The Background: Microorganisms in permafrost regions
Permafrost, ground frozen for at least two consecutive years, hosts diverse microbial communities despite harsh conditions. The microbial communities in permafrost environments are capable of orchestrating a wide array of biogeochemical processes. These include, but are not limited to, the degradation of soil organic matter, carbon fixation, methanogenesis, methanotrophy, and various aspects of nitrogen cycling. As global temperatures rise, permafrost thawing accelerates microbial activity, potentially increasing greenhouse gas emissions. This process could trigger both carbon-climate and non-carbon-climate feedbacks, exacerbating global climate warming. Understanding microbial community structure and functions in permafrost regions is thus vital for predicting biogeochemical responses to climate change and their feedbacks to climate warming. However, by conducting a comprehensive literature review, we find that most preceding investigations concerning permafrost microorganisms have been predominantly constrained to site-specific level and high-latitude permafrost region, the large-scale evidence of stratigraphic profiles of microbial communities and their functional potentials in high-altitude permafrost regions remains limited. That’s why we conduct this study based on the combination of regional-scale field sampling and high throughput sequencing to explore the microbial communities in alpine permafrost regions.
The Expedition: Large-scale sampling on the “Roof of the World”
The Tibetan Plateau, often referred to as the “Roof of the World”, is renowned for its severe climate and high altitude. The permafrost in this region extends across roughly 1.1 million square kilometers, encompassing 40% of the plateau. This vast frozen expanse creates an extreme environment where only the most resilient life forms can thrive. The plateau provides a great opportunity to explore the basic characteristics of microbial community in alpine permafrost regions. Our research team, led by Prof. Yuanhe Yang, at the Institute of Botany, Chinese Academy of Sciences (IBCAS), was driven by a profound curiosity to understand how microbial life has adapted to such inhospitable conditions and what this could mean for biogeochemical cycles in this unique alpine permafrost region. To unveil this issue, the IBCAS Sampling Team (Drs. Dan Kou, Yongliang Chen, and Chao Mao, the former members of Prof. Yuanhe Yang’s group) established 22 sampling sites along an ~1,000 km permafrost transect on the Tibetan Plateau during July and August in 2016. At each site, soil cores were extracted within five 1 m × 1 m quadrats along the diagonal lines of a 10 m × 10 m plot using a borehole drill. Soil samples were collected at depths of 0–10 cm and 30–50 cm, which represented the active layer. Simultaneously, permafrost samples were collected from the uppermost 50 cm permafrost thick layer. We homogenized soil samples from individual layers at each site using sterile hammering under low-temperature conditions. In this study, we analyzed the microbial community structure and functional potential of these soil samples using 16S rRNA amplicon and metagenomic sequencing technologies. After that, Luyao Kang (the first author) and Yutong Song (the second author) established a workflow for bioinformatics analysis, with additional support from Prof. Ye Deng at the Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences. To uncover the underlying drivers of microbial assemblage, we also assessed soil physicochemical properties alongside climatic, anthropogenic, and plant-related factors. Based on these measurements, we aimed to explore the large-scale stratigraphic profiles of the microbial community structure and functional potential across permafrost regions.
Executing this research demanded resilience in the face of numerous challenges. First, our field sampling expeditions pushed us to the limits, braving the harsh realities of high-altitude environments: biting cold, thin air, and treacherous terrain. The journey itself was an ordeal, with remote locations testing our logistical prowess. Second, back in the laboratory, we embarked on a steep learning curve. From acquiring and configuring computer servers to mastering cutting-edge genomic techniques and developing custom code, we built our analytical capabilities from the ground up. Simultaneously, we delved deep into microbial ecology, honing our theoretical knowledge to develop robust hypotheses. Overall, this multifaceted approach—combining physical endurance, technological innovation, and scientific insight—formed the bedrock of our study, allowing us to unlock the microbial secrets hidden in the permafrost regions.
Field sampling and laboratory measurements (credit: Chao Mao and Ziliang Li).
The Bigger Picture: Stratigraphic profiles of microbial community structure and functional potentials
Our study revealed clear vertical patterns in microbial diversity and function across permafrost soil profiles. Alpha diversity decreased with soil depth, while beta diversity increased, indicating more specialized communities in deeper layers. Thermoleophilia, a class of Actinobacteria, was notably prevalent in the deepest permafrost. Microbial community structure was primarily shaped by dispersal limitation and drift, with their relative importance varying along soil depth. Specifically, drift (and others) emerged as the primary driver of microbial assemblages in surface soils. Within the permafrost deposits, dispersal limitation took center stage, becoming the dominant force in structuring microbial communities.
Functional potential also shifted with soil depth, with deeper layers being enriched in genes associated with reduction processes, including dissimilatory nitrate reduction, denitrification, and several forms of anaerobic respiration. This pattern likely reflected the lower redox potential and more intricate trophic strategies employed by microorganisms in these environments. Moreover, the dominant microbial players changed across soil depths. Surface soils were characterized by α-Proteobacteria and Actinobacteria, while deeper layers showed a more diverse functional composition including Desulfobacterota, γ-Proteobacteria, Chloroflexota, Acidobacteriota, and Methylomirabilota. This vertical stratification highlights the complex microbial adaptations to varying environmental conditions across soil depths in permafrost regions.
Stratigraphic profiles of microbial communities and their functional potentials in alpine permafrost regions.
Overall, our study emphasizes the need to incorporate vertical microbial variations into future biogeochemical models. As climate warming accelerates permafrost thawing, our understanding about the response of microbial communities becomes crucial. This insight will enhance our ability to predict and manage the impacts of climate warming on these critical ecosystems, bridging the gap between microscopic processes and global environmental changes.