Alaskan palaeosols in modern times: Deciphering unique microbial diversity within the late-Holocene

Abstract

The Holocene Epoch (11,700 years ago to the present) marks the development of the present-day boreal ecosystems in interior Alaska. The composition and genetics of soil microbes have the potential to alter how nutrient cycling and vegetation respond to warming and cooling events, but very little is known about how boreal soils have varied over time. Here, we use DNA sequencing on both modern soils and well-preserved paleosols developed during several episodes of the Holocene to extract information on soil bacteria, archaea, and fungi present in interior Alaska during the past 8000 years (8 ka). Community composition of bacteria and fungi in the ancient paleosols was different from modern soils, with a higher relative abundance of Proteobacteria, Chloroflexi, and Verrucomicrobia in the modern soils. The most dramatic shift in interior Alaska’s soil microbiome occurred ca. 7 ka, when species diversity was lowered and functional diversity became higher after 7 ka. This suggests that function was truly low, the early Holocene ecosystems were functionally redundant, and/or that true functional diversity was not captured due to a lack of genetic resolution in existing sequence databases. The cause of this observed shift cannot be directly answered in this work; however, these data suggest that ca. 7 ka was a critical period when microbial taxa and function shifted dramatically. This is important for understanding how the soil microbiome responds to climate changes and impacts the succession of vegetation.

Millennial-Scale Microbiome Analysis Reveals Ancient Antimicrobial Resistance Conserved Despite Modern Selection Pressures

“…The projects in which the antiquity of the sample was not clearly established were also ignored. As a result, the nal number of projects was narrowed down to a total of ten, namely PRJEB47746 [4], PRJNA266334 [5], PRJNA343018 [6], PRJNA350710 [7], PRJNA505516 [8], PRJNA596250 [9], PRJNA601698 [10], PRJNA680161 [11], PRJNA438924 [12], and PRJDB5557 [13]. The age of the samples in these projects ranged from 7000 years ago to 1100 kilo years ago (Supplementary Table S1).…”

Profiling Antibiotic Resistance Determinants in Ancient Permafrost Microbiomes

“…The projects in which the antiquity of the sample was not clearly established were also ignored. As a result, the final number of projects was narrowed down to a total of ten, namely PRJEB47746 [4], PRJNA266334 [5], PRJNA343018 [6], PRJNA350710 [7], PRJNA505516 [8], PRJNA596250 [9], PRJNA601698 [10], PRJNA680161 [11], PRJNA438924 [12], and PRJDB5557 [13]. The age of the samples in these projects ranged from 7000 years ago to 1100 kilo years ago (Supplementary Table S1).…”