The Transition From Stochastic to Deterministic Bacterial Community Assembly During Permafrost Thaw Succession

Doherty, Stacey J.; Barbato, Robyn A.; Grandy, A. Stuart; Thomas, W. Kelley; Monteux, Sylvain; Dorrepaal, Ellen; Johansson, Margareta; Ernakovich, Jessica G.

doi:10.3389/fmicb.2020.596589

Cited by 43 publications

(39 citation statements)

References 65 publications

(102 reference statements)

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“…Specifically, the consistent rates of microbial respiration before and after rainfall (Figure 6A) did not reflect the increase we observed in aerobic microbial gene expression in the tussock tundra community following rainfall (Figure 4). This result is not unexpected because previous studies have also been unable to directly link microbial dynamics and carbon emissions [119], likely because respiration is the product of many processes in microbial communities. Here, the artificial conditions of the respiration rate incubations (i.e., N 2 gas for anoxic conditions, compressed air for oxic conditions) were intended to replicate field conditions, similar to previous incubation studies [38], but it is possible that other conditions in these incubations such as total O 2 availability and soil moisture differed from conditions in the soil mesocosms where microbial gene expression was sampled.…”

Section: Relating Microbial Expression To Rates Of Respiration and Ch 4 Productionmentioning

confidence: 64%

Rainfall Alters Permafrost Soil Redox Conditions, but Meta-Omics Show Divergent Microbial Community Responses by Tundra Type in the Arctic

2021

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Soil anoxia is common in the annually thawed surface (‘active’) layer of permafrost soils, particularly when soils are saturated, and supports anaerobic microbial metabolism and methane (CH4) production. Rainfall contributes to soil saturation, but can also introduce oxygen, causing soil oxidation and altering anoxic conditions. We simulated a rainfall event in soil mesocosms from two dominant tundra types, tussock tundra and wet sedge tundra, to test the impacts of rainfall-induced soil oxidation on microbial communities and their metabolic capacity for anaerobic CH4 production and aerobic respiration following soil oxidation. In both types, rainfall increased total soil O2 concentration, but in tussock tundra there was a 2.5-fold greater increase in soil O2 compared to wet sedge tundra due to differences in soil drainage. Metagenomic and metatranscriptomic analyses found divergent microbial responses to rainfall between tundra types. Active microbial taxa in the tussock tundra community, including bacteria and fungi, responded to rainfall with a decline in gene expression for anaerobic metabolism and a concurrent increase in gene expression for cellular growth. In contrast, the wet sedge tundra community showed no significant changes in microbial gene expression from anaerobic metabolism, fermentation, or methanogenesis following rainfall, despite an initial increase in soil O2 concentration. These results suggest that rainfall induces soil oxidation and enhances aerobic microbial respiration in tussock tundra communities but may not accumulate or remain in wet sedge tundra soils long enough to induce a community-wide shift from anaerobic metabolism. Thus, rainfall may serve only to maintain saturated soil conditions that promote CH4 production in low-lying wet sedge tundra soils across the Arctic.

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Section: Relating Microbial Expression To Rates Of Respiration and Ch 4 Productionmentioning

confidence: 64%

Rainfall Alters Permafrost Soil Redox Conditions, but Meta-Omics Show Divergent Microbial Community Responses by Tundra Type in the Arctic

2021

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“…Macro events in natural ecosystems, such as wildfire ( 5 ), permafrost thaw ( 42 , 43 ), flood ( 44 ), drought ( 45 ), and soil salinity ( 46 ), have been reported to contribute considerably to the change and secondary succession of microbial communities. As expected, disturbances, including mechanical stirring, grain acidification, and oxygen reduction, in the fermentation stage caused substantial changes in microbial diversity (Fig.…”

Section: Discussionmentioning

confidence: 99%

Deciphering Succession and Assembly Patterns of Microbial Communities in a Two-Stage Solid-State Fermentation System

Shen

Chen³

et al. 2021

Microbiol Spectr

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“…Permafrost is soil that remains continuously frozen for at least two years and underlies about 25% of terrestrial area in the Northern Hemisphere (Doherty et al 2020). It is estimated that permafrost soil contains approximately 1300 Pg of carbon which is equal to half of the global soil organic carbon (Schuur et al 2015;Zhou et al 2020).…”

Section: Introductionmentioning

confidence: 99%

Vertical distribution patterns and drivers of soil bacterial communities across the continuous permafrost region of northeastern China

Ren

2022

Ecol Process

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Background Soil microorganisms in the thawing permafrost play key roles in the maintenance of ecosystem function and regulation of biogeochemical cycles. However, our knowledge of patterns and drivers of permafrost microbial communities is limited in northeastern China. Therefore, we investigated the community structure of soil bacteria in the active, transition and permafrost layers based on 90 soil samples collected from 10 sites across the continuous permafrost region using high-throughput Illumina sequencing. Results Proteobacteria (31.59%), Acidobacteria (18.63%), Bacteroidetes (9.74%), Chloroflexi (7.01%) and Actinobacteria (6.92%) were the predominant phyla of the bacterial community in all soil layers; however, the relative abundances of the dominant bacterial taxa varied with soil depth. The bacterial community alpha-diversity based on the Shannon index and the phylogenetic diversity index both decreased significantly with depth across the transition from active layer to permafrost layer. Nonmetric multidimensional scaling analysis and permutation multivariate analysis of variance revealed that microbial community structures were significantly different among layers. Redundancy analysis and Spearman’s correlation analysis showed that soil properties differed between layers such as soil nutrient content, temperature and moisture mainly drove the differentiation of bacterial communities. Conclusions Our results revealed significant differences in bacterial composition and diversity among soil layers. Our findings suggest that the heterogeneous environmental conditions between the three soil horizons had strong influences on microbial niche differentiation and further explained the variability of soil bacterial community structures. This effort to profile the vertical distribution of bacterial communities may enable better evaluations of changes in microbial dynamics in response to permafrost thaw, which would be beneficial to ecological conservation of permafrost ecosystems.

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The Transition From Stochastic to Deterministic Bacterial Community Assembly During Permafrost Thaw Succession

Cited by 43 publications

References 65 publications

Rainfall Alters Permafrost Soil Redox Conditions, but Meta-Omics Show Divergent Microbial Community Responses by Tundra Type in the Arctic

Rainfall Alters Permafrost Soil Redox Conditions, but Meta-Omics Show Divergent Microbial Community Responses by Tundra Type in the Arctic

Deciphering Succession and Assembly Patterns of Microbial Communities in a Two-Stage Solid-State Fermentation System

Vertical distribution patterns and drivers of soil bacterial communities across the continuous permafrost region of northeastern China

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