Permafrost Microbial Community Structure Changes Across the Pleistocene-Holocene Boundary

Saidi‐Mehrabad, Alireza; Neuberger, Patrick; Hajihosseini, Morteza; Froese, Duane G.; Lanoil, Brian

doi:10.3389/fenvs.2020.00133

Cited by 12 publications

(16 citation statements)

References 69 publications

(104 reference statements)

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“…cellulose, xylan, and pectin; Tóth and Borsodi, 2014). Deinococcus-Thermus was detected in the older paleosols tested and has also been found in Holoceneaged samples collected in the central Yukon (Saidi-Mehrabad et al, 2020). Additionally, Pseudonocardiaceae, capable of degrading lignocellulose and chitin (Yeager et al, 2017), was detected in all of the paleosols tested, possibly indicating the presence of complex carbon in the ancient soils.…”

Section: Major Microbial Groups Found Throughout the Holocenementioning

confidence: 77%

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

et al. 2022

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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.

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Section: Major Microbial Groups Found Throughout the Holocenementioning

confidence: 77%

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

et al. 2022

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“…The permafrost origin is additionally important in driving the community structure, since significant differences in community composition were reported from late Pleistocene lacustrine-alluvial and Ice Complex (Yedoma) sediments (Rivkina et al, 2016). Recently, the transition from Pleistocene to Holocene was shown to initiate a major threshold-type shift in the composition and structure of permafrost microbial community in Central Yukon (Saidi-Mehrabad et al, 2020). These results draw particular attention to the potential effect of climate change on microbial activity and trace gas production.…”

Section: Introductionmentioning

confidence: 94%

“…The studied samples from ice wedges of the Mamontova Gora exposure demonstrate significant differences in the community composition of the lower and upper Ice Complex horizons, further confirming that these are different generations of ice wedges with different origin (Figures 10,11). We assume that the observed differences are related more to the genesis than the differential preservation of DNA since the microbial community structure within an epoch is relatively stable over time (Shade et al, 2013), while once the system surpasses a threshold, microbial parameters rapidly shift to a new stable state (Saidi-Mehrabad et al, 2020).…”

Section: Ice Complexes: Ice Wedgesmentioning

confidence: 99%

“…The microbial community structure in permafrost soils is supposed to be relatively stable over time (Shade et al, 2013), but rapidly shift to a new stable state under changing conditions, experiencing threshold behavior (Saidi-Mehrabad et al, 2020). Ground freezing and permafrost development are natural thresholds, but they can occur either simultaneously with sediment accumulation, or significantly later.…”

Section: Introductionmentioning

confidence: 99%

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Microbial and Geochemical Evidence of Permafrost Formation at Mamontova Gora and Syrdakh, Central Yakutia

et al. 2021

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Biotracers marking the geologic history and permafrost evolution in Central Yakutia, including Yedoma Ice Complex (IC) deposits, were identified in a multiproxy analysis of water chemistry, isotopic signatures, and microbial datasets. The key study sections were the Mamontova Gora and Syrdakh exposures, well covered in the literature. In the Mamontova Gora section, two distinct IC strata with massive ice wedges were described and sampled, the upper and lower IC strata, while previously published studies focused only on the lower IC horizon. Our results suggest that these two IC horizons differ in water origin of wedge ice and in their cryogenic evolution, evidenced by the differences in their chemistry, water isotopic signatures and the microbial community compositions. Microbial community similarity between ground ice and host deposits is shown to be a proxy for syngenetic deposition and freezing. High community similarity indicates syngenetic formation of ice wedges and host deposits of the lower IC horizon at the Mamontova Gora exposure. The upper IC horizon in this exposure has much lower similarity metrics between ice wedge and host sediments, and we suggest epigenetic ice wedge development in this stratum. We found a certain correspondence between the water origin and the degree of evaporative transformation in ice wedges and the microbial community composition, notably, the presence of Chloroflexia bacteria, represented by Gitt-GS-136 and KD4-96 classes. These bacteria are absent at the ice wedges of lower IC stratum at Mamontova Gora originating from snowmelt, but are abundant in the Syrdakh ice wedges, where the meltwater underwent evaporative isotopical fractionation. Minor evaporative transformation of water in the upper IC horizon of Mamontova Gora, whose ice wedges formed by meltwater that was additionally fractionated corresponds with moderate abundance of these classes in its bacterial community.

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“…Permafrost thaw leads to rapid changes in microbial community composition and function, including shifts in several metabolites and genes involving nitrogen and carbon cycling in response to permafrost thaw, and during a thaw event, community function within permafrost quickly converges to that of the active layer ( Mackelprang et al, 2011 ; Coolen and Orsi, 2015 ; Monteux et al, 2018 ; Johnston et al, 2019 ; Messan et al, 2020 ; Saidi-Mehrabad et al, 2020 ). Consistent with the pattern of permafrost thaw affecting soil microbial communities, Inglese et al (2017) found that active layer detachments, a form of permafrost disturbance, significantly affect fungal and Archaeal community composition of the active layer.…”

Section: Introductionmentioning

confidence: 99%

Unearthing Shifts in Microbial Communities Across a Soil Disturbance Gradient

2022

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Permafrost, an important source of soil disturbance, is particularly vulnerable to climate change in Alaska where 85% of the land is underlained with discontinuous permafrost. Boreal forests, home to plants integral to subsistence diets of many Alaska Native communities, are not immune to the effects of climate change. Soil disturbance events, such as permafrost thaw, wildfires, and land use change can influence abiotic conditions, which can then affect active layer soil microbial communities. In a previous study, we found negative effects on boreal plants inoculated with microbes impacted by soil disturbance compared to plants inoculated with microbes from undisturbed soils. Here, we identify key shifts in microbial communities altered by soil disturbance using 16S rRNA gene sequencing and make connections between microbial community changes and previously observed plant growth. Additionally, we identify further community shifts in potential functional mechanisms using long read metagenomics. Across a soil disturbance gradient, microbial communities differ significantly based on the level of soil disturbance. Consistent with the earlier study, the family Acidobacteriaceae, which consists of known plant growth promoters, was abundant in undisturbed soil, but practically absent in most disturbed soil. In contrast, Comamonadaceae, a family with known agricultural pathogens, was overrepresented in most disturbed soil communities compared to undisturbed. Within our metagenomic data, we found that soil disturbance level is associated with differences in microbial community function, including mechanisms potentially involved in plant pathogenicity. These results indicate that a decrease in plant growth can be linked to changes in the microbial community and functional composition driven by soil disturbance and climate change. Together, these results build a genomic understanding of how shifting soil microbiomes may affect plant productivity and ecosystem health as the Arctic warms.

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Permafrost Microbial Community Structure Changes Across the Pleistocene-Holocene Boundary

Cited by 12 publications

References 69 publications

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

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

Microbial and Geochemical Evidence of Permafrost Formation at Mamontova Gora and Syrdakh, Central Yakutia

Unearthing Shifts in Microbial Communities Across a Soil Disturbance Gradient

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