Examination of Soil Microbial Communities After Permafrost Thaw Subsequent to an Active Layer Detachment in the High Arctic

Inglese, Cara; Christiansen, Casper T.; Lamhonwah, Daniel; Moniz, Kristy; Montross, Scott; Lamoureux, Scott F.; Lafrenière, Melissa J.; Grogan, Paul; Walker, Virginia K.

doi:10.1657/aaar0016-066

Cited by 17 publications

(17 citation statements)

References 45 publications

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“…The continuity between soils and sediments in geochemistry and microbial communities in the present study and others (10) suggests that microbiomes respond very slowly to submergence. Furthermore, local edaphic factors, rather than global factors, have been identified as the main direct shaping force of arctic microbiomes (40); local edaphic factors include components such as pH, moisture, carbon, nitrogen, phosphorus, and trace elements (17, 34, 45, 46). pH and NO 2 − -N were the two major structuring factors identified by the network analysis.…”

Section: Discussionmentioning

confidence: 99%

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Geochemical-Compositional-Functional Changes in Arctic Soil Microbiomes Post Land Submergence Revealed by Metagenomics

Wang

Guo

et al. 2019

Microb. Environ.

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Lakes of meltwater in the Artic have become one of the transforming landscape changes under global warming. We herein compared microbial communities between sediments and bank soils at an arctic lake post land submergence using geochemistry, 16S rRNA amplicons, and metagenomes. The results obtained showed that each sample had approximately 2,609 OTUs on average and shared 1,716 OTUs based on the 16S rRNA gene V3–V4 region. Dominant phyla in sediments and soils included Proteobacteria , Acidobacteria , Actinobacteria , Gemmatimonadetes , and Nitrospirae ; sediments contained a unique phylum, Euryarchaeota , with the phylum Thaumarchaeota being primarily present in bank soils. Among the top 35 genera across all sites, 17 were more abundant in sediments, while the remaining 18 were more abundant in bank soils; seven out of the top ten genera across all sites were only from sediments. A redundancy analysis separated sediment samples from soil samples based on the components of nitrite and ammonium. Metagenome results supported the role of nitrite because most of the genes for denitrification and methane metabolic genes were more abundant in sediments than in soils, while the abundance of phosphorus-utilizing genes was similar and, thus, was not a significant explanatory factor. We identified several modules from the global networks of OTUs that were closely related to some geochemical factors, such as pH and nitrite. Collectively, the present results showing consistent changes in geochemistry, microbiome compositions, and functional genes suggest an ecological mechanism across molecular and community levels that structures microbiomes post land submergence.

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Section: Discussionmentioning

confidence: 99%

“…Furthermore, soil microbiomes appear to be associated with an array of environmental factors. Significant geochemical factors affecting microbiome assembly include organic carbon, moisture, pH, phosphorus (17, 34, 45), redox potential and oxidative stress (25, 28), nanoparticles (21), and temperature (5).…”

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confidence: 99%

Geochemical-Compositional-Functional Changes in Arctic Soil Microbiomes Post Land Submergence Revealed by Metagenomics

Wang

Guo

et al. 2019

Microb. Environ.

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“…Over the past decade, several studies (i.e., [1,3,[21][22][23][24][25][26][27][28][29]) have addressed microbial communities along a soil column that includes both seasonally thawed and permanently frozen horizons; see [30] for a review. However, these studies dealt with samples that contained a relatively small amount of organic carbon (<5-10% of C org ) and therefore characterized the bacterial activity and diversity in the mineral rather than the organic frozen layer.…”

Section: Introductionmentioning

confidence: 99%

Bacterial Number and Genetic Diversity in a Permafrost Peatland (Western Siberia): Testing a Link with Organic Matter Quality and Elementary Composition of a Peat Soil Profile

et al. 2021

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Permafrost peatlands, containing a sizable amount of soil organic carbon (OC), play a pivotal role in soil (peat) OC transformation into soluble and volatile forms and greatly contribute to overall natural CO2 and CH4 emissions to the atmosphere under ongoing permafrost thaw and soil OC degradation. Peat microorganisms are largely responsible for the processing of this OC, yet coupled studies of chemical and bacterial parameters in permafrost peatlands are rather limited and geographically biased. Towards testing the possible impact of peat and peat pore water chemical composition on microbial population and diversity, here we present results of a preliminary study of the western Siberia permafrost peatland discontinuous permafrost zone. The quantitative evaluation of microorganisms and determination of microbial diversity along a 100 cm thick peat soil column, which included thawed and frozen peat and bottom mineral horizon, was performed by RT-PCR and 16S rRNA gene-based metagenomic analysis, respectively. Bacteria (mainly Proteobacteria, Acidobacteria, Actinobacteria) strongly dominated the microbial diversity (99% sequences), with a negligible proportion of archaea (0.3–0.5%). There was a systematic evolution of main taxa according to depth, with a maximum of 65% (Acidobacteria) encountered in the active layer, or permafrost boundary (50–60 cm). We also measured C, N, nutrients and ~50 major and trace elements in peat (19 samples) as well as its pore water and dispersed ice (10 samples), sampled over the same core, and we analyzed organic matter quality in six organic and one mineral horizon of this core. Using multiparametric statistics (PCA), we tested the links between the total microbial number and 16S rRNA diversity and chemical composition of both the solid and fluid phase harboring the microorganisms. Under climate warming and permafrost thaw, one can expect a downward movement of the layer of maximal genetic diversity following the active layer thickening. Given a one to two orders of magnitude higher microbial number in the upper (thawed) layers compared to bottom (frozen) layers, an additional 50 cm of peat thawing in western Siberia may sizably increase the total microbial population and biodiversity of active cells.

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“…Much of the boreal forests across Alaska are underlain by discontinuous permafrost that is not immune to the pressures of climate change. Permafrost thaw is associated with direct and indirect changes in plant communities due to significant shifts in soil hydrology which in turn affect nutrient availability and carbon dynamics ( Schuur et al, 2007 ; Yang et al, 2013 ; Inglese et al, 2017 ; Sewell et al, 2020 ), yet only few studies have explored the biotic mechanism contributing to changes in plant community with thaw ( Hewitt et al, 2016 ; Schütte et al, 2019 ; Seitz et al, 2021 ).…”

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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Examination of Soil Microbial Communities After Permafrost Thaw Subsequent to an Active Layer Detachment in the High Arctic

Cited by 17 publications

References 45 publications

Geochemical-Compositional-Functional Changes in Arctic Soil Microbiomes Post Land Submergence Revealed by Metagenomics

Geochemical-Compositional-Functional Changes in Arctic Soil Microbiomes Post Land Submergence Revealed by Metagenomics

Bacterial Number and Genetic Diversity in a Permafrost Peatland (Western Siberia): Testing a Link with Organic Matter Quality and Elementary Composition of a Peat Soil Profile

Unearthing Shifts in Microbial Communities Across a Soil Disturbance Gradient

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