Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale

Microbiome

Paula B. Matheus Carnevali¹  Shufei Lei¹  Spencer Diamond¹  Adi Lavy¹  Allison Sharrar¹  Jillian F. Banfield²  Raphaël Méheust³  Alex D. Thomas⁴  Alexander Crits-Christoph⁵  Matthew R. Olm⁶  Susan Hubbard⁷  Nicola Falco⁷  Wenming Dong⁷  Peter Nico⁷  Nicholas Bouskill⁷  Dipankar Dwivedi⁷  Kenneth H. Williams⁷  Michelle E. Newcomer⁷  Haruko Wainwright⁷ 

[1] Department of Earth and Planetary Science, University of California, Berkeley, USA;Department of Earth and Planetary Science, University of California, Berkeley, USA;Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA;Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA;Innovative Genomics Institute, Berkley, CA, USA;Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA;Chan Zuckerberg Biohub, San Francisco, CA, USA;Department of Earth and Planetary Science, University of California, Berkeley, USA;Innovative Genomics Institute, Berkley, CA, USA;Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA;Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA;Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA;Current affiliation: Department of Microbiology and Immunology, Stanford University, Palo Alto, CA, USA;Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA;

关键词: Microbiome;    Floodplain;    Soil;    Watershed;    Genome-resolved metagenomics;    Metatranscriptomics;   

DOI  :  10.1186/s40168-020-00957-z

来源: Springer

【 摘 要 】

BackgroundBiogeochemical exports from watersheds are modulated by the activity of microorganisms that function over micron scales. Here, we tested the hypothesis that meander-bound regions share a core microbiome and exhibit patterns of metabolic potential that broadly predict biogeochemical processes in floodplain soils along a river corridor.ResultsWe intensively sampled the microbiomes of floodplain soils located in the upper, middle, and lower reaches of the East River, Colorado. Despite the very high microbial diversity and complexity of the soils, we reconstructed 248 quality draft genomes representative of subspecies. Approximately one third of these bacterial subspecies was detected across all three locations at similar abundance levels, and ~ 15% of species were detected in two consecutive years. Within the meander-bound floodplains, we did not detect systematic patterns of gene abundance based on sampling position relative to the river. However, across meanders, we identified a core floodplain microbiome that is enriched in capacities for aerobic respiration, aerobic CO oxidation, and thiosulfate oxidation with the formation of elemental sulfur. Given this, we conducted a transcriptomic analysis of the middle floodplain. In contrast to predictions made based on the prominence of gene inventories, the most highly transcribed genes were relatively rare amoCAB and nxrAB (for nitrification) genes, followed by genes involved in methanol and formate oxidation, and nitrogen and CO2 fixation. Within all three meanders, low soil organic carbon correlated with high activity of genes involved in methanol, formate, sulfide, hydrogen, and ammonia oxidation, nitrite oxidoreduction, and nitrate and nitrite reduction. Overall, the results emphasize the importance of sulfur, one-carbon and nitrogen compound metabolism in soils of the riparian corridor.ConclusionsThe disparity between the scale of a microbial cell and the scale of a watershed currently limits the development of genomically informed predictive models describing watershed biogeochemical function. Meander-bound floodplains appear to serve as scaling motifs that predict aggregate capacities for biogeochemical transformations, providing a foundation for incorporating riparian soil microbiomes in watershed models. Widely represented genetic capacities did not predict in situ activity at one time point, but rather they define a reservoir of biogeochemical potential available as conditions change.8muhHv3_-7zzU2wL3D8t9_Video abstract

【 授权许可】

CC BY