversity. Further analyses of representative functional genes affiliated with N₂ fixation (nifH), methane oxidation (pmoA), and sulfate reduction (dsrB, and aprA), suggested functional redundancy within the shallow aquifer microbiomes. While more diversified functional gene taxa were observed for the suspended microbial communities than the attached ones except for pmoA, different levels of changes over time and space were observed between these functional genes. Notably, deterministic and stochastic ecological processes shaped the assembly of microbial communities and functional gene reservoirs differently. While homogenous selection was the prevailing process controlling assembly of microbial communities, the neutral processes (e.g., dispersal limitation, drift and others) were more important for the functional genes. The results suggest complex and changing shallow aquifer microbiomes, whose functionality and assembly vary even between the spatially proximate habitats and fractions. As a result, this research underscored the importance to include all the interface components for a more holistic understanding of the biogeochemical processes in aquifer ecosystems, which is also instructive for practical applications.

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Research Organization:: Univ. of Illinois at Urbana-Champaign, IL (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: FC26-05NT42588

OSTI ID:: 1810109

Journal Information:: Water Research, Journal Name: Water Research Vol. 202; ISSN 0043-1354

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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54 ENVIRONMENTAL SCIENCES
Shallow aquifer microbiomes
community assembly
functional genes
multiplex PCR
suspended vs attached microbial communities
temporal-spatial affects

Title: Differential structure and functional gene response to geochemistry associated with the suspended and attached shallow aquifer microbiomes from the Illinois Basin, IL

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