Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in <scp>A</scp>laska

Deng, Jie; Gu, Yunfu; Zhang, Jin; Xue, Kai; Qin, Yujia; Yuan, Mengting; Yin, Huaqun; He, Zhili; Wu, Liyou; Schuur, Edward A. G.; Tiedje, James M.; Zhou, Jizhong

doi:10.1111/mec.13015

Cited by 114 publications

(129 citation statements)

References 61 publications

(105 reference statements)

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“…Raw sequences were divided into sample libraries using the unique barcodes and shorted by removing the primer and barcode sequence. Forward and reverse reads with at least 10‐bp overlaps and less than 4‐bp mismatches were merged using FLASH (Deng et al, ). QIIME (Version 1.7.0, http://qiime.org/index.html) was used to perform the quality filtering of the raw tags.…”

Section: Methodsmentioning

confidence: 99%

Grass and maize vegetation systems restore saline‐sodic soils in the Songnen Plain of northeast China

et al. 2018

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Establishment of an appropriate vegetation system for reclamation of saline‐sodic soils requires studies for specific salt‐affected region(s). The phytoremediation of saline‐sodic soils has not been well documented in the Songnen Plain of northeast China. Thus, in this study, we aimed to investigate the effects of grass (G) and maize (Zea mays L.; M) vegetation systems, which were established for 5 years, on soil properties of 10 typical saline‐sodic sampling sites across the Songnen Plain, in comparison with respective nonvegetated areas that were used as controls (CK) for the evaluation of variability among the sampling sites. Physicochemical properties, such as soil moisture, bulk density, porosity, saturated hydraulic conductivity, aggregate stability, pH, electric conductivity, total salt, organic C, total N, and C/N ratio, were analyzed. G and M vegetation significantly produced a 108% and 153% improvement in soil quality, respectively. Additionally, metagenomic analysis of the soil bacterial community revealed that vegetation enhanced the ability of the bacteria to survive in saline‐sodic soils, relative to the control. The composition of the bacterial community was highly correlated with all of the soil physicochemical properties. G vegetation had better effects than M vegetation in enhancing soil organic C, total N and aggregate stability, whereas M vegetation more favorably adjusted soil pH, physical structure, and bacterial community than G vegetation did. Collectively, these findings demonstrate that M vegetation has a greater impact than G vegetation on repairing saline‐sodic soils in the Songnen Plain of northeast China.

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Section: Methodsmentioning

confidence: 99%

Grass and maize vegetation systems restore saline‐sodic soils in the Songnen Plain of northeast China

et al. 2018

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“…Changes in soil microbial function could mediate effects of permafrost thaw on plant communities. Thaw impacts soil microbial community structure (Blazewicz, Petersen, Waldrop, & Firestone, ; Deng et al, ; Hultman et al, ; Tas et al, ), decomposition (Hicks Pries, Schuur, Vogel, & Natali, ) and activity (Coolen & Orsi, ; Mackelprang et al, ; McCalley et al, ; Neumann, Blazewicz, Conaway, Turetsky, & Waldrop, ). Mackelprang et al () found that permafrost thaw leads to rapid shifts in many microbial, phylogenetic and functional gene abundances and pathways.…”

Section: Introductionmentioning

confidence: 99%

Effect of permafrost thaw on plant and soil fungal community in a boreal forest: Does fungal community change mediate plant productivity response?

Schütte

Henning

et al. 2019

Journal of Ecology

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Permafrost thaw is leading to rapid shifts in boreal ecosystem function. Permafrost thaw affects soil carbon turnover through changes in soil hydrology; however, the biotic mechanisms regulating plant community response remain elusive. Here, we measured the response of fungal community composition and soil nutrient content in an intact permafrost plateau forest soil and an adjacent thermokarst bog and evaluated their potential to mediate shifts in plant composition. We used barcoded amplicon targeting ITS2 and 28S rRNA genes to determine fungal community composition. Next, we used the soils from the permafrost plateau and the thermokarst bog as soil inoculum in a greenhouse experiment to measure whether shifts in fungal community and soil water level regulate plant productivity and composition. Overall, we found that fungal community composition differed significantly between the thawed and intact permafrost sites, but soil nutrient content did not. Relative abundance of mycorrhizal fungal taxa decreased while relative abundance of putative fungal pathogens increased with permafrost thaw. In the greenhouse, we found that ecto‐ and arbuscular‐associated host plants had higher productivity in permafrost‐intact soils relative to thawed soils. However, productivity of non‐mycorrhizal tussock grass was more affected by soil water levels than soil communities. Synthesis. Our results suggest that fungal communities are crucial in mediating plant community response to permafrost thaws inducing hydrology changes.

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“…Within cold regions, both soils and permafrost niches appear to be dominated by bacterial (mainly Proteobacterial, Actinobacterial and Acidobacterial), archaeal (mostly Euryarchaeota) and fungal (dominated by Ascomycota) lineages [7,23,24,25 ] (Table 1). While these studies have provided a comprehensive, and reasonably consistent, survey of microbial diversity at the specific sites sampled, few of these studies have any temporal component; that is, they are single time-point analyses which provide, at best, a baseline for future assessments of the effects of environmental change.…”

Section: Microbial Diversity In Cold Environmentsmentioning

confidence: 99%

Microbial diversity and functional capacity in polar soils

Makhalanyane

Goethem

Cowan

2016

Current Opinion in Biotechnology

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Global change is disproportionately affecting cold environments (polar and high elevation regions), with potentially negative impacts on microbial diversity and functional processes. In most cold environments the combination of low temperatures, and physical stressors, such as katabatic wind episodes and limited water availability result in biotic systems, which are in trophic terms very simple and primarily driven by microbial communities. Metagenomic approaches have provided key insights on microbial communities in these systems and how they may adapt to stressors and contribute towards mediating crucial biogeochemical cycles. Here we review, the current knowledge regarding edaphic-based microbial diversity and functional processes in Antarctica, and the Artic. Such insights are crucial and help to establish a baseline for understanding the impact of climate change on Polar Regions. AddressCentre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria 0028, South Africa Corresponding author: Cowan, Don Arthur (don.cowan@up.ac.za) IntroductionThe Congress of Parties (COP) 21 meeting in Paris (November 2015) highlighted the urgency of global climate change, and the critical need to reduce global average temperatures through curbing greenhouse gas emissions [1]. Nowhere are the effects of global change more apparent than in cold environments (polar and alpine regions), which are subject to accelerated rates of warming compared to other ecosystems [2 ,3]. Climatic models have predicted that temperatures in high latitude regions of the Northern Hemisphere are likely to increase by between 0.38C and 4.88C before the end of the twenty first century [4]. There is also evidence that regions in the Southern Hemisphere have experienced the fastest warming globally, with average increases of as much as 2.48C in the last fifty years [5].A major consequence of climate change in cold environments is the thawing of submerged and surface ice, which alters the hydrology of the systems and may have adverse effects on microbial processes [6 ]. In cold environments, microorganisms (bacteria, archaea and fungi) are major constituents of the total biomass, and are estimated to mediate the cycling of key biogeochemical elements such as nitrogen and carbon, with potentially important implications for the productivity of these systems [7]. Although the precise contribution of microbial processes to global change processes are not well known, there are efforts to incorporate biological processes into Earth systems models with the realization that they may be crucial in regulating soil organic matter (SOM) [8 ]. For instance, permafrost (defined as ground which remains frozen for at least two years) in cold environments stores roughly 1600 Pg of carbon, which if released would significantly contribute towards increasing global CO 2 levels [9]. The current contribution of microbial communities to constraining carbon losses in permafrost and the influence on CO 2 levels remains virtually unknown. In ...

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Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska

Cited by 114 publications

References 61 publications

Grass and maize vegetation systems restore saline‐sodic soils in the Songnen Plain of northeast China

Grass and maize vegetation systems restore saline‐sodic soils in the Songnen Plain of northeast China

Effect of permafrost thaw on plant and soil fungal community in a boreal forest: Does fungal community change mediate plant productivity response?

Microbial diversity and functional capacity in polar soils

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