TY - JOUR
T1 - Assessing Microbial Community Patterns During Incipient Soil Formation From Basalt
AU - Sengupta, Aditi
AU - Stegen, James C.
AU - Meira Neto, Antonio A.
AU - Wang, Yadi
AU - Neilson, Julia W.
AU - Chorover, Jon
AU - Troch, Peter A.
AU - Maier, Raina M.
N1 - Funding Information:
A. S., J. N., A. A. M. N., Y. W., J. C., P. T., and R. M. wish to acknowledge support of NSF‐funded projects EAR‐1344552, EAR‐1340912, EAR‐1417097, and Philecology Foundation of Fort Worth Texas. A. A. M. N. would like to acknowledge the support received by the Brazilian Scientific Mobility Program promoted by CAPES. Additional funding supports were provided by the Water, Environmental, and Energy Solutions (WEES) initiative at the University of Arizona and by the office of Research, Discovery and Innovation's Accelerate for Success Grant at the University of Arizona. We would also like to acknowledge Daniel Laubitz at the University of Arizona Genomics Core for method development and sequencing of low‐ template samples. J. C. S. was supported by the U.S. Department of Energy (DOE), Office of Biological and Environmental Research (BER), as part of Subsurface Biogeochemical Research Program's Scientific Focus Area (SFA) at Pacific Northwest National Laboratory (PNNL). PNNL is operated for DOE by Battelle Memorial Institute under contract DE‐AC06‐76RLO 1830. The authors declare that they have no conflicts of interest. Conforming with the AGU data policy, data are available from the supporting information. Supporting data as two tables, three supporting data sets, and 13 figures are included in the supporting information file, sequence data are deposited at Sequence Read Archive SRP116044 (Accession PRJNA392820), and R code for Null Modeling can be found at https://github.com/stegen/Stegen_ etal_ISME_2013.
PY - 2019/4
Y1 - 2019/4
N2 - Microbial dynamics drive the biotic machinery of early soil evolution. However, integrated knowledge of microbial community establishment, functional associations, and community assembly processes in incipient soil is lacking. This study presents a novel approach of combining microbial phylogenetic profiling, functional predictions, and community assembly processes to analyze drivers of microbial community establishment in an emerging soil system. Rigorous submeter sampling of a basalt-soil lysimeter after 2 years of irrigation revealed that microbial community colonization patterns and associated soil parameters were depth dependent. Phylogenetic analysis of 16S rRNA gene sequences indicated the presence of diverse bacterial and archaeal phyla, with high relative abundance of Actinomyceles on the surface and a consistently high abundance of Proteobacteria (Alpha, Beta, Gamma, and Delta) at all depths. Despite depth-dependent variation in community diversity, predicted functional gene analysis suggested that microbial metabolisms did not differ with depth, thereby suggesting redundancy in functional potential throughout the system. Null modeling revealed that microbial community assembly patterns were predominantly governed by variable selection. The relative influence of variable selection decreased with depth, indicating unique and relatively harsh environmental conditions near the surface and more benign conditions with depth. Additionally, community composition near the center of the domain was influenced by high levels of dispersal, suggesting that spatial processes interact with deterministic selection imposed by the environment. These results suggest that for oligotrophic systems, there are major differences in the length scales of variation between vertical and horizontal dimensions with the vertical dimension dominating variation in physical, chemical, and biological features.
AB - Microbial dynamics drive the biotic machinery of early soil evolution. However, integrated knowledge of microbial community establishment, functional associations, and community assembly processes in incipient soil is lacking. This study presents a novel approach of combining microbial phylogenetic profiling, functional predictions, and community assembly processes to analyze drivers of microbial community establishment in an emerging soil system. Rigorous submeter sampling of a basalt-soil lysimeter after 2 years of irrigation revealed that microbial community colonization patterns and associated soil parameters were depth dependent. Phylogenetic analysis of 16S rRNA gene sequences indicated the presence of diverse bacterial and archaeal phyla, with high relative abundance of Actinomyceles on the surface and a consistently high abundance of Proteobacteria (Alpha, Beta, Gamma, and Delta) at all depths. Despite depth-dependent variation in community diversity, predicted functional gene analysis suggested that microbial metabolisms did not differ with depth, thereby suggesting redundancy in functional potential throughout the system. Null modeling revealed that microbial community assembly patterns were predominantly governed by variable selection. The relative influence of variable selection decreased with depth, indicating unique and relatively harsh environmental conditions near the surface and more benign conditions with depth. Additionally, community composition near the center of the domain was influenced by high levels of dispersal, suggesting that spatial processes interact with deterministic selection imposed by the environment. These results suggest that for oligotrophic systems, there are major differences in the length scales of variation between vertical and horizontal dimensions with the vertical dimension dominating variation in physical, chemical, and biological features.
KW - bacterial/archaeal phylogenetic analysis
KW - incipient soil system
KW - null modeling
KW - scale and dimensions of variation
KW - terrestrial basalt
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U2 - 10.1029/2017JG004315
DO - 10.1029/2017JG004315
M3 - Article
AN - SCOPUS:85064512451
VL - 124
SP - 941
EP - 958
JO - Journal of Geophysical Research: Atmospheres
JF - Journal of Geophysical Research: Atmospheres
SN - 2169-897X
IS - 4
ER -