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Soil microbes respond to four-year warming and precipitation alteration

Cite this dataset

Qi, Qi et al. (2022). Soil microbes respond to four-year warming and precipitation alteration [Dataset]. Dryad.


The alpine grasslands of the Tibetan Plateau store 23.2 Pg soil organic carbon (SOC), which becomes susceptible to microbial degradation with climate warming. However, accurate prediction of how the soil carbon (C) stock changes under future climate warming is hampered by our limited understanding of below-ground complex microbial communities. Here, we show that 4 years of warming strongly stimulated methane (CH4) uptake by 93.8% and aerobic respiration (CO2) by % in the soils of alpine grassland ecosystem. Due to no significant effects of warming on net ecosystem CO2 exchange (NEE), the warming-stimulated CH4 uptake enlarged the carbon sink capacity of whole ecosystem. Furthermore, precipitation alternation didn’t alter such warming effects, despite the significant effects of precipitation on NEE and soil CH4 fluxes were observed. Metagenomic sequencing revealed that warming led to significant shifts in the overall microbial community structure and the abundances of functional genes, which contrasted to no detectable changes after 2 years of warming. Carbohydrate utilization genes were significantly increased by warming, corresponding with significant increases in soil aerobic respiration. Increased methanotrophic genes and decreased methanogenic genes were observed under warming, which significantly (R2 = 0.59, P < 0.001) correlated with warming-enhanced CH4 uptakes. Furthermore, 212 metagenome-assembled genomes (MAGs) were recovered, including many populations involved in the degradation of various organic matter and a highly-abundant methylotrophic population of the Methyloceanibacter genus. Collectively, our results provide compelling evidence that specific microbial functional traits for CH4 and CO2 cycling processes respond to climate warming with differential effects on soil greenhouse gas emissions. Alpine grasslands may play huge roles in mitigating climate warming through such microbially-enhanced CH4 uptake.


Soil temperature and moisture were automatically monitored by 5-TM probe sensors at the soil depth of 5 cm with an EM-to data logger (Meter, Inc., Pullman, WA, USA) in each plot. 

Soil aerobic respiration (soil CO2 flux) was automatically measured once an hour by the LI-8150 Multiplexer composed of LI -8100-104 long-term chambers (Li-Cor Inc., Lincoln, NE, USA) and a LI-8100 Automated soil CO2 flux system (Wang et al., 2014). As for soil CH4 fluxes, gas samples were collected from all plots twice or three times per month between 9:00 a.m. and 12:00 p.m. on sunny days (Qi et al., 2021). Specifically, a stainless steel collar was inserted 10 cm into the soil in each plot and a static opaque chamber (40 cm in length ´ 40 cm in width ´ 40 cm in height) was used to collect gas samples from soil at this site (Yuan et al., 2021). At each measurement, 60 mL gas sample was collected in each plot and analyzed within 24 hours using gas chromatography (Agilent 7890A; Agilent Technologies, Santa Clara, CA, USA) to present a one-day average flux.

Similar with soil CH4 fluxes, ecosystem C fluxes were also measured twice or three times per month between 9:00 a.m. and 12:00 p.m. on sunny days (Qi et al., 2021). We used a LI-6400 infrared gas analyzer (LI-COR, Inc., Lincoln, NE, USA) with a transparent chamber (0.4 m in length × 0.4 m in width × 0.6 m in height) to measure net ecosystem CO2 exchange (NEE). Ecosystem respiration (ER) was measured by using the similar method with the transparent chamber covered by an opaque cloth. Gross ecosystem production (GEP) was estimated as the difference between NEE and ER (Qi et al., 2021). In this study, the more negative NEE represents more CO2 sequestration by terrestrial ecosystem.


National Natural Science Foundation of China, Award: 41825016

National Natural Science Foundation of China, Award: 41907209

National Natural Science Foundation of China, Award: 41877048

Second Tibetan Plateau Scientific Expedition, Award: 2019QZKK0503